diff options
Diffstat (limited to 'sci-biology')
474 files changed, 2219 insertions, 13028 deletions
diff --git a/sci-biology/ABI-connectivity-data/ABI-connectivity-data-0.1-r1.ebuild b/sci-biology/ABI-connectivity-data/ABI-connectivity-data-0.1-r1.ebuild index b882373e2..fe4926644 100644 --- a/sci-biology/ABI-connectivity-data/ABI-connectivity-data-0.1-r1.ebuild +++ b/sci-biology/ABI-connectivity-data/ABI-connectivity-data-0.1-r1.ebuild @@ -1,13 +1,13 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 inherit check-reqs DESCRIPTION="Connectivity data from the Allen Mouse Brain data portal" HOMEPAGE="https://github.com/IBT-FMI/ABI-connectivity-data_generator" -SRC_URI="http://chymera.eu/distfiles/${P}.tar.xz" +SRC_URI="https://resources.chymera.eu/distfiles/${P}.tar.xz" LICENSE="fairuse" SLOT="0" diff --git a/sci-biology/ABI-connectivity-data/ABI-connectivity-data-0.2.ebuild b/sci-biology/ABI-connectivity-data/ABI-connectivity-data-0.2.ebuild index b882373e2..fe4926644 100644 --- a/sci-biology/ABI-connectivity-data/ABI-connectivity-data-0.2.ebuild +++ b/sci-biology/ABI-connectivity-data/ABI-connectivity-data-0.2.ebuild @@ -1,13 +1,13 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 inherit check-reqs DESCRIPTION="Connectivity data from the Allen Mouse Brain data portal" HOMEPAGE="https://github.com/IBT-FMI/ABI-connectivity-data_generator" -SRC_URI="http://chymera.eu/distfiles/${P}.tar.xz" +SRC_URI="https://resources.chymera.eu/distfiles/${P}.tar.xz" LICENSE="fairuse" SLOT="0" diff --git a/sci-biology/ABI-connectivity-data/metadata.xml b/sci-biology/ABI-connectivity-data/metadata.xml index 6de417d21..4f11f95ba 100644 --- a/sci-biology/ABI-connectivity-data/metadata.xml +++ b/sci-biology/ABI-connectivity-data/metadata.xml @@ -9,4 +9,7 @@ <email>sci@gentoo.org</email> <name>Gentoo Science Project</name> </maintainer> + <upstream> + <remote-id type="github">IBT-FMI/ABI-connectivity-data_generator</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/ABI-expression-data/ABI-expression-data-0.2.ebuild b/sci-biology/ABI-expression-data/ABI-expression-data-0.2.ebuild index 0d53f2a90..2016de083 100644 --- a/sci-biology/ABI-expression-data/ABI-expression-data-0.2.ebuild +++ b/sci-biology/ABI-expression-data/ABI-expression-data-0.2.ebuild @@ -8,7 +8,7 @@ inherit check-reqs DESCRIPTION="Gene expression data form the Allen Mouse Brain data portal" HOMEPAGE="https://github.com/IBT-FMI/ABI-expression-data_generator" SRC_URI=" - http://chymera.eu/distfiles/${P}.tar.xz + https://resources.chymera.eu/distfiles/${P}.tar.xz " LICENSE="fairuse" diff --git a/sci-biology/BEP032tools/BEP032tools-0.0.1_alpha.ebuild b/sci-biology/BEP032tools/BEP032tools-0.0.1_alpha.ebuild new file mode 100644 index 000000000..ec394603d --- /dev/null +++ b/sci-biology/BEP032tools/BEP032tools-0.0.1_alpha.ebuild @@ -0,0 +1,44 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..11} ) + +inherit distutils-r1 + +MY_HASH="a7059ef691e74aeb018edaf37df49c99f6efed60" + +DESCRIPTION="Conversion and validation tools for BEP 032" +HOMEPAGE="https://github.com/INT-NIT/BEP032tools" +SRC_URI="https://github.com/INT-NIT/BEP032tools/archive/${MY_HASH}.tar.gz -> ${P}.gh.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64" + +RDEPEND=" + dev-python/pandas[${PYTHON_USEDEP}] + dev-python/pynwb[${PYTHON_USEDEP}] + dev-python/neo[${PYTHON_USEDEP}] +" +BDEPEND=" + dev-python/parameterized[${PYTHON_USEDEP}] +" + +S="${WORKDIR}/${PN}-${MY_HASH}" + +# Require nixio +EPYTEST_DESELECT=( + "bep032tools/generator/tests/test_BEP032Generator.py::Test_BEP032Data_ece::test_data_file_conversion_0_nix" + "bep032tools/generator/tests/test_BEP032Generator.py::Test_BEP032Data_ece::test_data_file_conversion_multi_split" + "bep032tools/generator/tests/test_BEP032Generator.py::Test_BEP032Data_ice::test_data_file_conversion_0_nix" +) +# Require dynamically fetched data +EPYTEST_DESELECT+=( + "bep032tools/generator/tests/test_nwb2bidsgenerator.py::TestNwbBIDSGenerator::test_nwb_to_bids" + "bep032tools/generator/tests/test_nwb2bidsgenerator.py::TestNwbBIDSGenerator::test_validation" +) + +distutils_enable_tests pytest diff --git a/sci-biology/BEP032tools/Manifest b/sci-biology/BEP032tools/Manifest new file mode 100644 index 000000000..1e97ed9b1 --- /dev/null +++ b/sci-biology/BEP032tools/Manifest @@ -0,0 +1 @@ +DIST BEP032tools-0.0.1_alpha.gh.tar.gz 79175 BLAKE2B dc3d999401d2d4361bfc66b72a39fa02bd6148a377bf63b5bdcc788f4018e486e89743b35ad8f61e232b22f79fed6199dad462aaab60e3bbd1425de117b9c576 SHA512 bf929e5f00cfdd47bbdb9f2240bab97468da5bcb72857e8272eb25857ce7d525b6a97cbc459ace8629d67eb9238b8ddd537e2b6269b73d0173a945b39d5eb59e diff --git a/sci-biology/symap/metadata.xml b/sci-biology/BEP032tools/metadata.xml index ae9640ffb..8d24d17e7 100644 --- a/sci-biology/symap/metadata.xml +++ b/sci-biology/BEP032tools/metadata.xml @@ -1,8 +1,16 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> + <maintainer type="person"> + <email>gentoo@chymera.eu</email> + <name>Horea Christian</name> + </maintainer> <maintainer type="project"> <email>sci@gentoo.org</email> <name>Gentoo Science Project</name> </maintainer> + <upstream> + <remote-id type="github">INT-NIT/BEP032tools</remote-id> + <remote-id type="pypi">BEP032tools</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/BRAKER/metadata.xml b/sci-biology/BRAKER/metadata.xml index 138cb7705..aa4766e73 100644 --- a/sci-biology/BRAKER/metadata.xml +++ b/sci-biology/BRAKER/metadata.xml @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">Gaius-Augustus/BRAKER</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/BlastToSam/BlastToSam-1.1.ebuild b/sci-biology/BlastToSam/BlastToSam-1.1.ebuild deleted file mode 100644 index 775889330..000000000 --- a/sci-biology/BlastToSam/BlastToSam-1.1.ebuild +++ /dev/null @@ -1,32 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit git-r3 java-pkg-2 java-ant-2 - -DESCRIPTION="Convert NCBI BLAST+ Pairwise/XML (-outfmt 0 or 5) output to SAM v1.4" -HOMEPAGE="https://github.com/AstrorEnales/BlastToSam" -EGIT_REPO_URI="https://github.com/AstrorEnales/BlastToSam.git" -EGIT_COMMIT="8f543ff1640b64e44701cb534e2959ff46469b2e" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -RDEPEND=">=virtual/jre-1.5:*" -DEPEND="${RDEPEND} - >=virtual/jdk-1.5:* - dev-java/ant-core - dev-java/jython -" - -src_compile() { - ant compile || die -} - -src_install() { - java-pkg_dojar build/jar/BlastToSam.jar - java-pkg_dolauncher - dodoc README.md -} diff --git a/sci-biology/BlastToSam/metadata.xml b/sci-biology/BlastToSam/metadata.xml deleted file mode 100644 index 5a3c7d51d..000000000 --- a/sci-biology/BlastToSam/metadata.xml +++ /dev/null @@ -1,15 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="github">AstrorEnales/BlastToSam</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-biology/CAT/CAT-1.3.ebuild b/sci-biology/CAT/CAT-1.3.ebuild index a2c4233c9..508ca4c36 100644 --- a/sci-biology/CAT/CAT-1.3.ebuild +++ b/sci-biology/CAT/CAT-1.3.ebuild @@ -4,9 +4,7 @@ EAPI=7 DESCRIPTION="Codon usage bias (composition) and its statistical significance" -HOMEPAGE=" - https://bigd.big.ac.cn/tools/cat - http://cbb.big.ac.cn/Software" +HOMEPAGE="https://bigd.big.ac.cn/tools/cat" SRC_URI="ftp://download.big.ac.cn/bigd/tools/${PN}${PV}.tar.gz -> ${P}.tar.gz" LICENSE="GPL-3+" diff --git a/sci-biology/FLASH/metadata.xml b/sci-biology/FLASH/metadata.xml index 0f267b755..7dc91092f 100644 --- a/sci-biology/FLASH/metadata.xml +++ b/sci-biology/FLASH/metadata.xml @@ -10,6 +10,6 @@ <name>Gentoo Biology Project</name> </maintainer> <upstream> - <remote-id type="sourceforge">downloads</remote-id> + <remote-id type="sourceforge">flashpage</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/Fastaq/Fastaq-3.17.0.ebuild b/sci-biology/Fastaq/Fastaq-3.17.0.ebuild index 28ff526f6..443fb3342 100644 --- a/sci-biology/Fastaq/Fastaq-3.17.0.ebuild +++ b/sci-biology/Fastaq/Fastaq-3.17.0.ebuild @@ -1,9 +1,10 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 -PYTHON_COMPAT=( python3_{7,8,9} ) +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools inherit distutils-r1 @@ -15,4 +16,6 @@ LICENSE="GPL-3" SLOT="0" KEYWORDS="~amd64" -distutils_enable_tests nose +distutils_enable_tests pytest +# Nominally upstream still uses nose, though it does not encumber us, and tests pass: +# https://github.com/sanger-pathogens/Fastaq/issues/84 diff --git a/sci-biology/GAL/GAL-0.2.2_p20200508.ebuild b/sci-biology/GAL/GAL-0.2.2_p20200508.ebuild index 1aa7e99be..f02907368 100644 --- a/sci-biology/GAL/GAL-0.2.2_p20200508.ebuild +++ b/sci-biology/GAL/GAL-0.2.2_p20200508.ebuild @@ -1,7 +1,7 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 inherit perl-module @@ -10,16 +10,15 @@ COMMIT="94af39622aab5ba48eb693f2327f6e90f1d202ed" DESCRIPTION="Genome Annotation Library (incl. fasta_tool)" HOMEPAGE="https://github.com/The-Sequence-Ontology/GAL" SRC_URI="https://github.com/The-Sequence-Ontology/GAL/archive/${COMMIT}.tar.gz -> ${P}.tar.gz" +S="${WORKDIR}/${PN}-${COMMIT}" LICENSE="( GPL-1+ Artistic )" SLOT="0" -KEYWORDS="" +KEYWORDS="~amd64" RESTRICT="test" DEPEND=" - >=dev-lang/perl-5.6.1 - dev-perl/Module-Build dev-perl/Config-Std virtual/perl-Data-Dumper dev-perl/Data-Types @@ -29,6 +28,7 @@ DEPEND=" dev-perl/Number-Format virtual/perl-Scalar-List-Utils dev-perl/Set-IntSpan-Fast + dev-perl/Statistics-Descriptive dev-perl/Statistics-Descriptive-Discrete dev-perl/Template-Toolkit dev-perl/Text-Graph @@ -36,7 +36,12 @@ DEPEND=" dev-perl/Text-Table dev-perl/Exception-Class dev-perl/Test-Warn - dev-perl/URI" + dev-perl/URI + sci-biology/fasta +" RDEPEND="${DEPEND}" +BDEPEND="dev-perl/Module-Build" -S="${WORKDIR}/${PN}-${COMMIT}" +PATCHES=( + "${FILESDIR}/Build.PL.patch" +) diff --git a/sci-biology/GAL/files/Build.PL.patch b/sci-biology/GAL/files/Build.PL.patch index 6d881f249..eee4fb60d 100644 --- a/sci-biology/GAL/files/Build.PL.patch +++ b/sci-biology/GAL/files/Build.PL.patch @@ -1,16 +1,11 @@ -diff -ruN GAL_0.2.2.orig/Build.PL GAL_0.2.2/Build.PL ---- GAL_0.2.2.orig/Build.PL 2014-01-30 01:35:11.000000000 +0100 -+++ GAL_0.2.2/Build.PL 2016-01-02 12:09:16.212623256 +0100 -@@ -6,26 +6,6 @@ - my $class = Module::Build->subclass - ( - class => 'Module::Build::Custom', -- code => q{ -- sub ACTION_build { -- my $self = shift; -- $self->SUPER::ACTION_build; -- $self->dispatch('installdeps'); -- } +diff --git a/Build.PL b/Build.PL +index 5915ca8..61eceb3 100644 +--- a/Build.PL ++++ b/Build.PL +@@ -12,19 +12,6 @@ my $class = Module::Build->subclass + $self->SUPER::ACTION_build; + $self->dispatch('installdeps'); + } - sub ACTION_install { - my $self = shift; - print "\n\nGAL does not do a system wide install\n\n"; @@ -24,7 +19,6 @@ diff -ruN GAL_0.2.2.orig/Build.PL GAL_0.2.2/Build.PL - print "remove the entire subroutine (ACTION_install) where this message\n"; - print "is printed run Build realclean and re-install.\n\n"; - } -- }, + }, ); - my $builder = $class->new( diff --git a/sci-biology/GAL/metadata.xml b/sci-biology/GAL/metadata.xml index 138cb7705..480ba370b 100644 --- a/sci-biology/GAL/metadata.xml +++ b/sci-biology/GAL/metadata.xml @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">The-Sequence-Ontology/GAL</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/LINKS/LINKS-1.8.7.ebuild b/sci-biology/LINKS/LINKS-1.8.7.ebuild deleted file mode 100644 index 898898b94..000000000 --- a/sci-biology/LINKS/LINKS-1.8.7.ebuild +++ /dev/null @@ -1,50 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -DESCRIPTION="Scaffold genome assemblies by Chromium/PacBio/Nanopore reads" -HOMEPAGE="https://github.com/bcgsc/LINKS" -SRC_URI="https://github.com/bcgsc/LINKS/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="GPL-3" -SLOT="0" -KEYWORDS="" - -RESTRICT="test" - -RDEPEND=" - >=dev-lang/perl-1.6 - dev-lang/swig - dev-util/cppcheck -" -# sci-biology/btl_bloomfilter - -src_compile(){ - cd btllib | die "Cannot chdir to bundled btllib/" - ./compile-wrappers || die "Failed to compile bundled btllib" - # baah, this also does some kind of install - # SUCCESS: sdsl was installed successfully! - # The sdsl include files are located in $foo'/LINKS/btllib/external/sdsl-lite/installdir/include'. - # The library files are located in $foo'/LINKS/btllib/external/sdsl-lite/installdir/lib'. - # - # Sample programs can be found in the examples-directory. - # A program 'example.cpp' can be compiled with the command: - # g++ -std=c++11 -DNDEBUG -O3 [-msse4.2] \ - # -I$foo/LINKS/btllib/external/sdsl-lite/installdir/include -L$foo/LINKS/btllib/external/sdsl-lite/installdir/lib \ - # example.cpp -lsdsl -ldivsufsort -ldivsufsort64 - # - # Tests in the test-directory - # A cheat sheet in the extras/cheatsheet-directory. - # Have fun! - # [2/3] Installing files. - # Installing extras/python/_btllib.so to $foo/LINKS/btllib/python - # Installing $foo/LINKS/btllib/extras/python/btllib.py to $foo/LINKS/btllib/python -} - -src_install(){ - sed -e 's#$(bin)/../src/##' -i bin/LINKS-make || die - sed -e 's#perl $(bin)/##' -i bin/LINKS-make || die - dobin bin/LINKS bin/LINKS-make src/LINKS_CPP bin/*.pl tools/*.pl - dodoc README.md -} diff --git a/sci-biology/LINKS/LINKS-2.0.1.ebuild b/sci-biology/LINKS/LINKS-2.0.1.ebuild new file mode 100644 index 000000000..c1c9cc5d8 --- /dev/null +++ b/sci-biology/LINKS/LINKS-2.0.1.ebuild @@ -0,0 +1,21 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DESCRIPTION="Scaffold genome assemblies by Chromium/PacBio/Nanopore reads" +HOMEPAGE="https://github.com/bcgsc/LINKS" +SRC_URI="https://github.com/bcgsc/LINKS/releases/download/v${PV}/links-v${PV}.tar.gz -> ${P}.tar.gz" +S="${WORKDIR}/links-${PV}" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64" + +RDEPEND=" + >=dev-lang/perl-1.6 + dev-util/cppcheck +" +DEPEND="${RDEPEND} + dev-lang/swig +" diff --git a/sci-biology/LINKS/Manifest b/sci-biology/LINKS/Manifest index bc5133d76..e57aae29d 100644 --- a/sci-biology/LINKS/Manifest +++ b/sci-biology/LINKS/Manifest @@ -1 +1 @@ -DIST LINKS-1.8.7.tar.gz 13550877 BLAKE2B ee77f295b0dfc70494b985075c1be794492178c050117f7d775d9cfb2a0dc2ab96030fae2b05075955b03ed99683586fd1b0688a99cd741671be762021bc06e8 SHA512 1b869229275eddc7cb9ae2df1d4f9422741b845df50d438761a8afd4ea172244ded1a70e4fba42045e09a0ae23f8a64e2233d66a261698c13aba1b231576015c +DIST LINKS-2.0.1.tar.gz 4566466 BLAKE2B 0713278c17b5d6fce3d6c0bbfffd2decd71599464b9d4c7da5b82997dfc6f2e1be7435dc26bc96eb6ce23ba0bd8136f8ca714e327de465137e0435ebdaa19d9c SHA512 2bbcc264da6dbe361d8224e2a123983c4f09a4b051490d599f193e3f02463e4e8ff2fadf72b8be2df6adee6db886b76d59eee179648cfed6a025c31d7fe2c696 diff --git a/sci-biology/MaSuRCA/MaSuRCA-4.0.1.ebuild b/sci-biology/MaSuRCA/MaSuRCA-4.0.1.ebuild index 8e6d2925e..7b070e595 100644 --- a/sci-biology/MaSuRCA/MaSuRCA-4.0.1.ebuild +++ b/sci-biology/MaSuRCA/MaSuRCA-4.0.1.ebuild @@ -1,17 +1,19 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 DESCRIPTION="de Bruijn and OLC assembler for Sanger, Roche 454, Illumina, Pacbio, Nanopore" HOMEPAGE="http://www.genome.umd.edu/masurca.html http://bioinformatics.oxfordjournals.org/content/29/21/2669 - https://biorxiv.org/content/biorxiv/early/2016/07/26/066100.full.pdf" + https://github.com/alekseyzimin/masurca" SRC_URI="https://github.com/alekseyzimin/masurca/releases/download/v${PV}/${P}.tar.gz" LICENSE="BSD GPL-2 GPL-3" SLOT="0" -KEYWORDS="~amd64" +# Known to produce build failure: +# https://github.com/alekseyzimin/masurca/issues/323 +KEYWORDS="" DEPEND=" >=dev-lang/perl-5.8 diff --git a/sci-biology/MaSuRCA/MaSuRCA-4.1.0.ebuild b/sci-biology/MaSuRCA/MaSuRCA-4.1.0.ebuild new file mode 100644 index 000000000..7b070e595 --- /dev/null +++ b/sci-biology/MaSuRCA/MaSuRCA-4.1.0.ebuild @@ -0,0 +1,29 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DESCRIPTION="de Bruijn and OLC assembler for Sanger, Roche 454, Illumina, Pacbio, Nanopore" +HOMEPAGE="http://www.genome.umd.edu/masurca.html + http://bioinformatics.oxfordjournals.org/content/29/21/2669 + https://github.com/alekseyzimin/masurca" +SRC_URI="https://github.com/alekseyzimin/masurca/releases/download/v${PV}/${P}.tar.gz" + +LICENSE="BSD GPL-2 GPL-3" +SLOT="0" +# Known to produce build failure: +# https://github.com/alekseyzimin/masurca/issues/323 +KEYWORDS="" + +DEPEND=" + >=dev-lang/perl-5.8 + app-arch/bzip2 +" +RDEPEND="${DEPEND}" + +src_compile(){ + ./install.sh || die +} +src_install(){ + dobin masurca +} diff --git a/sci-biology/MaSuRCA/Manifest b/sci-biology/MaSuRCA/Manifest index 330ac8de3..fd6029f04 100644 --- a/sci-biology/MaSuRCA/Manifest +++ b/sci-biology/MaSuRCA/Manifest @@ -1 +1,2 @@ DIST MaSuRCA-4.0.1.tar.gz 26502309 BLAKE2B 658c3a85d3d16bc966f50def9b0f98503f25f89893a18f6b7c361592dc2b20875f4c2b78e55e7279e47d0d381e9f973185da7cf7a1529c617c82b0789dea4183 SHA512 5a52dc6667b501ef5ee33f8c30a516a466b39b061ae3bee93f3e6a9cc9dd21503365671d93858165290b3200c859772324fdb12f8bdab235b3ff08c158c4dd66 +DIST MaSuRCA-4.1.0.tar.gz 26532049 BLAKE2B 93cf8cc2bcb4d2c56961f66c0e045ad7776011b4a5f78e5944c5e9b74004c553fc38e542a163aa2efca0aff0e2726fc38eea1aba8f2da287c5154c9eae4e9bcf SHA512 6de57abff87de2fd8c30bcc7efbd6c37358d37eab518d36ccbe48f036af6e1bc22a655abb59f32df613d99c84a5deca272c8c894395f255bcbceb4da5368e64a diff --git a/sci-biology/MaSuRCA/metadata.xml b/sci-biology/MaSuRCA/metadata.xml index 138cb7705..8a631d677 100644 --- a/sci-biology/MaSuRCA/metadata.xml +++ b/sci-biology/MaSuRCA/metadata.xml @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">alekseyzimin/masurca</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/MeV/metadata.xml b/sci-biology/MeV/metadata.xml index bd7adb92f..334d55097 100644 --- a/sci-biology/MeV/metadata.xml +++ b/sci-biology/MeV/metadata.xml @@ -9,6 +9,6 @@ <name>Gentoo Biology Project</name> </maintainer> <upstream> - <remote-id type="sourceforge">downloads</remote-id> + <remote-id type="sourceforge">mev-tm4</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/MolBioLib/Manifest b/sci-biology/MolBioLib/Manifest deleted file mode 100644 index fcfe68414..000000000 --- a/sci-biology/MolBioLib/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST MolBioLib_public.version5.tar.gz 2414384 BLAKE2B 845ac366ed41886cc0d3d96376dc9a97bae3d84bfc41d5f9e5be4fa274a6d64a981fcbcc12de28e1518212313af12330b08cac5488e7db9a2738c7846b981cb7 SHA512 056c38bcb65b845b32678fb8c5d758023154c07085414194e98e58281e61e475dca7321c8d684955c88bf459bc92c9d39f8b6091d0b804581e6f6e6ecabe3832 diff --git a/sci-biology/MolBioLib/MolBioLib-5.ebuild b/sci-biology/MolBioLib/MolBioLib-5.ebuild deleted file mode 100644 index bbbbeb605..000000000 --- a/sci-biology/MolBioLib/MolBioLib-5.ebuild +++ /dev/null @@ -1,40 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -DOCS_BUILDER="doxygen" -DOCS_DEPEND="media-gfx/graphviz" - -inherit docs - -DESCRIPTION="C++11 framework for bioinformatics tasks" -HOMEPAGE="https://sourceforge.net/projects/molbiolib" -SRC_URI="https://sourceforge.net/projects/molbiolib/files/MolBioLib_public.version${PV}.tar.gz" - -LICENSE="GPL-3" -SLOT="0" -KEYWORDS="" # does not build - -# contains bundled samtools-0.1.18 and bamtools (pezmaster31-bamtools-d553a62) -# which contains jsoncpp, also needs app-doc/doxygen -DEPEND=" - dev-lang/perl - sys-devel/gcc:* - sys-devel/clang:* - >=sci-biology/samtools-0.1.18:0.1-legacy - <sci-biology/samtools-1:0.1-legacy" -RDEPEND="${DEPEND}" -CDEPEND="doc? ( app-doc/doxygen )" - -S="${WORKDIR}"/MolBioLib - -src_compile(){ - perl MakeAllApps.pl || die - docs_compile -} - -src_install() { - einstalldocs - # TODO: install this -} diff --git a/sci-biology/MolBioLib/metadata.xml b/sci-biology/MolBioLib/metadata.xml deleted file mode 100644 index 3b9e38617..000000000 --- a/sci-biology/MolBioLib/metadata.xml +++ /dev/null @@ -1,15 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="sourceforge">molbiolib</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-biology/OBO-Edit/Manifest b/sci-biology/OBO-Edit/Manifest deleted file mode 100644 index 328ce0bca..000000000 --- a/sci-biology/OBO-Edit/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST OBO-Edit_unix_install4j-2.3.1.sh 44841394 BLAKE2B cdde5fa8bd3ce505bc18471a3924f35f6bdcac426a260c65568cdc0a70027c86d095c05e85441e770b4a6d3d0d8de3da1a3808bc3c3758e51e708e60864c0ab4 SHA512 3a48c20c02727057e3dfc7e94cf5e414942a63a9b2339e2bc6bb19e8f45ac0289904e1e6cf7b83efa53bf32b7f188c36d0deb539e169710ea2f326c5ea323603 diff --git a/sci-biology/OBO-Edit/OBO-Edit-2.3.1.ebuild b/sci-biology/OBO-Edit/OBO-Edit-2.3.1.ebuild deleted file mode 100644 index 321d3901c..000000000 --- a/sci-biology/OBO-Edit/OBO-Edit-2.3.1.ebuild +++ /dev/null @@ -1,73 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit java-pkg-2 - -MY_PV="${PV//./_}" - -DESCRIPTION="Java-based editor optimized for the OBO biological ontology file format" -HOMEPAGE="http://www.oboedit.org/" # no https, invalid certificate -SRC_URI="https://downloads.sourceforge.net/project/geneontology/OBO-Edit%202%20%5BLatest%20versions%5D/OBO-Edit%20${PV}/oboedit_${MY_PV}_unix_install4j.sh -> ${PN}_unix_install4j-${PV}.sh" - -LICENSE="OBO-Edit" # Artistic-like -SLOT="0" -KEYWORDS="" - -DEPEND="app-arch/rpm2targz" -RDEPEND="virtual/jre" - -S="${WORKDIR}" - -pkg_setup() { - einfo "Fixing java access violations ..." - # learned from bug #387227 - # opened a bug #402507 to get this .systemPrefs directory pre-created for everybody - addpredict /opt/icedtea-bin-7.2.0/jre/.systemPrefs - addpredict /usr/local/bin/OBO-Edit -} - -src_prepare(){ - default - dodir /opt/OBO-Edit2/.install4j /usr/bin - cp "${DISTDIR}"/"${PN}"_unix_install4j-"${PV}".sh "${WORKDIR}" || die - - # /var/tmp/portage/sci-biology/OBO-Edit-2.1.1.6/image//opt/OBO-Edit2/.install4j/response.varfile - sed -e "s#\"\${D}\"#"${D}"#g" "${FILESDIR}"/response.varfile | \ - sed -e "s#\"\${HOME}\"#"${HOME}"#g" | \ - sed -e "s@sys.symlinkDir=/usr/local/bin@#sys.symlinkDir=/usr/local/bin@" \ - > "${D}"/opt/OBO-Edit2/.install4j/response.varfile || die "sed failed" - cp -r "${D}"/opt/OBO-Edit2/.install4j "${HOME}" || die - - # for user root install4j writes into /opt/icedtea-bin-7.2.0/jre/.systemPrefs or whatever it - # found via JAVA_HOME or similar variables - # for other users it writes into $HOME/.java/.userPrefs/ - - # trick setting -Djava.util.prefs.systemRoot="${TMPDIR}" does not work - sed \ - -e "s@/bin/java\" -Dinstall4j.jvmDir=\"\$app_java_home\"@/bin/java\" -Duser.home="${HOME}" -Dinstall4j.jvmDir="${HOME}" -Dsys.symlinkDir="${D}"/usr/bin -Djava.util.prefs.systemRoot="${HOME}"@" \ - -i "${WORKDIR}"/"${PN}"_unix_install4j-"${PV}".sh \ - || die "failed to set userHome and jvmDir where JAVA .systemPrefs can be found" - - chmod u+rx "${WORKDIR}/${PN}"_unix_install4j-"${PV}".sh || die -} - -src_install(){ - # it looks install4j removes the target installation direcotry before writing into it :(( - # - # cat "${TMPDIR}"/.install4j/response.varfile - # chmod a-w "${TMPDIR}"/.install4j/response.varfile - - INSTALL4J_KEEP_TEMP="yes" \ - sh "${WORKDIR}"/"${PN}"_unix_install4j-"${PV}".sh -q \ - --varfile="${HOME}"/.install4j/response.varfile \ - --destination="${D}"/opt/OBO-Edit2 \ - -dir "${D}"/opt/OBO-Edit2 \ - || die "Failed to run the self-extracting ${WORKDIR}/${PN}_unix_install4j-${PV}.sh file" - - find . -name firstrun -delete || die - - echo "PATH=/opt/OBO-Edit2" > 99OBO-Edit || die - doenvd 99OBO-Edit -} diff --git a/sci-biology/OBO-Edit/files/response.varfile b/sci-biology/OBO-Edit/files/response.varfile deleted file mode 100644 index 8c4361d01..000000000 --- a/sci-biology/OBO-Edit/files/response.varfile +++ /dev/null @@ -1,10 +0,0 @@ -#install4j response file for OBO-Edit2 2.1.1-b6 -#Tue Feb 07 03:08:04 MET 2012 -sys.component.89$Boolean=false -createDesktopLinkAction$Boolean=false -oboedit.memoryAlloc$Integer=3456 -sys.programGroupDisabled$Boolean=true -sys.component.61$Boolean=true -sys.symlinkDir="${D}"usr/bin -sys.languageId=en -sys.installationDir="${D}"opt/OBO-Edit2 diff --git a/sci-biology/OBO-Edit/metadata.xml b/sci-biology/OBO-Edit/metadata.xml deleted file mode 100644 index acbbc35a4..000000000 --- a/sci-biology/OBO-Edit/metadata.xml +++ /dev/null @@ -1,15 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="sourceforge">geneontology</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-biology/RAILS/metadata.xml b/sci-biology/RAILS/metadata.xml index 138cb7705..a3f152e56 100644 --- a/sci-biology/RAILS/metadata.xml +++ b/sci-biology/RAILS/metadata.xml @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">bcgsc/RAILS</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/RSeQC/Manifest b/sci-biology/RSeQC/Manifest deleted file mode 100644 index 5319e5fa5..000000000 --- a/sci-biology/RSeQC/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -DIST RSeQC-4.0.0.tar.gz 101873 BLAKE2B 0a63ef39d3aa27e8ad419ad4d4e335563d870600d03e131fd02e4d4fd8fb403007f8b3a7ec0d57e8731ac616c6a4e07f3d6664668ea0e79aef911c1e54088afb SHA512 77ec4ad2c0f460b8bafe00dcfac6b1d9ddf65f933a55892c376eb7009f5820531dd167acc675b07186e81daa2a904914643dfcb7c220ef7b290d0c8ad3833c42 -DIST fetchChromSizes 2695 BLAKE2B a41f8e0085121f097c0fe93922b221b276f00a5d6af1da76f347ca121882e5d899d482900f51a0da4bff22b0b3158f0e274a67c60d7b7499c1bc3ead96beccd6 SHA512 23405beabb4f42b5cc5b569d9948d070e354ef2be10030b51ba3510865ab4e25bee8aab7283d9b6cbd7df454159a6f89e58ad8f5ee6a541046ad5a72f65019e8 diff --git a/sci-biology/RSeQC/RSeQC-4.0.0-r1.ebuild b/sci-biology/RSeQC/RSeQC-4.0.0-r1.ebuild deleted file mode 100644 index 9df8930e5..000000000 --- a/sci-biology/RSeQC/RSeQC-4.0.0-r1.ebuild +++ /dev/null @@ -1,34 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7,8,9} ) - -inherit distutils-r1 - -DESCRIPTION="Utilities for RNA-seq data quality control" -HOMEPAGE="https://sourceforge.net/projects/rseqc/" -SRC_URI="https://sourceforge.net/projects/rseqc/files/RSeQC-${PV}.tar.gz - https://sourceforge.net/projects/rseqc/files/other/fetchChromSizes" - -LICENSE="GPL-3" -SLOT="0" -KEYWORDS="~amd64" - -BDEPEND=" - dev-python/cython[${PYTHON_USEDEP}] - dev-python/nose[${PYTHON_USEDEP}] -" -RDEPEND=" - >=sci-biology/pysam-0.7.5[${PYTHON_USEDEP}] - sci-biology/bx-python[${PYTHON_USEDEP}] - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/pyBigWig[${PYTHON_USEDEP}] -" - -python_prepare_all() { - distutils-r1_python_prepare_all - # avoid file collision with bx-python - rm lib/psyco_full.py || die -} diff --git a/sci-biology/RSeQC/metadata.xml b/sci-biology/RSeQC/metadata.xml deleted file mode 100644 index 5c8442330..000000000 --- a/sci-biology/RSeQC/metadata.xml +++ /dev/null @@ -1,15 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="sourceforge">rseqc</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-biology/SOAPdenovo2/Manifest b/sci-biology/SOAPdenovo2/Manifest deleted file mode 100644 index f732ff7a8..000000000 --- a/sci-biology/SOAPdenovo2/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST SOAPdenovo2-242.tar.gz 1534059 BLAKE2B e72b8b8005a807e1f949d092a1b582ed75ddbd3f4a1f014f86754ae69e279b93758693f36942e16183095fcfcc843a637fab39b08cfa6b8cbeffaf8b07c3050a SHA512 eaa2020aa9054588805bd69bb2e1d70be5bfcad31d52a33ed8f7accd4006db1ec980b20f846a6e1c0ee0ec8a493c38febb9022ce6a59c14d03fe43a3ca50569b diff --git a/sci-biology/SOAPdenovo2/SOAPdenovo2-242.ebuild b/sci-biology/SOAPdenovo2/SOAPdenovo2-242.ebuild deleted file mode 100644 index 33fd4a2a3..000000000 --- a/sci-biology/SOAPdenovo2/SOAPdenovo2-242.ebuild +++ /dev/null @@ -1,40 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -DESCRIPTION="Whole genome shotgun assembler (sparse de Bruijn graph) (now MEGAHIT)" -HOMEPAGE="https://github.com/aquaskyline/SOAPdenovo2 - https://gigascience.biomedcentral.com/articles/10.1186/2047-217X-1-18" -SRC_URI="https://github.com/aquaskyline/SOAPdenovo2/archive/r${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="GPL-3" -SLOT="0" -KEYWORDS="" # fails to compile - -DEPEND="dev-libs/libaio - sci-biology/samtools:0.1-legacy" -RDEPEND="${DEPEND}" - -S="${WORKDIR}"/"${PN}"-r"${PV}" # version is 2.04-r241 - -src_prepare(){ - #eapply "${FILESDIR}"/SOAPdenovo2-r241-Makefile.patch - # this will be partly covered by - # https://github.com/aquaskyline/SOAPdenovo2/pull/44 - # - for f in Makefile standardPregraph/Makefile sparsePregraph/Makefile; do - sed -e 's#^INCLUDES =#INCLUDES = -I/usr/include/bam-0.1-legacy -I./inc#;s#-lbam#-lbam-0.1-legacy#' -i $f || die - done - rm -f standardPregraph/*.a standardPregraph/inc/sam.h standardPregraph/inc/bam.h standardPregraph/inc/bgzf.h \ - sparsePregraph/inc/sam.h sparsePregraph/inc/bam.h sparsePregraph/inc/bgzf.h standardPregraph/inc/zlib.h \ - standardPregraph/inc/zconf.h sparsePregraph/inc/zlib.h sparsePregraph/inc/zconf.h standardPregraph/inc/*.so \ - sparsePregraph/*.a || die - find -type f -name "*.h" -exec sed -i -e 's/#include "sam.h"/#include "bam-0.1-legacy\/sam.h"/g' {} + || die - find -type f -name "*.h" -exec sed -i -e 's/#include "bgzf.h"/#include "bam-0.1-legacy\/bgzf.h"/g' {} + || die - find -type f -name "*.h" -exec sed -i -e 's/#include "sam.h"/#include "bam-0.1-legacy\/sam.h"/g' {} + || die - find -type f -name "*.c*" -exec sed -i -e 's/#include "bam.h"/#include "bam-0.1-legacy\/bam.h"/g' {} + || die - find -type f -name "*.c*" -exec sed -i -e 's/#include "bgzf.h"/#include "bam-0.1-legacy\/bgzf.h"/g' {} + || die - find -type f -name "*.c*" -exec sed -i -e 's/#include "sam.h"/#include "bam-0.1-legacy\/sam.h"/g' {} + || die - default -} diff --git a/sci-biology/SOAPdenovo2/files/SOAPdenovo2-r241-Makefile.patch b/sci-biology/SOAPdenovo2/files/SOAPdenovo2-r241-Makefile.patch deleted file mode 100644 index a710c2d86..000000000 --- a/sci-biology/SOAPdenovo2/files/SOAPdenovo2-r241-Makefile.patch +++ /dev/null @@ -1,204 +0,0 @@ ---- sparsePregraph/Makefile.ori 2017-01-03 21:34:59.000000000 +0100 -+++ sparsePregraph/Makefile 2018-04-22 22:07:47.303546845 +0200 -@@ -1,28 +1,28 @@ --CC= g++ -+CXX ?= g++ - ifdef debug --CFLAGS= -O0 -g -fomit-frame-pointer -+CXXFLAGS ?= -O0 -g -fomit-frame-pointer - else --CFLAGS= -O3 -fomit-frame-pointer -w -+CXXFLAGS ?= -O3 -fomit-frame-pointer -w - endif - --DFLAGS= --OBJS= build_graph.o build_edge.o multi_threads.o \ -- build_preArc.o pregraph_sparse.o io_func.o\ -- global.o convert_soapdenovo.o --PROG= --INCLUDES= -I./inc --SUBDIRS= . --LIBPATH= -L/usr/lib64 --LIBS= -pthread -lz -L./inc -+DFLAGS = -+OBJS = build_graph.o build_edge.o multi_threads.o \ -+ build_preArc.o pregraph_sparse.o io_func.o\ -+ global.o convert_soapdenovo.o -+PROG = -+INCLUDES = -I./inc -+SUBDIRS = . -+LIBPATH = -L/usr/lib64 -+LIBS = -pthread -lz -L./inc - EXTRA_FLAGS= --VERSION = 1.0.3 -+VERSION = 1.0.3 - - ifdef 127mer --CFLAGS += -D_127MER_ -+CXXFLAGS += -D_127MER_ - PROG = pregraph_sparse_127mer.v$(VERSION) - - else --CFLAGS += -D_63MER_ -+CXXFLAGS += -D_63MER_ - PROG = pregraph_sparse_63mer.v$(VERSION) - endif - -@@ -38,22 +38,22 @@ - endif - - ifneq (,$(findstring $(shell uname -m), x86_64)) --CFLAGS += -m64 -+CXXFLAGS += -m64 - endif - - ifneq (,$(findstring $(shell uname -m), ia64)) --CFLAGS += -+CXXFLAGS += - endif - - ifneq (,$(findstring $(shell uname -m), ppc64)) --CFLAGS += -mpowerpc64 -+CXXFLAGS += -mpowerpc64 - endif - - .SUFFIXES:.cpp .o - - .cpp.o: - @printf "Compiling $<... \r" -- @$(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< || echo "Error in command: $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $<" -+ @$(CXX) -c $(CXXFLAGS) $(DFLAGS) $(INCLUDES) $< || echo "Error in command: $(CXX) -c $(CXXFLAGS) $(DFLAGS) $(INCLUDES) $<" - - all: $(OBJS) - @printf "$(PROG) objects generated. \n" -@@ -66,7 +66,7 @@ - - pregraph_sparse: clean envTest $(OBJS) - @printf "Linking... \r" -- @$(CC) $(CFLAGS)$(INCLUDES) -o $(PROG) $(OBJS) $(LIBPATH) $(LIBS) $(ENTRAFLAGS) -+ @$(CXX) $(CXXFLAGS)$(INCLUDES) -o $(PROG) $(OBJS) $(LIBPATH) $(LIBS) $(ENTRAFLAGS) - @printf "$(PROG) compilation done. \n" - - clean: ---- Makefile.ori 2017-01-03 21:34:59.000000000 +0100 -+++ Makefile 2018-04-22 22:09:16.526124921 +0200 -@@ -1,17 +1,17 @@ - MAKEFLAGS += --no-print-directory --CC = g++ -+CXX ?= g++ - ifdef debug --CFLAGS= -O0 -g -fomit-frame-pointer -+CXXFLAGS ?= -O0 -g -fomit-frame-pointer - else --CFLAGS= -O3 -fomit-frame-pointer -+CXXFLAGS ?= -O3 -fomit-frame-pointer - endif - - SUBDIRS = sparsePregraph standardPregraph fusion --PROG= SOAPdenovo-63mer SOAPdenovo-127mer SOAPdenovo-fusion --INCLUDES= -I./sparsePregraph/inc -I./standardPregraph/inc -+PROG = SOAPdenovo-63mer SOAPdenovo-127mer SOAPdenovo-fusion -+INCLUDES = -I./sparsePregraph/inc -I./standardPregraph/inc - --LIBPATH= -L/lib64 -L/usr/lib64 -L./sparsePregraph/inc -L./standardPregraph/inc --LIBS= -pthread -lz -lm -+LIBPATH = -L./sparsePregraph/inc -L./standardPregraph/inc -+LIBS = -pthread -lz -lm - EXTRA_FLAGS= - - BIT_ERR = 0 -@@ -25,15 +25,15 @@ - endif - - ifneq (,$(findstring $(shell uname -m), x86_64)) --CFLAGS += -m64 -+CXXFLAGS += -m64 - endif - - ifneq (,$(findstring $(shell uname -m), ia64)) --CFLAGS += -+CXXFLAGS += - endif - - ifneq (,$(findstring $(shell uname -m), ppc64)) --CFLAGS += -mpowerpc64 -+CXXFLAGS += -mpowerpc64 - endif - - -@@ -46,20 +46,20 @@ - SOAPdenovo-63mer: - @cd sparsePregraph;make 63mer=1 debug=1;cd ..; - @cd standardPregraph;make 63mer=1 debug=1;cd ..; -- @$(CC) sparsePregraph/*.o standardPregraph/*.o $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-63mer -+ @$(CXX) sparsePregraph/*.o standardPregraph/*.o $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-63mer - SOAPdenovo-127mer: - @cd sparsePregraph;make 127mer=1 debug=1;cd ..; - @cd standardPregraph;make 127mer=1 debug=1;cd ..; -- @$(CC) sparsePregraph/*.o standardPregraph/*.o $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-127mer -+ @$(CXX) sparsePregraph/*.o standardPregraph/*.o $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-127mer - else - SOAPdenovo-63mer: - @cd sparsePregraph;make 63mer=1;cd ..; - @cd standardPregraph;make 63mer=1;cd ..; -- @$(CC) sparsePregraph/*.o standardPregraph/*.o $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-63mer -+ @$(CXX) sparsePregraph/*.o standardPregraph/*.o $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-63mer - SOAPdenovo-127mer: - @cd sparsePregraph;make 127mer=1;cd ..; - @cd standardPregraph;make 127mer=1;cd ..; -- @$(CC) sparsePregraph/*.o standardPregraph/*.o $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-127mer -+ @$(CXX) sparsePregraph/*.o standardPregraph/*.o $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-127mer - endif - - clean: ---- standardPregraph/Makefile.ori 2017-01-03 21:34:59.000000000 +0100 -+++ standardPregraph/Makefile 2018-04-22 22:10:33.108337752 +0200 -@@ -5,13 +5,13 @@ - # - ################################### - --CC= gcc -+CC ?= gcc - GCCVERSIONMAJOR := $(shell expr `$(CC) -dumpversion | cut -f1 -d.` \>= 4) - GCCVERSIONMINOR := $(shell expr `$(CC) -dumpversion | cut -f2 -d.` \>= 4) - ifdef debug --CFLAGS= -O0 -g -fomit-frame-pointer #-msse4.2 -+CFLAGS ?= -O0 -g -fomit-frame-pointer #-msse4.2 - else --CFLAGS= -O3 -fomit-frame-pointer -w #-msse4.2 -+CFLAGS ?= -O3 -fomit-frame-pointer -w #-msse4.2 - endif - DFLAGS= - OBJS= arc.o attachPEinfo.o bubble.o check.o compactEdge.o \ -@@ -24,12 +24,12 @@ - prlRead2path.o prlReadFillGap.o read2scaf.o readInterval.o stack.o\ - readseq1by1.o scaffold.o searchPath.o seq.o splitReps.o \ - cutTip_graph2.o linearEdge.o kmerhash.o read2edge.o iterate.o --PROG= SOAPdenovo-63mer --INCLUDES= -Iinc --SUBDIRS= . --LIBPATH= -L/lib64 -L/usr/lib64 -L./inc --LIBS= -pthread -lz -lm --EXTRA_FLAGS= -+PROG = SOAPdenovo-63mer -+INCLUDES = -Iinc -+SUBDIRS = . -+LIBPATH = -L./inc -+LIBS = -pthread -lz -lm -+EXTRA_FLAGS = - - BIT_ERR = 0 - ifeq (,$(findstring $(shell uname -m), x86_64 ppc64 ia64)) ---- fusion/Makefile.ori 2017-01-03 21:34:59.000000000 +0100 -+++ fusion/Makefile 2018-04-22 22:11:21.209727636 +0200 -@@ -6,8 +6,8 @@ - libdir = - mandir = - --CC = gcc --CCOPT = -O3 -fprefetch-loop-arrays -funroll-loops -fomit-frame-pointer -w -+CC ?= gcc -+CCOPT ?= -O3 -fprefetch-loop-arrays -funroll-loops -fomit-frame-pointer -w - LIBS = -lm -lpthread - INCDIRS = -Iinc/ - CFLAGS = ${CCOPT} ${INCDIRS} diff --git a/sci-biology/SOAPdenovo2/files/soapdenovo2.1 b/sci-biology/SOAPdenovo2/files/soapdenovo2.1 deleted file mode 100644 index 337618ace..000000000 --- a/sci-biology/SOAPdenovo2/files/soapdenovo2.1 +++ /dev/null @@ -1,22 +0,0 @@ -.TH soapdenovo2 1 "February 09, 2013" "version 2.2.3" "USER COMMANDS" -.SH NAME -soapdenovo2 \- Short-read assembly method that can build a de novo draft assembly -.SH SYNOPSIS -.B soapdenovo_63mer soapdenovo_127mer - -.SH Introduction - -SOAPdenovo is a novel short-read assembly method that can build a de novo draft assembly for the human-sized genomes. The program is specially designed to assemble Illumina GA short reads. It creates new opportunities for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost effective way. - -1) Support large kmer up to 127 to utilize long reads. Three version are provided. - I. The 31mer version support kmer only <=31. - II. The 63mer version support kmer only <=63 and doubles the memory consumption than 31mer version, even being used with kmer <=31. - III. The 127mer version support kmer only <=127 and double the memory consumption than 63mer version, even being used with kmer <=63. - -Please notice that, with longer kmer, the quantity of nodes would decrease significantly, thus the memory consumption is usually smaller than double with shifted version. - -For more information, look at the MANUAL in /usr/share/doc/soapdenovo2 or on soapdenovo web site. - -.SH AUTHOR -Olivier Sallou (olivier.sallou (at) irisa.fr) - Man page and packaging - diff --git a/sci-biology/SOAPdenovo2/metadata.xml b/sci-biology/SOAPdenovo2/metadata.xml deleted file mode 100644 index 138cb7705..000000000 --- a/sci-biology/SOAPdenovo2/metadata.xml +++ /dev/null @@ -1,12 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-biology/SPAdes/Manifest b/sci-biology/SPAdes/Manifest index e10186934..cf724a82a 100644 --- a/sci-biology/SPAdes/Manifest +++ b/sci-biology/SPAdes/Manifest @@ -1,4 +1,4 @@ -DIST SPAdes-3.15.1.tar.gz 13686155 BLAKE2B fb0ff0de93302268e1fc28199be3e14ef670aeab91fca82f2e895f899c9cd8d5380c31d4fe2e884737a917ff04a94cf55d25b91a27b47c91aa3e7c7408b9bd87 SHA512 b2ee4719937912f2b6326b67f602dc62f4be319ccf2774380a487da67fc2e32adcfa417ac5fcf4c5494f80152aab561b87e30a2d36abfe50ed1c48396b44d9d9 -DIST SPAdes-3.15.1_manual.html 78200 BLAKE2B b78da09ae94a46fbf4df19ba668276e6129083e7b50f66f86da137f8ed6435a2300b133be58fe25edb0cbb598aeb66e9310425574408bc419a3e3dff18893b15 SHA512 c3571abc87ffea1c54d7f0d42ce73955a7d101a4a61ecd104538832d193eab19c8813cf0a732f2bbe428724c24be283db89165900c2d49a7f3142770de4ca3b6 -DIST SPAdes-3.15.1_rnaspades_manual.html 8624 BLAKE2B b549a6cae6b02c98cae08fd5d8975210f3593c47f2b4757f19a9445a759e332229620885a6fa2f1dc0662096974548e3d0362079d12c47e6738c0261d755a2af SHA512 2d0b169efd8aa7064d59bed8ad406477c72150f23ae0438227903645071c8f66f26fe062f7dd44b584edf8ef7c709ad6c220237e68917ec23c63cfb3139666b8 -DIST SPAdes-3.15.1_truspades_manual.html 10821 BLAKE2B eb466697f774d3421053cf0fd290c82d9b2059cafd787f10c616c1363537c59960cb8ca41a8a02983ec199e0e1a27567c5850009ad6d2173df45e38f7d3120f7 SHA512 1f3bcdbe5397a23ee94820f6aaf3b85c48aca357276f58f66607140d25529c28b31298c5c8e681df3c61dabed478ac67abeb0975885aa9b7e365e14d6aac06fd +DIST SPAdes-3.15.5.tar.gz 13692466 BLAKE2B c4fe59e6b253c91a6e409cf3c2e5a8181f3c0e93892e3b87f603aa75a6d025d5f1466a87ada5c86d6602f74de9048639e9b057d2abfbe449265f9c1796c608d1 SHA512 98b17f1ab0019a45e6abaf1bc7128a5edb5102120d50a47ddfbd5e30fc7130c7895a096cef16ba8e40be71c8a1f0feff38da54f02f9d2e62bd39d2d91a54f9bd +DIST SPAdes-3.15.5_manual.html 91156 BLAKE2B e5776ec98e972f52eb630cb2048f8cd12318f0cfc020ce464bbe72e14f3716b72199d5ea34f219351d79b3fd0f4201c99f68ca487edde0d258d8794aea1f4675 SHA512 b21cc705a1f3a224dad882fce26e15dfd6d249c46627172189b285584a11d2846d0fa3c4b5aa01ca6436a494cec552122cffd4b79f6cc31446a03d610486dfaa +DIST SPAdes-3.15.5_rnaspades_manual.html 8624 BLAKE2B b549a6cae6b02c98cae08fd5d8975210f3593c47f2b4757f19a9445a759e332229620885a6fa2f1dc0662096974548e3d0362079d12c47e6738c0261d755a2af SHA512 2d0b169efd8aa7064d59bed8ad406477c72150f23ae0438227903645071c8f66f26fe062f7dd44b584edf8ef7c709ad6c220237e68917ec23c63cfb3139666b8 +DIST SPAdes-3.15.5_truspades_manual.html 10821 BLAKE2B eb466697f774d3421053cf0fd290c82d9b2059cafd787f10c616c1363537c59960cb8ca41a8a02983ec199e0e1a27567c5850009ad6d2173df45e38f7d3120f7 SHA512 1f3bcdbe5397a23ee94820f6aaf3b85c48aca357276f58f66607140d25529c28b31298c5c8e681df3c61dabed478ac67abeb0975885aa9b7e365e14d6aac06fd diff --git a/sci-biology/SPAdes/SPAdes-3.15.1.ebuild b/sci-biology/SPAdes/SPAdes-3.15.1.ebuild deleted file mode 100644 index 853524984..000000000 --- a/sci-biology/SPAdes/SPAdes-3.15.1.ebuild +++ /dev/null @@ -1,55 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -DESCRIPTION="De novo de Bruijn genome assembler overcoming uneven coverage" -HOMEPAGE="https://cab.spbu.ru/software/spades" -SRC_URI=" - https://github.com/ablab/spades/releases/download/v${PV}/${P}.tar.gz - https://cab.spbu.ru/files/release${PV}/manual.html -> ${P}_manual.html - https://cab.spbu.ru/files/release${PV}/rnaspades_manual.html -> ${P}_rnaspades_manual.html - https://cab.spbu.ru/files/release${PV}/truspades_manual.html -> ${P}_truspades_manual.html" -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="" - -DEPEND=" - sys-libs/zlib - app-arch/bzip2 - dev-python/regex" -RDEPEND="${DEPEND}" -BDEPEND="dev-util/cmake" -# BUG: -# SPAdes uses bundled while modified copy of dev-libs/boost (only headers are used, -# not *.so or *.a are even used) -# -# BUG: "${S}"/ext/src/ contains plenty of bundled 3rd-party tools. Drop them all and properly DEPEND on their -# existing packages -# nlopt -# llvm -# python_libs -# bamtools -# ConsensusCore -# ssw -# jemalloc -# htrie -# getopt_pp -# cppformat -# cityhash -# samtools -# bwa - -# BUG: "${S}"/ext/tools/ contains even two version of bwa, being installed as bwa-spades binary? -# bwa-0.7.12 -# bwa-0.6.2 - -src_compile(){ - PREFIX="${ED}"/usr ./spades_compile.sh || die -} - -src_install(){ - # BUG: move *.py files to standard site-packages/ subdirectories - insinto /usr/share/"${PN}" - dodoc "${DISTDIR}"/${P}_*manual.html -} diff --git a/sci-biology/SPAdes/SPAdes-3.15.5.ebuild b/sci-biology/SPAdes/SPAdes-3.15.5.ebuild new file mode 100644 index 000000000..026dd0476 --- /dev/null +++ b/sci-biology/SPAdes/SPAdes-3.15.5.ebuild @@ -0,0 +1,42 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..12} ) +inherit python-single-r1 + +DESCRIPTION="De novo de Bruijn genome assembler overcoming uneven coverage" +HOMEPAGE="https://cab.spbu.ru/software/spades" +SRC_URI=" + https://github.com/ablab/spades/releases/download/v${PV}/${P}.tar.gz + https://cab.spbu.ru/files/release${PV}/manual.html -> ${P}_manual.html + https://cab.spbu.ru/files/release${PV}/rnaspades_manual.html -> ${P}_rnaspades_manual.html + https://cab.spbu.ru/files/release${PV}/truspades_manual.html -> ${P}_truspades_manual.html +" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64" +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +DEPEND=" + sys-libs/zlib + app-arch/bzip2 + dev-python/regex + ${PYTHON_DEPS} +" +RDEPEND="${DEPEND}" +BDEPEND="dev-build/cmake" + +# Remove for next release: +# https://github.com/ablab/spades/issues/1238#issuecomment-1904427831 +PATCHES=( + "${FILESDIR}/${P}-gcc13.patch" +) + +src_install(){ + einstalldocs + # WORKAROUND: This script does both compile and install in one go + PREFIX="${ED}"/usr ./spades_compile.sh || die +} diff --git a/sci-biology/SPAdes/files/SPAdes-3.15.5-gcc13.patch b/sci-biology/SPAdes/files/SPAdes-3.15.5-gcc13.patch new file mode 100644 index 000000000..3dd3f8c02 --- /dev/null +++ b/sci-biology/SPAdes/files/SPAdes-3.15.5-gcc13.patch @@ -0,0 +1,49 @@ +From 3e802fa51d156fc958c36e25d607f20bf756f0bf Mon Sep 17 00:00:00 2001 +From: Bo YU <tsu.yubo@gmail.com> +Date: Wed, 19 Jul 2023 18:42:04 +0800 +Subject: [PATCH] fix build issues due to gcc-13 + +Signed-off-by: Bo YU <tsu.yubo@gmail.com> +--- + ext/include/llvm/Support/Signals.h | 1 + + src/common/pipeline/library_data.hpp | 1 + + src/common/sequence/nucl.hpp | 2 ++ + 3 files changed, 4 insertions(+) + +diff --git a/assembler/ext/include/llvm/Support/Signals.h b/assembler/ext/include/llvm/Support/Signals.h +index e0a18e72f..148216b8f 100644 +--- a/ext/include/llvm/Support/Signals.h ++++ b/ext/include/llvm/Support/Signals.h +@@ -14,6 +14,7 @@ + #ifndef LLVM_SUPPORT_SIGNALS_H + #define LLVM_SUPPORT_SIGNALS_H + ++#include <cstdint> + #include <string> + + namespace llvm { +diff --git a/assembler/src/common/pipeline/library_data.hpp b/assembler/src/common/pipeline/library_data.hpp +index 3cbaf0adb..1ffaa7b37 100644 +--- a/src/common/pipeline/library_data.hpp ++++ b/src/common/pipeline/library_data.hpp +@@ -8,6 +8,7 @@ + + #include <map> + #include <string> ++#include <cstdint> + + // Forward decls for LLVM YAML API + namespace llvm { namespace yaml { class IO; template<typename T> struct MappingTraits; } } +diff --git a/assembler/src/common/sequence/nucl.hpp b/assembler/src/common/sequence/nucl.hpp +index 9c7d6de13..e10e7f583 100755 +--- a/src/common/sequence/nucl.hpp ++++ b/src/common/sequence/nucl.hpp +@@ -8,6 +8,8 @@ + #ifndef NUCL_HPP_ + #define NUCL_HPP_ + ++#include <cstdint> ++ + #include "utils/verify.hpp" + + /** diff --git a/sci-biology/SPAdes/metadata.xml b/sci-biology/SPAdes/metadata.xml index 0845ad7a4..5f573393e 100644 --- a/sci-biology/SPAdes/metadata.xml +++ b/sci-biology/SPAdes/metadata.xml @@ -10,8 +10,11 @@ <name>Gentoo Biology Project</name> </maintainer> <longdescription> -truSPAdes includes support for Illumina TruSeq Synthetic Long Read technology reads. -hammer and ionhammer are read error correcting modules for Illumina /IonTorrent reads, resp. -dipspades is assembly module for highly polymorphic diploid genomes -</longdescription> + truSPAdes includes support for Illumina TruSeq Synthetic Long Read technology reads. + hammer and ionhammer are read error correcting modules for Illumina /IonTorrent reads, resp. + dipspades is assembly module for highly polymorphic diploid genomes + </longdescription> + <upstream> + <remote-id type="github">ablab/spades</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/Trinotate/Manifest b/sci-biology/Trinotate/Manifest deleted file mode 100644 index 30ecd61fa..000000000 --- a/sci-biology/Trinotate/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST Trinotate-3.2.1.tar.gz 29794455 BLAKE2B b630b4750540aeefaed598d34038ebc4bf0147f998d9a45038759b1f02cd210835b88cdc7e8e5b8e194ade05b410f8e76ea562c09dcbf09bfa56cfffafa207c3 SHA512 0c2c5021156651644cfcec09bdd19f45c4dd5ab5dd63effbacca3ffc13a32ff3b2050d8fe860e4302ade142f350c895303925542aa730c16abe0721654f8cad7 diff --git a/sci-biology/Trinotate/Trinotate-3.2.1.ebuild b/sci-biology/Trinotate/Trinotate-3.2.1.ebuild deleted file mode 100644 index ca61abdf4..000000000 --- a/sci-biology/Trinotate/Trinotate-3.2.1.ebuild +++ /dev/null @@ -1,44 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit perl-module - -DESCRIPTION="Annotation and analysis pipeline for de novo assembled transcriptomes" -HOMEPAGE="https://github.com/Trinotate/Trinotate.github.io/wiki" -SRC_URI="https://github.com/Trinotate/Trinotate/archive/${PN}-v${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="BSD-BroadInstitute" -SLOT="0" -KEYWORDS="" - -DEPEND="" -RDEPEND="${DEPEND} - sci-biology/ncbi-tools++ - sci-biology/trinityrnaseq - sci-biology/TransDecoder -" - -# http://www.cbs.dtu.dk/cgi-bin/sw_request?rnammer -# >=sci-biology/rnammer-2.3.2 -# -# http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?signalp -# >=sci-biology/signalp-4 -# -# http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?tmhmm - -# We suggest you rename this version of hmmsearch from hmmer-2 package to 'hmmsearch2'. -# In the 'rnammer' software configuration, edit the rnammer script to point -# $HMMSEARCH_BINARY = "/path/to/hmmsearch2"; - -S="${WORKDIR}/${PN}-${PN}-v${PV}" - -src_install(){ - perl_set_version - dobin Trinotate - insinto /usr/share/"${PN}" - doins -r admin sample_data util TrinotateWeb - perl_domodule -r PerlLib/* - dodoc notes README.md README.txt Changelog.txt -} diff --git a/sci-biology/Trinotate/metadata.xml b/sci-biology/Trinotate/metadata.xml deleted file mode 100644 index eaf731f09..000000000 --- a/sci-biology/Trinotate/metadata.xml +++ /dev/null @@ -1,15 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="github">Trinotate/Trinotate</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-biology/VarScan/VarScan-2.4.4.ebuild b/sci-biology/VarScan/VarScan-2.4.4.ebuild index 72a3c94df..039a68f06 100644 --- a/sci-biology/VarScan/VarScan-2.4.4.ebuild +++ b/sci-biology/VarScan/VarScan-2.4.4.ebuild @@ -18,9 +18,11 @@ KEYWORDS="~amd64" DEPEND=" >=virtual/jdk-1.5:* - !sci-biology/VarScan-bin" +" RDEPEND=">=virtual/jre-1.5:* - sci-biology/bam-readcount" + sci-biology/bam-readcount + !sci-biology/VarScan-bin +" S="${WORKDIR}"/net/sf/varscan diff --git a/sci-biology/VelvetOptimiser/metadata.xml b/sci-biology/VelvetOptimiser/metadata.xml index 138cb7705..cc34f33b5 100644 --- a/sci-biology/VelvetOptimiser/metadata.xml +++ b/sci-biology/VelvetOptimiser/metadata.xml @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">tseemann/VelvetOptimiser</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/abacas/abacas-1.3.1.ebuild b/sci-biology/abacas/abacas-1.3.1.ebuild index 9abddf036..c347b508b 100644 --- a/sci-biology/abacas/abacas-1.3.1.ebuild +++ b/sci-biology/abacas/abacas-1.3.1.ebuild @@ -6,8 +6,8 @@ EAPI=7 inherit optfeature DESCRIPTION="Order and orientate DNA contigs even via 6-frame protein alignments" -HOMEPAGE="http://abacas.sourceforge.net" -SRC_URI="https://downloads.sourceforge.net/project/abacas/abacas.1.3.1.pl" +HOMEPAGE="https://abacas.sourceforge.net" +SRC_URI="https://downloads.sourceforge.net/project/abacas/abacas.${PV}.pl" LICENSE="GPL-2+" SLOT="0" @@ -21,7 +21,7 @@ RDEPEND="${DEPEND} S="${WORKDIR}" src_prepare(){ - cp -p "${DISTDIR}"/abacas.1.3.1.pl abacas.pl || die + cp -p "${DISTDIR}"/abacas.${PV}.pl abacas.pl || die sed \ -i 's#/usr/local/bin/perl#/usr/bin/perl#' \ -i abacas.pl || die diff --git a/sci-biology/abacas/metadata.xml b/sci-biology/abacas/metadata.xml index 0f267b755..0bb7ca029 100644 --- a/sci-biology/abacas/metadata.xml +++ b/sci-biology/abacas/metadata.xml @@ -10,6 +10,6 @@ <name>Gentoo Biology Project</name> </maintainer> <upstream> - <remote-id type="sourceforge">downloads</remote-id> + <remote-id type="sourceforge">abacas</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/afni/Manifest b/sci-biology/afni/Manifest index 2f909b5c4..d1e783ff1 100644 --- a/sci-biology/afni/Manifest +++ b/sci-biology/afni/Manifest @@ -1,3 +1,4 @@ -DIST afni-19.3.12.tar.gz 42337320 BLAKE2B f8f3347e38b7c4b3d720c3c49d5bc50f1057b1d3945e6a33b8415e84e7e539577e5eb351cfc61c53269b6a465619f900b9edcb25830ea056a53f54beb683b0ad SHA512 c4f9303312a89a6e87285646f58223df40b07329cf155bf251a48e8e63302988f103a97363d0666ddd8e9f62f762cf0c219bfc995265b4fe1f1ff5f782025371 -DIST afni-20.1.16.tar.gz 43355499 BLAKE2B ad7750e64dd9f4c2ca7e5c67bd99faeb8595a41d8a16192e77202f3d307e912083affc11dcbb5da3530079b9e3cf3c2b6b470050f57d5d7af2bb35cc2322772f SHA512 e6fdb8baea6165865bae5bb186375bd65e862564c48470523a8fe026a12f00715fd21bd852bd77c4077ea444a97642c4c3d2ca8060640ba5ddd57bd7883901a6 -DIST afni-20.3.03.tar.gz 43263734 BLAKE2B 7fdaf3de874edff9b32950a2724ba8b4cbcdda538b09effb12658a042326d5c8badf48f1a4dfb4555eb069347099cf3cdb08c4fe1a12999e6eca3ca6f8dca639 SHA512 3c5007f59d6c46093d38f9419c72aa36fb5701314690811f757d9568561b386cf3cd602ddf910ae08fd071ea7ae1e51f5762081217f7a29b23e32f1490f5db65 +DIST afni-24.0.04.gh.tar.gz 52888143 BLAKE2B db414b9ac9489aaab824e6f99cae54a1982e600d3b6d93a01cf3f175220ab76923a53ce6da647e4d8be87d3b50699c1b9603f8f0de43d812d34ceb1a65bde19d SHA512 aff673b63453a18c1f687775a6316614ee7495ff583e86c341aa0eed40d5f99b15cb599dea79baf05f8f8b77fea292436e3adc51b906dc13589968a8bdffa3d8 +DIST afni-24.0.08.gh.tar.gz 52917832 BLAKE2B 4cf61f3474c2c69d8373fbf9413c2236fbda77408535b142e6860effbf49ebcc6007ef9fb18943c07299b4815be6692477cc79423d7ac5a09bfe3d125565058c SHA512 90a9c8a48e1084dcc19d90e62b313057f0e71e87740f6ac63a305d19a4ded8ee01722b55546d2aaa2d4dfbfd0a206d4a9d25969592646c101cabe4743b8962c6 +DIST gifti-d3e873d8539d9b469daf7db04093da1d7e73d4f7.tar.gz 107745 BLAKE2B b8162fe08446d5c934762e8dce051e93c8c90fd574dca55757988ccc45be20bfdd07b7a401ef6c536afbe097e6bc05fd3b7f09c4404af4fad4e21fbada7109de SHA512 c458074c6976245cffc48c1e1e57811ec3c0cc5959345bdbc8d674eed6c8a8f93e9f9762bf3acce7142e004dc37930d14bed8cfb97c5b7e92b3f39598da924e2 +DIST nifti-da476fd27f46098f37f5c9c4c1baee01e559572c.tar.gz 451578 BLAKE2B 6bb92ae3ab48dba435b067f7ec0b6d417658ee1a46efe05070bf18fd6d46b8339eaffd09c2fea4971d2685f211496a700b36c255ffb164994636e535b64fe4f5 SHA512 df92345ed580e8bf0579f2ea3ed55a4c4c678a0fe3bfad1e62379e5bf16961272bb2d3e7fda89b96b503cda51c1bf2fb8eb74adba6aad9c73b6830d7d884d1f5 diff --git a/sci-biology/afni/afni-19.3.12.ebuild b/sci-biology/afni/afni-19.3.12.ebuild deleted file mode 100644 index db19930fd..000000000 --- a/sci-biology/afni/afni-19.3.12.ebuild +++ /dev/null @@ -1,72 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit toolchain-funcs - -DESCRIPTION="An open-source environment for processing and displaying functional MRI data" -HOMEPAGE="http://afni.nimh.nih.gov/" -SRC_URI="https://github.com/afni/afni/archive/AFNI_${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="GPL-3+" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -RDEPEND="dev-libs/expat - media-libs/glu - media-libs/netpbm - media-libs/qhull - media-video/mpeg-tools - sci-libs/gsl - sys-devel/llvm:* - virtual/jpeg:0 - x11-libs/libGLw - x11-libs/libXft - x11-libs/libXi - x11-libs/libXpm - x11-libs/motif[-static-libs]" - -# x11-libs/motif[static-libs] breaks the build. -# See upstream discussion -# http://afni.nimh.nih.gov/afni/community/board/read.php?1,85348,85348#msg-85348 - -DEPEND="${RDEPEND} - app-shells/tcsh" - -S="${WORKDIR}/${PN}-AFNI_${PV}/src" -BUILD="linux_fedora_19_64" -BIN_CONFLICTS=(qdelaunay whirlgif djpeg cjpeg qhull rbox count mpeg_encode) - -src_prepare() { - find -type f -exec sed -i -e "s/-lXp //g" {} + - cp other_builds/Makefile.${BUILD} Makefile || die "Could not copy Makefile" - # Unbundle imcat - sed -e "s/ imcat / /g" \ - -i Makefile.INCLUDE || die "Could not edit includes files." - sed -e "s~CC = /usr/bin/gcc -O2 -m64~CC = $(tc-getCC) \$(CFLAGS)~" \ - -e "s~CCMIN = /usr/bin/gcc -m64~CCMIN = $(tc-getCC) \$(CFLAGS)~" \ - -e "s~LD = /usr/bin/gcc~LD = $(tc-getCC)~" \ - -e "s~AR = /usr/bin/ar~AR = $(tc-getAR)~" \ - -e "s~RANLIB = /usr/bin/ranlib~RANLIB = $(tc-getRANLIB)~" \ - -i Makefile || die "Could not edit Makefile" - # they provide somewhat problematic makefiles :( - sed -e "s~ifeq ($(CC),gcc)~ifeq (1,1)~"\ - -i SUMA/SUMA_Makefile || die "Could not edit SUMA/SUMA_Makefile" - # upstream checks if $CC is EXACTLY gcc, else sets variables for Mac - find "${S}" -iname "*Makefile*" | xargs sed -e "s~/usr/~${EROOT}/usr/~g;" -i - eapply_user -} - -src_compile() { - emake -j1 all plugins suma_exec -} - -src_install() { - emake INSTALLDIR="${ED}/usr/bin" -j1 install install_plugins - emake INSTALLDIR="${ED}/usr/$(get_libdir)" -j1 install_lib - for CONFLICT in ${BIN_CONFLICTS[@]}; do - rm "${ED}/usr/bin/${CONFLICT}" - done -} diff --git a/sci-biology/afni/afni-20.1.16.ebuild b/sci-biology/afni/afni-20.1.16.ebuild deleted file mode 100644 index e2ed432c8..000000000 --- a/sci-biology/afni/afni-20.1.16.ebuild +++ /dev/null @@ -1,73 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit toolchain-funcs - -DESCRIPTION="An open-source environment for processing and displaying functional MRI data" -HOMEPAGE="http://afni.nimh.nih.gov/" -SRC_URI="https://github.com/afni/afni/archive/AFNI_${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="GPL-3+" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -RDEPEND="dev-libs/expat - media-libs/glu - media-libs/netpbm - media-libs/qhull - media-video/mpeg-tools - sci-libs/gsl - sys-devel/llvm:* - virtual/jpeg:0 - x11-libs/libGLw - x11-libs/libXft - x11-libs/libXi - x11-libs/libXpm - x11-libs/motif[-static-libs]" - -# x11-libs/motif[static-libs] breaks the build. -# See upstream discussion -# http://afni.nimh.nih.gov/afni/community/board/read.php?1,85348,85348#msg-85348 - -DEPEND="${RDEPEND} - app-shells/tcsh" - -S="${WORKDIR}/${PN}-AFNI_${PV}/src" -BUILD="linux_fedora_19_64" -BIN_CONFLICTS=(qdelaunay whirlgif djpeg cjpeg qhull rbox count mpeg_encode) - -src_prepare() { - eapply "${FILESDIR}/${P}-python.patch" || die - find -type f -exec sed -i -e "s/-lXp //g" {} + - cp other_builds/Makefile.${BUILD} Makefile || die "Could not copy Makefile" - # Unbundle imcat - sed -e "s/ imcat / /g" \ - -i Makefile.INCLUDE || die "Could not edit includes files." - sed -e "s~CC = /usr/bin/gcc -O2 -m64~CC = $(tc-getCC) \$(CFLAGS)~" \ - -e "s~CCMIN = /usr/bin/gcc -m64~CCMIN = $(tc-getCC) \$(CFLAGS)~" \ - -e "s~LD = /usr/bin/gcc~LD = $(tc-getCC)~" \ - -e "s~AR = /usr/bin/ar~AR = $(tc-getAR)~" \ - -e "s~RANLIB = /usr/bin/ranlib~RANLIB = $(tc-getRANLIB)~" \ - -i Makefile || die "Could not edit Makefile" - # they provide somewhat problematic makefiles :( - sed -e "s~ifeq ($(CC),gcc)~ifeq (1,1)~"\ - -i SUMA/SUMA_Makefile || die "Could not edit SUMA/SUMA_Makefile" - # upstream checks if $CC is EXACTLY gcc, else sets variables for Mac - find "${S}" -iname "*Makefile*" | xargs sed -e "s~/usr/~${EROOT}/usr/~g;" -i - default -} - -src_compile() { - emake -j1 all plugins suma_exec -} - -src_install() { - emake INSTALLDIR="${ED}/usr/bin" -j1 install install_plugins - emake INSTALLDIR="${ED}/usr/$(get_libdir)" install_lib - for CONFLICT in ${BIN_CONFLICTS[@]}; do - rm "${ED}/usr/bin/${CONFLICT}" - done -} diff --git a/sci-biology/afni/afni-20.3.03.ebuild b/sci-biology/afni/afni-20.3.03.ebuild deleted file mode 100644 index 3185a297a..000000000 --- a/sci-biology/afni/afni-20.3.03.ebuild +++ /dev/null @@ -1,77 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit toolchain-funcs - -DESCRIPTION="An open-source environment for processing and displaying functional MRI data" -HOMEPAGE="http://afni.nimh.nih.gov/" -SRC_URI="https://github.com/afni/afni/archive/AFNI_${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="GPL-3+" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -RDEPEND="dev-libs/expat - media-libs/glu - media-libs/netpbm - media-libs/qhull - media-video/mpeg-tools - sci-libs/gsl - sys-devel/llvm:* - virtual/jpeg:0 - x11-libs/libGLw - x11-libs/libXft - x11-libs/libXi - x11-libs/libXpm - x11-libs/motif[-static-libs]" - -# x11-libs/motif[static-libs] breaks the build. -# See upstream discussion -# http://afni.nimh.nih.gov/afni/community/board/read.php?1,85348,85348#msg-85348 - -DEPEND="${RDEPEND} - app-shells/tcsh" - -S="${WORKDIR}/${PN}-AFNI_${PV}/src" -BUILD="linux_fedora_19_64" -BIN_CONFLICTS=(qdelaunay whirlgif djpeg cjpeg qhull rbox count mpeg_encode) - -#PATCHES=( -# "${FILESDIR}/${P}-python.patch" -#) - -src_prepare() { - eapply "${FILESDIR}/${P}-python.patch" || die - find -type f -exec sed -i -e "s/-lXp //g" {} + - cp other_builds/Makefile.${BUILD} Makefile || die "Could not copy Makefile" - # Unbundle imcat - sed -e "s/ imcat / /g" \ - -i Makefile.INCLUDE || die "Could not edit includes files." - sed -e "s~CC = /usr/bin/gcc -O2 -m64~CC = $(tc-getCC) \$(CFLAGS)~" \ - -e "s~CCMIN = /usr/bin/gcc -m64~CCMIN = $(tc-getCC) \$(CFLAGS)~" \ - -e "s~LD = /usr/bin/gcc~LD = $(tc-getCC)~" \ - -e "s~AR = /usr/bin/ar~AR = $(tc-getAR)~" \ - -e "s~RANLIB = /usr/bin/ranlib~RANLIB = $(tc-getRANLIB)~" \ - -i Makefile || die "Could not edit Makefile" - # they provide somewhat problematic makefiles :( - sed -e "s~ifeq ($(CC),gcc)~ifeq (1,1)~"\ - -i SUMA/SUMA_Makefile || die "Could not edit SUMA/SUMA_Makefile" - # upstream checks if $CC is EXACTLY gcc, else sets variables for Mac - find "${S}" -iname "*Makefile*" | xargs sed -e "s~/usr/~${EROOT}/usr/~g;" -i - default -} - -src_compile() { - emake -j1 all plugins suma_exec -} - -src_install() { - emake INSTALLDIR="${ED}/usr/bin" -j1 install install_plugins - emake INSTALLDIR="${ED}/usr/$(get_libdir)" install_lib - for CONFLICT in ${BIN_CONFLICTS[@]}; do - rm "${ED}/usr/bin/${CONFLICT}" - done -} diff --git a/sci-biology/afni/afni-24.0.04-r1.ebuild b/sci-biology/afni/afni-24.0.04-r1.ebuild new file mode 100644 index 000000000..557fbd579 --- /dev/null +++ b/sci-biology/afni/afni-24.0.04-r1.ebuild @@ -0,0 +1,110 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..12} ) + +DISTUTILS_USE_PEP517=setuptools +inherit cmake distutils-r1 toolchain-funcs + +GTS_HASH="962155a01f5a1b87bd64e3e3d880b4dbc2347ac7" +NIFTI_HASH="da476fd27f46098f37f5c9c4c1baee01e559572c" +GIFTI_HASH="d3e873d8539d9b469daf7db04093da1d7e73d4f7" + +DESCRIPTION="Advanced Normalitazion Tools for neuroimaging" +HOMEPAGE="http://stnava.github.io/ANTs/" +SRC_URI=" + https://github.com/afni/afni/archive/refs/tags/AFNI_${PV}.tar.gz -> ${P}.gh.tar.gz + https://github.com/NIFTI-Imaging/nifti_clib/archive/${NIFTI_HASH}.tar.gz -> nifti-${NIFTI_HASH}.tar.gz + https://github.com/NIFTI-Imaging/gifti_clib/archive/${GIFTI_HASH}.tar.gz -> gifti-${GIFTI_HASH}.tar.gz + " + +SLOT="0" +LICENSE="GPL-3+" +KEYWORDS="~amd64 ~x86" +IUSE="test whirlgif" +RESTRICT="!test? ( test )" + +RDEPEND=" + dev-libs/glib:2 + dev-libs/libf2c + dev-libs/expat + dev-build/ninja + media-libs/freeglut + media-libs/glu + media-libs/netpbm + media-libs/qhull + media-video/mpeg-tools + sci-libs/gsl + sci-libs/gts + sys-devel/llvm:* + sys-libs/libomp + virtual/jpeg-compat:62 + x11-libs/libGLw + x11-libs/libXft + x11-libs/libXi + x11-libs/libXmu + x11-libs/libXpm + x11-libs/libXt + x11-libs/motif[-static-libs] + " +DEPEND=" + ${RDEPEND} + app-shells/tcsh + " + +S="${WORKDIR}/afni-AFNI_${PV}" + +src_prepare() { + tar xf "${DISTDIR}/nifti-${NIFTI_HASH}.tar.gz" || die + tar xf "${DISTDIR}/gifti-${GIFTI_HASH}.tar.gz" || die + cmake_src_prepare + default + } + +src_configure() { + if use !whirlgif; then + eapply "${FILESDIR}/${P}-whirlgif.patch" + fi + export CFLAGS="-pthread ${CFLAGS}" + export GIT_REPO_VERSION=3.0.1.1 + local mycmakeargs=( + -DLIBDIR=/usr/$(get_libdir) + -DNIFTI_INSTALL_LIBRARY_DIR=/usr/$(get_libdir) + -DGIFTI_INSTALL_LIBRARY_DIR=/usr/$(get_libdir) + -DGIFTI_INSTALL_LIB_DIR=/usr/$(get_libdir) + -DAFNI_INSTALL_LIBRARY_DIR=/usr/$(get_libdir) + -DCMAKE_INSTALL_LIBDIR=/usr/$(get_libdir) + -DCOMP_COREBINARIES=ON + -DUSE_SYSTEM_NIFTI=OFF + -DUSE_SYSTEM_GIFTI=OFF + -DUSE_SYSTEM_XMHTML=OFF + -DUSE_SYSTEM_GTS=ON + -DFETCHCONTENT_SOURCE_DIR_NIFTI_CLIB="${WORKDIR}/nifti_clib-${NIFTI_HASH}" + -DFETCHCONTENT_SOURCE_DIR_GIFTI_CLIB="${WORKDIR}/gifti_clib-${GIFTI_HASH}" + -DCOMP_GUI=ON + -DCOMP_PLUGINS=ON + -DUSE_OMP=ON + -DCOMP_PYTHON=OFF + -DUSE_SYSTEM_F2C=ON + ) + tc-export CC + cmake_src_configure +} + +src_compile() { + cmake_src_compile + pushd src/python_scripts + distutils-r1_src_compile + popd +} + +src_install() { + cmake_src_install + pushd src/python_scripts + distutils-r1_src_install + popd + cd "${D}" + rm usr/bin/mpeg_encode +} diff --git a/sci-biology/afni/afni-24.0.08-r1.ebuild b/sci-biology/afni/afni-24.0.08-r1.ebuild new file mode 100644 index 000000000..20293877f --- /dev/null +++ b/sci-biology/afni/afni-24.0.08-r1.ebuild @@ -0,0 +1,114 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..12} ) + +DISTUTILS_USE_PEP517=setuptools +inherit cmake distutils-r1 toolchain-funcs + +GTS_HASH="962155a01f5a1b87bd64e3e3d880b4dbc2347ac7" +NIFTI_HASH="da476fd27f46098f37f5c9c4c1baee01e559572c" +GIFTI_HASH="d3e873d8539d9b469daf7db04093da1d7e73d4f7" + +DESCRIPTION="Advanced Normalitazion Tools for neuroimaging" +HOMEPAGE="http://stnava.github.io/ANTs/" +SRC_URI=" + https://github.com/afni/afni/archive/refs/tags/AFNI_${PV}.tar.gz -> ${P}.gh.tar.gz + https://github.com/NIFTI-Imaging/nifti_clib/archive/${NIFTI_HASH}.tar.gz -> nifti-${NIFTI_HASH}.tar.gz + https://github.com/NIFTI-Imaging/gifti_clib/archive/${GIFTI_HASH}.tar.gz -> gifti-${GIFTI_HASH}.tar.gz + " + +SLOT="0" +LICENSE="GPL-3+" +KEYWORDS="~amd64 ~x86" +IUSE="test whirlgif" +RESTRICT="!test? ( test )" + +RDEPEND=" + dev-libs/glib:2 + dev-libs/libf2c + dev-libs/expat + dev-build/ninja + media-libs/freeglut + media-libs/glu + media-libs/netpbm + media-libs/qhull + media-video/mpeg-tools + sci-libs/gsl + sci-libs/gts + sys-devel/llvm:* + sys-libs/libomp + virtual/jpeg-compat:62 + x11-libs/libGLw + x11-libs/libXft + x11-libs/libXi + x11-libs/libXmu + x11-libs/libXpm + x11-libs/libXt + x11-libs/motif[-static-libs] + " +DEPEND=" + ${RDEPEND} + app-shells/tcsh + " +# Prospectively: +#Update jpeg-compat to virtual/jpeg:0 +# look for xmhtlm + +S="${WORKDIR}/afni-AFNI_${PV}" + + #tar xf "${DISTDIR}/${GTS_HASH}.tar.gz" || die +src_prepare() { + tar xf "${DISTDIR}/nifti-${NIFTI_HASH}.tar.gz" || die + tar xf "${DISTDIR}/gifti-${GIFTI_HASH}.tar.gz" || die + cmake_src_prepare + default + } + +src_configure() { + if use !whirlgif; then + eapply "${FILESDIR}/${PN}-24.0.04-whirlgif.patch" + fi + export CFLAGS="-pthread ${CFLAGS}" + export GIT_REPO_VERSION=3.0.1.1 + local mycmakeargs=( + -DLIBDIR=/usr/$(get_libdir) + -DNIFTI_INSTALL_LIBRARY_DIR=/usr/$(get_libdir) + -DGIFTI_INSTALL_LIBRARY_DIR=/usr/$(get_libdir) + -DGIFTI_INSTALL_LIB_DIR=/usr/$(get_libdir) + -DAFNI_INSTALL_LIBRARY_DIR=/usr/$(get_libdir) + -DCMAKE_INSTALL_LIBDIR=/usr/$(get_libdir) + -DCOMP_COREBINARIES=ON + -DUSE_SYSTEM_NIFTI=OFF + -DUSE_SYSTEM_GIFTI=OFF + -DUSE_SYSTEM_XMHTML=OFF + -DUSE_SYSTEM_GTS=ON + -DFETCHCONTENT_SOURCE_DIR_NIFTI_CLIB="${WORKDIR}/nifti_clib-${NIFTI_HASH}" + -DFETCHCONTENT_SOURCE_DIR_GIFTI_CLIB="${WORKDIR}/gifti_clib-${GIFTI_HASH}" + -DCOMP_GUI=ON + -DCOMP_PLUGINS=ON + -DUSE_OMP=ON + -DCOMP_PYTHON=OFF + -DUSE_SYSTEM_F2C=ON + ) + tc-export CC + cmake_src_configure +} + +src_compile() { + cmake_src_compile + pushd src/python_scripts + distutils-r1_src_compile + popd +} + +src_install() { + cmake_src_install + pushd src/python_scripts + distutils-r1_src_install + popd + cd "${D}" + rm usr/bin/mpeg_encode +} diff --git a/sci-biology/afni/afni-9999.ebuild b/sci-biology/afni/afni-9999.ebuild deleted file mode 100644 index c6e4c669b..000000000 --- a/sci-biology/afni/afni-9999.ebuild +++ /dev/null @@ -1,70 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit git-r3 toolchain-funcs - -DESCRIPTION="An open-source environment for processing and displaying functional MRI data" -HOMEPAGE="http://afni.nimh.nih.gov/" -SRC_URI="" -EGIT_REPO_URI="https://github.com/AFNI/AFNI" - -LICENSE="GPL-3+" -SLOT="0" -KEYWORDS="" -IUSE="" - -RDEPEND="dev-libs/expat - media-libs/glu - media-libs/netpbm - media-libs/qhull - media-video/mpeg-tools - sci-libs/gsl - sys-devel/llvm:* - virtual/jpeg:0 - x11-libs/libGLw - x11-libs/libXft - x11-libs/libXi - x11-libs/libXpm - x11-libs/motif[-static-libs]" - -# x11-libs/motif[static-libs] breaks the build. -# See upstream discussion -# http://afni.nimh.nih.gov/afni/community/board/read.php?1,85348,85348#msg-85348 - -DEPEND="${RDEPEND} - app-shells/tcsh" - -S="${WORKDIR}/${P}/src" -BUILD="linux_fedora_19_64" -BIN_CONFLICTS=(qdelaunay whirlgif djpeg cjpeg qhull rbox count mpeg_encode) - -src_prepare() { - find -type f -exec sed -i -e "s/-lXp //g" {} + - cp other_builds/Makefile.${BUILD} Makefile || die "Could not copy Makefile" - sed -e "s~CC = /usr/bin/gcc -O2 -m64~CC = $(tc-getCC) \$(CFLAGS)~" \ - -e "s~CCMIN = /usr/bin/gcc -m64~CCMIN = $(tc-getCC) \$(CFLAGS)~" \ - -e "s~LD = /usr/bin/gcc~LD = $(tc-getCC)~" \ - -e "s~AR = /usr/bin/ar~AR = $(tc-getAR)~" \ - -e "s~RANLIB = /usr/bin/ranlib~RANLIB = $(tc-getRANLIB)~" \ - -i Makefile || die "Could not edit Makefile" - # they provide somewhat problematic makefiles :( - sed -e "s~ifeq ($(CC),gcc)~ifeq (1,1)~"\ - -i SUMA/SUMA_Makefile || die "Could not edit SUMA/SUMA_Makefile" - # upstream checks if $CC is EXACTLY gcc, else sets variables for Mac - find "${S}" -iname "*Makefile*" | xargs sed -e "s~/usr/~${EROOT}/usr/~g;" -i - eapply_user -} - -src_compile() { - emake -j1 all plugins suma_exec -} - -src_install() { - emake INSTALLDIR="${ED}/usr/bin" -j1 install install_plugins - emake INSTALLDIR="${ED}/usr/$(get_libdir)" -j1 install_lib - for CONFLICT in ${BIN_CONFLICTS[@]}; do - rm "${ED}/usr/bin/${CONFLICT}" - done -} diff --git a/sci-biology/afni/files/afni-20.1.16-python.patch b/sci-biology/afni/files/afni-20.1.16-python.patch deleted file mode 100644 index 24ed98405..000000000 --- a/sci-biology/afni/files/afni-20.1.16-python.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- a/other_builds/Makefile.linux_fedora_19_64 2020-10-09 07:07:58.348874414 -0400 -+++ b/other_builds/Makefile.linux_fedora_19_64 2020-10-10 01:15:22.337755934 -0400 -@@ -11,8 +11,6 @@ - - # ------------------------------ - # python from C --IPYTHON = -DSELENIUM_READY -I/usr/include/python2.7 --LDPYTHON = -lpython2.7 - - # ---------------------------------------------------------------------- - # X configuration diff --git a/sci-biology/afni/files/afni-20.3.03-python.patch b/sci-biology/afni/files/afni-20.3.03-python.patch deleted file mode 100644 index 24ed98405..000000000 --- a/sci-biology/afni/files/afni-20.3.03-python.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- a/other_builds/Makefile.linux_fedora_19_64 2020-10-09 07:07:58.348874414 -0400 -+++ b/other_builds/Makefile.linux_fedora_19_64 2020-10-10 01:15:22.337755934 -0400 -@@ -11,8 +11,6 @@ - - # ------------------------------ - # python from C --IPYTHON = -DSELENIUM_READY -I/usr/include/python2.7 --LDPYTHON = -lpython2.7 - - # ---------------------------------------------------------------------- - # X configuration diff --git a/sci-biology/afni/files/afni-24.0.04-whirlgif.patch b/sci-biology/afni/files/afni-24.0.04-whirlgif.patch new file mode 100644 index 000000000..a357799e6 --- /dev/null +++ b/sci-biology/afni/files/afni-24.0.04-whirlgif.patch @@ -0,0 +1,39 @@ +diff --git a/packaging/installation_components.txt b/packaging/installation_components.txt +index 127193338..ba8825a7b 100644 +--- a/packaging/installation_components.txt ++++ b/packaging/installation_components.txt +@@ -347,7 +347,6 @@ uniq_images, corebinaries + unu, corebinaries + waver, corebinaries + whereami, corebinaries +-whirlgif, corebinaries + 3dMax, tcsh + 3dPAR2AFNI.pl, tcsh + @1dDiffMag, tcsh +diff --git a/src/CMakeLists_binaries.txt b/src/CMakeLists_binaries.txt +index d53368390..8c8e9e1fb 100644 +--- a/src/CMakeLists_binaries.txt ++++ b/src/CMakeLists_binaries.txt +@@ -209,7 +209,6 @@ foreach( + uniq_images + unu + whereami +- whirlgif + ) + + add_afni_executable(${target} ${target}.c) +diff --git a/src/Makefile.INCLUDE b/src/Makefile.INCLUDE +index f44103def..7ac08a87d 100644 +--- a/src/Makefile.INCLUDE ++++ b/src/Makefile.INCLUDE +@@ -3495,11 +3495,6 @@ help_format:help_format.o + ibinom:ibinom.o + $(CC) -o ibinom ibinom.o $(LFLAGS) $(LLIBS) + +-## GIF animation +- +-whirlgif:whirlgif.h whirlgif.c +- $(CC) -o whirlgif whirlgif.c $(INFLAGS) $(LFLAGS) $(LLIBS) +- + extor.o:extor.c + $(CCFAST) -c extor.c $(INFLAGS) diff --git a/sci-biology/afni/metadata.xml b/sci-biology/afni/metadata.xml index acf637dca..39ec69d08 100644 --- a/sci-biology/afni/metadata.xml +++ b/sci-biology/afni/metadata.xml @@ -13,4 +13,10 @@ Analysis of Functional NeuroImages (AFNI) is an open-source environment for processing and displaying functional MRI data—a technique for mapping human brain activity. </longdescription> + <use> + <flag name="whirlgif">Build optional whirlgif binary</flag> + </use> + <upstream> + <remote-id type="github">afni/afni</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/aghermann/aghermann-1.1.2-r2.ebuild b/sci-biology/aghermann/aghermann-1.1.2-r2.ebuild index 4606fa9df..b0ac5fe00 100644 --- a/sci-biology/aghermann/aghermann-1.1.2-r2.ebuild +++ b/sci-biology/aghermann/aghermann-1.1.2-r2.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=7 @@ -13,7 +13,7 @@ SRC_URI="http://johnhommer.com/code/aghermann/source/${P}.tar.xz" LICENSE="GPL-2+" SLOT="0" -KEYWORDS="" +KEYWORDS="~amd64" REQUIRED_USE="${LUA_REQUIRED_USE}" diff --git a/sci-biology/angsd/metadata.xml b/sci-biology/angsd/metadata.xml index 138cb7705..ed9e5b12d 100644 --- a/sci-biology/angsd/metadata.xml +++ b/sci-biology/angsd/metadata.xml @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">ANGSD/angsd</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/ants/Manifest b/sci-biology/ants/Manifest index 867a142eb..ef2d97caf 100644 --- a/sci-biology/ants/Manifest +++ b/sci-biology/ants/Manifest @@ -1,2 +1,2 @@ -DIST ants-2.3.4.tar.gz 2455843 BLAKE2B c00a2d3edebc0a121fa3b6618982c64fd986db9ea6aed1a1b2c7ced2f77ab154837a47e5bcb01f432b937160de2248b30a2bb7b526952852946e686858334e12 SHA512 084161505671a19530bec40c8209a67510d7de6e9d5afd151b806755ca703dadbea17c0a8d5c6472c7a81185821e17213ebf1488bc0325bfe858af783e8e6575 -DIST ants_testdata-2.3.4.tar.xz 25056552 BLAKE2B 6478ffe0c98fd3700a6de201f1271339276b45b461b02d4753acdcd1335c83196aa2ed89a89b5b4b0b3df33026f77b231ba1418c9eb7a2380356d4e224f9b310 SHA512 a266fbf2de0003ee689a9369c424c97c92cdf7e4d08ba713623948276d96c9f0f02ab14480c329f462db0059217138680bfe39654f9ec4ac99bf947f51da853d +DIST ants-2.4.3.tar.gz 2474986 BLAKE2B 56a057673ff65e7ed3037ee34cea481e960122f32d2fd04b347644126793a2ba0a9249823b45e360abf2019136659b3ba4a24e49677458d69cc0b614266faca1 SHA512 50b42e30bec9077a00450253a39a8296ca841a3b3511f623a759071e6fbda9b6ab480b4f26566c621dc85107913f2782f2a1c4ecdeaa8361dc132209a432c544 +DIST ants_testdata-2.4.3.tar.xz 25058064 BLAKE2B ca3bb9998d7ded8fc9821a341a3a5b847a40fe93cccbc61458b5a6f9bab102a14fa297aad2425a5602b70c51e756edab2609213b01e06f7dc63eca2e67846351 SHA512 2689bdf1cb6bc4e608511efab574c8a0a5de839a376e9af91e277bae352744fa58463258ea604ea73041b7b596a3ab3a36e0f5a28c098ee5e7a1a9f8b8873779 diff --git a/sci-biology/ants/ants-2.3.4.ebuild b/sci-biology/ants/ants-2.4.3.ebuild index 756fde11d..2dfa2a56d 100644 --- a/sci-biology/ants/ants-2.3.4.ebuild +++ b/sci-biology/ants/ants-2.4.3.ebuild @@ -1,22 +1,22 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 CMAKE_MAKEFILE_GENERATOR="emake" - inherit cmake MY_PN="ANTs" DESCRIPTION="Advanced Normalitazion Tools for neuroimaging" -HOMEPAGE="http://stnava.github.io/ANTs/" +HOMEPAGE="https://stnava.github.io/ANTs/" SRC_URI=" https://github.com/ANTsX/ANTs/archive/v${PV}.tar.gz -> ${P}.tar.gz test? ( - http://chymera.eu/distfiles/ants_testdata-${PV}.tar.xz + https://resources.chymera.eu/distfiles/ants_testdata-${PV}.tar.xz ) " +S="${WORKDIR}/${MY_PN}-${PV}" SLOT="0" LICENSE="BSD" @@ -25,49 +25,40 @@ IUSE="test vtk" RESTRICT="!test? ( test )" DEPEND=" + !vtk? ( =sci-libs/itk-5.3*[fftw,-vtkglue] ) vtk? ( - ~sci-libs/itk-5.1.0[vtkglue] - sci-libs/vtk + =sci-libs/itk-5.3*[fftw,vtkglue] + =sci-libs/vtk-9.2* ) - !vtk? ( ~sci-libs/itk-5.1.0 ) " RDEPEND="${DEPEND}" -PATCHES=( - "${FILESDIR}/${P}-version.patch" - "${FILESDIR}/${P}-libdir.patch" -) - -S="${WORKDIR}/${MY_PN}-${PV}" - src_unpack() { default if use test; then - mkdir -p "${S}/.ExternalData/MD5" || die "Could not create test data directory." - tar xvf "${DISTDIR}/ants_testdata-${PV}.tar.xz" -C "${S}/.ExternalData/MD5/" > /dev/null || die "Could not unpack test data." + mkdir -p "${S}/.ExternalData/SHA512" || die "Could not create test data directory." + tar xvf "${DISTDIR}/ants_testdata-${PV}.tar.xz" -C "${S}/.ExternalData/SHA512/" > /dev/null || die "Could not unpack test data." fi } src_configure() { local mycmakeargs=( + -DBUILD_EXAMPLES=OFF -DUSE_SYSTEM_ITK=ON - -DITK_DIR="${EPREFIX}/usr/include/ITK-5.1/" + -DITK_USE_SYSTEM_FFTW=ON + -DITK_DIR="${EPREFIX}/usr/include/ITK-5.3/" -DBUILD_TESTING="$(usex test ON OFF)" -DUSE_VTK=$(usex vtk ON OFF) -DUSE_SYSTEM_VTK=$(usex vtk ON OFF) - -DANTS_SNAPSHOT_VERSION:STRING=${PV} ) use vtk && mycmakeargs+=( - -DVTK_DIR="${EPREFIX}/usr/include/vtk-8.1/" - ) - use test && mycmakeargs+=( - -DExternalData_OBJECT_STORES="${S}/.ExternalData/MD5" + -DVTK_DIR="${EPREFIX}/usr/include/vtk-9.2/" ) cmake_src_configure } src_install() { - BUILD_DIR="${WORKDIR}/${P}_build/ANTS-build" + BUILD_DIR="${WORKDIR}/${MY_PN}-${PV}_build/ANTS-build" cmake_src_install cd "${S}/Scripts" || die "scripts dir not found" dobin *.sh diff --git a/sci-biology/ants/files/ants-2.3.1_p20191013-logic.patch b/sci-biology/ants/files/ants-2.3.1_p20191013-logic.patch deleted file mode 100644 index 932da9954..000000000 --- a/sci-biology/ants/files/ants-2.3.1_p20191013-logic.patch +++ /dev/null @@ -1,37 +0,0 @@ -From b2c828ff8e5ce537d7096af04b086e965fede9e8 Mon Sep 17 00:00:00 2001 -From: "Gabriel A. Devenyi" <gdevenyi@gmail.com> -Date: Mon, 7 Oct 2019 22:01:51 -0400 -Subject: [PATCH] Fix install logic - ---- - ANTS.cmake | 3 ++- - SuperBuild.cmake | 2 ++ - 2 files changed, 4 insertions(+), 1 deletion(-) - -diff --git a/ANTS.cmake b/ANTS.cmake -index a1baf845..95ffdc74 100644 ---- a/ANTS.cmake -+++ b/ANTS.cmake -@@ -172,7 +172,8 @@ install(PROGRAMS Scripts/ANTSpexec.sh - COMPONENT SCRIPTS - ) - --if(BUILD_SHARED_LIBS AND NOT (USE_SYSTEM_ITK AND USE_SYSTEM_VTK)) -+#Only install ITK/VTK libraries if shared build and superbuild is used -+if(BUILD_SHARED_LIBS AND ((NOT USE_SYSTEM_ITK) OR ((NOT USE_SYSTEM_VTK) AND USE_VTK))) - install(DIRECTORY ${CMAKE_BINARY_DIR}/../staging/lib/ - DESTINATION lib) - endif() -diff --git a/SuperBuild.cmake b/SuperBuild.cmake -index f4630e64..32b930c2 100644 ---- a/SuperBuild.cmake -+++ b/SuperBuild.cmake -@@ -207,6 +207,8 @@ list(APPEND ${CMAKE_PROJECT_NAME}_SUPERBUILD_EP_VARS - CMAKE_C_COMPILER_LAUNCHER:STRING - CMAKE_CXX_COMPILER_LAUNCHER:STRING - CMAKE_CUDA_COMPILER_LAUNCHER:STRING -+ USE_SYSTEM_ITK:BOOL -+ USE_SYSTEM_VTK:BOOL - ) - - _expand_external_project_vars() diff --git a/sci-biology/ants/files/ants-2.3.1_p20191013-paths.patch b/sci-biology/ants/files/ants-2.3.1_p20191013-paths.patch deleted file mode 100644 index aaea92808..000000000 --- a/sci-biology/ants/files/ants-2.3.1_p20191013-paths.patch +++ /dev/null @@ -1,40 +0,0 @@ -diff --git a/Examples/CMakeLists.txt b/Examples/CMakeLists.txt ---- a/Examples/CMakeLists.txt -+++ b/Examples/CMakeLists.txt -@@ -16,8 +16,9 @@ -+include(GNUInstallDirs) - install(TARGETS antsUtilities -- RUNTIME DESTINATION bin -+ RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR} - COMPONENT RUNTIME_antsUtilities -- LIBRARY DESTINATION lib -+ LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} - COMPONENT RUNTIME_antsUtilities -- ARCHIVE DESTINATION lib -+ ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR} - COMPONENT DEVELOPMENT_antsUtilities - ) -@@ -38,8 +38,8 @@ - install(TARGETS l_${ANTS_FUNCTION_NAME} ${ANTS_FUNCTION_NAME} -- RUNTIME DESTINATION bin -+ RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR} - COMPONENT RUNTIME_${ANTS_FUNCTION_NAME} -- LIBRARY DESTINATION lib -+ LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} - COMPONENT RUNTIME_${ANTS_FUNCTION_NAME} -- ARCHIVE DESTINATION lib -+ ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR} - COMPONENT DEVELOPMENT_${ANTS_FUNCTION_NAME} - ) -@@ -61,8 +61,8 @@ - install(TARGETS l_${ANTS_FUNCTION_NAME} ${ANTS_FUNCTION_NAME} -- RUNTIME DESTINATION bin -+ RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR} - COMPONENT RUNTIME_${ANTS_FUNCTION_NAME} -- LIBRARY DESTINATION lib -+ LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} - COMPONENT RUNTIME_${ANTS_FUNCTION_NAME} -- ARCHIVE DESTINATION lib -+ ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR} - COMPONENT DEVELOPMENT_${ANTS_FUNCTION_NAME} - ) diff --git a/sci-biology/ants/files/ants-2.3.4-libdir.patch b/sci-biology/ants/files/ants-2.3.4-libdir.patch deleted file mode 100644 index b593c2778..000000000 --- a/sci-biology/ants/files/ants-2.3.4-libdir.patch +++ /dev/null @@ -1,117 +0,0 @@ -From 329a7be631b33294d9cf3d58e8cdeb62e0aa993c Mon Sep 17 00:00:00 2001 -From: Philip A Cook <cookpa@pennmedicine.upenn.edu> -Date: Fri, 26 Jun 2020 18:23:08 +0000 -Subject: [PATCH] ENH: Use GNUInstallDirs CMake module - -Trying to enable installation to the correct lib dir for each platform ---- - Common.cmake | 7 +++++-- - Examples/CMakeLists.txt | 32 ++++++++++++++++---------------- - 2 files changed, 21 insertions(+), 18 deletions(-) - -diff --git a/Common.cmake b/Common.cmake -index 5e52d7f1..1e604113 100644 ---- a/Common.cmake -+++ b/Common.cmake -@@ -103,8 +103,6 @@ if(PLATFORM_CHECK) - endif() - endif() - -- -- - #------------------------------------------------------------------------- - # Augment compiler flags - #------------------------------------------------------------------------- -@@ -124,3 +122,8 @@ if(NOT CMAKE_POSITION_INDEPENDENT_CODE) - set(CMAKE_POSITION_INDEPENDENT_CODE ON) - endif() - endif() -+ -+#------------------------------------------------------------------------- -+# Define install dirs for different platforms -+#------------------------------------------------------------------------- -+include(GNUInstallDirs) -diff --git a/Examples/CMakeLists.txt b/Examples/CMakeLists.txt -index 61781f56..cb352748 100644 ---- a/Examples/CMakeLists.txt -+++ b/Examples/CMakeLists.txt -@@ -1,4 +1,4 @@ --SET(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib") -+SET(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_LIBDIR}") - ## Note that the antsUtilities can always be built static. It will then be linked - ## Directly into the other libraries. - add_library(antsUtilities antsUtilities.cxx -@@ -14,11 +14,11 @@ add_library(antsUtilities antsUtilities.cxx - ) - target_link_libraries(antsUtilities ${ITK_LIBRARIES} ) - install(TARGETS antsUtilities -- RUNTIME DESTINATION bin -+ RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR} - COMPONENT RUNTIME_antsUtilities -- LIBRARY DESTINATION lib -+ LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} - COMPONENT RUNTIME_antsUtilities -- ARCHIVE DESTINATION lib -+ ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR} - COMPONENT DEVELOPMENT_antsUtilities - ) - -@@ -34,22 +34,22 @@ macro(STATIC_ANTS_BUILD ANTS_FUNCTION_NAME EXTRA_LIBS) - - if (ANTS_INSTALL_LIBS_ONLY) - install(TARGETS l_${ANTS_FUNCTION_NAME} -- # RUNTIME DESTINATION bin -+ # RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR} - # COMPONENT RUNTIME_${ANTS_FUNCTION_NAME} -- LIBRARY DESTINATION lib -+ LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} - COMPONENT RUNTIME_${ANTS_FUNCTION_NAME} -- ARCHIVE DESTINATION lib -+ ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR} - COMPONENT DEVELOPMENT_${ANTS_FUNCTION_NAME} - ) - else() - add_executable( ${ANTS_FUNCTION_NAME} cli_${ANTS_FUNCTION_NAME}.cxx ) - target_link_libraries( ${ANTS_FUNCTION_NAME} l_${ANTS_FUNCTION_NAME} ) - install(TARGETS l_${ANTS_FUNCTION_NAME} ${ANTS_FUNCTION_NAME} -- RUNTIME DESTINATION bin -+ RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR} - COMPONENT RUNTIME_${ANTS_FUNCTION_NAME} -- LIBRARY DESTINATION lib -+ LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} - COMPONENT RUNTIME_${ANTS_FUNCTION_NAME} -- ARCHIVE DESTINATION lib -+ ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR} - COMPONENT DEVELOPMENT_${ANTS_FUNCTION_NAME} - ) - endif() -@@ -68,11 +68,11 @@ macro(DYNAMIC_ANTS_BUILD ANTS_FUNCTION_NAME EXTRA_LIBS) - - if (ANTS_INSTALL_LIBS_ONLY) - install(TARGETS l_${ANTS_FUNCTION_NAME} -- # RUNTIME DESTINATION bin -+ # RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR} - # COMPONENT RUNTIME_${ANTS_FUNCTION_NAME} -- LIBRARY DESTINATION lib -+ LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} - COMPONENT RUNTIME_${ANTS_FUNCTION_NAME} -- ARCHIVE DESTINATION lib -+ ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR} - COMPONENT DEVELOPMENT_${ANTS_FUNCTION_NAME} - ) - else() -@@ -80,11 +80,11 @@ macro(DYNAMIC_ANTS_BUILD ANTS_FUNCTION_NAME EXTRA_LIBS) - target_link_libraries( ${ANTS_FUNCTION_NAME} l_${ANTS_FUNCTION_NAME} ) - - install(TARGETS l_${ANTS_FUNCTION_NAME} ${ANTS_FUNCTION_NAME} -- RUNTIME DESTINATION bin -+ RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR} - COMPONENT RUNTIME_${ANTS_FUNCTION_NAME} -- LIBRARY DESTINATION lib -+ LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} - COMPONENT RUNTIME_${ANTS_FUNCTION_NAME} -- ARCHIVE DESTINATION lib -+ ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR} - COMPONENT DEVELOPMENT_${ANTS_FUNCTION_NAME} - ) - endif() diff --git a/sci-biology/ants/files/ants-2.3.4-version.patch b/sci-biology/ants/files/ants-2.3.4-version.patch deleted file mode 100644 index 487151d69..000000000 --- a/sci-biology/ants/files/ants-2.3.4-version.patch +++ /dev/null @@ -1,17 +0,0 @@ ---- a/ANTS.cmake 2020-06-08 12:11:14.000000000 -0400 -+++ b/ANTS.cmake 2020-08-03 16:44:00.826633506 -0400 -@@ -37,7 +37,6 @@ - set(${PROJECT_NAME}_VERSION_MAJOR 0) - set(${PROJECT_NAME}_VERSION_MINOR 0) - set(${PROJECT_NAME}_VERSION_PATCH 0) -- set(${PROJECT_NAME}_VERSION_TWEAK 0) - set(${PROJECT_NAME}_VERSION "snapshot-${ANTS_SNAPSHOT_VERSION}") - endif() - -@@ -46,7 +45,6 @@ - set(${PROJECT_NAME}_VERSION_MAJOR 0) - set(${PROJECT_NAME}_VERSION_MINOR 0) - set(${PROJECT_NAME}_VERSION_PATCH 0) -- set(${PROJECT_NAME}_VERSION_TWEAK 0) - set(${PROJECT_NAME}_VERSION "0.0.0.0") - endif() diff --git a/sci-biology/ants/metadata.xml b/sci-biology/ants/metadata.xml index 9f969ddf9..e8372d21b 100644 --- a/sci-biology/ants/metadata.xml +++ b/sci-biology/ants/metadata.xml @@ -21,4 +21,7 @@ <use> <flag name="vtk">Optional support for a number of surface enabled tools (via sci-libs/vtk).</flag> </use> + <upstream> + <remote-id type="github">ANTsX/ANTs</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/arachne/Manifest b/sci-biology/arachne/Manifest deleted file mode 100644 index c70683996..000000000 --- a/sci-biology/arachne/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST arachne-46233.tar.gz 5161566 BLAKE2B dc9381fae80477e4a2439e24cbcf9bc462c7a4effb06c26a9f74ad1740f86a96273c3dae142d0065aad08d6340e9508528c35ee6914a8405b66327bfc4ec89da SHA512 4ab293e7f4477dd6aeba7c6bc1a78d168cbb811d7f67cbcbc1eea094a7b6bd180bdde6fb1b7c8256ff473dba3d748a43bd426d971575f1c0793289a0b200dc2b diff --git a/sci-biology/arachne/arachne-46233.ebuild b/sci-biology/arachne/arachne-46233.ebuild deleted file mode 100644 index b34d00134..000000000 --- a/sci-biology/arachne/arachne-46233.ebuild +++ /dev/null @@ -1,39 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -DESCRIPTION="Whole genome shotgun OLC assembler for Sanger reads (overlap-layout-contig)" -HOMEPAGE="https://genome.cshlp.org/content/12/1/177.abstract" -SRC_URI="ftp://ftp.broadinstitute.org/pub/crd/ARACHNE/latest_source_code/${P}.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="" -IUSE="doc openmp" - -DEPEND="dev-libs/xerces-c - doc? ( virtual/latex-base app-text/dvipsk )" -RDEPEND="${DEPEND}" - -# needs >=g++-4.7 but does not compile with 5.3.0 - -# --disable-openmp to disable requirement for OpenMP-capable compiler -src_configure() { - local myconf=() - use openmp || myconf+=( --disable-openmp ) - econf ${myconf[@]} -} - -# set the following environment variables -# http://www.broadinstitute.org/crd/wiki/index.php/Setup -# -# ARACHNE_PRE -# ARACHNE_BIN_DIR -# ARACHNE_PRETTY_HELP - -pkg_postinst(){ - einfo "Please add these to your ~/.bashrc" - einfo "limit stacksize 100000" - einfo "limit datasize unlimited" -} diff --git a/sci-biology/arachne/metadata.xml b/sci-biology/arachne/metadata.xml deleted file mode 100644 index 138cb7705..000000000 --- a/sci-biology/arachne/metadata.xml +++ /dev/null @@ -1,12 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-biology/bambus/bambus-2.33.ebuild b/sci-biology/bambus/bambus-2.33-r2.ebuild index e92c8c8da..1cb7aad1b 100644 --- a/sci-biology/bambus/bambus-2.33.ebuild +++ b/sci-biology/bambus/bambus-2.33-r2.ebuild @@ -1,7 +1,7 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 inherit perl-module toolchain-funcs @@ -11,7 +11,7 @@ HOMEPAGE=" https://sourceforge.net/projects/amos/files/bambus" SRC_URI=" https://sourceforge.net/projects/amos/files/bambus/${PV}/${P}.tar.gz - http://mira-assembler.sourceforge.net/docs/scaffolding_MIRA_BAMBUS.pdf" # no https + https://mira-assembler.sourceforge.net/docs/scaffolding_MIRA_BAMBUS.pdf" LICENSE="Artistic" SLOT="0" @@ -66,28 +66,12 @@ src_prepare() { einfo "bambus-2.33/src/TIGR_Foundation_CC/OptionResult.cc:/*! Uses same syntax as getopt" #rm -rf src/TIGR_Foundation_CC || die "Failed to rm -rf src/TIGR_Foundation_CC/, we use it from sci-biology/tigr-foundation-libs" #sed -i 's:TIGR_Foundation_CC::' src/Makefile || die "Failed to zap last pointer to local copy of tigr-foundation-libs" - cd src/TIGR_Foundation_CC || die "Failed to cd src/TIGR_Foundation_CC/" - sed -e "s:/export/usr/local:${ED}/usr:g" -i Makefile || die -} - -src_compile() { - emake DESTDIR="${ED}/usr" - - # TODO: - #ld -L../TIGR_Foundation_CC/ -shared -fPIC -o grommit grommit.o -L. -lgraph -lTigrFoundation - # ld: warning: creating a DT_TEXTREL in object. - # - # * QA Notice: The following files contain runtime text relocations - # * Text relocations force the dynamic linker to perform extra - # * work at startup, waste system resources, and may pose a security - # * risk. On some architectures, the code may not even function - # * properly, if at all. - # * For more information, see http://hardened.gentoo.org/pic-fix-guide.xml - # * Please include the following list of files in your report: - # * TEXTREL usr/bin/grommit } src_install() { + pushd src/TIGR_Foundation_CC || die + sed -e "s:/export/usr/local:${ED}/usr:g" -i Makefile || die + popd || die emake DESTDIR="${ED}/usr" install # cvs HEAD of amos now contains even more updated files: /usr/bin/printScaff /usr/bin/untangle /usr/lib/TIGR/AsmLib.pm for f in FASTArecord.pm FASTAreader.pm Foundation.pm FASTAgrammar.pm AsmLib.pm; do rm "${ED}"/usr/lib/TIGR/$f; done || die @@ -102,13 +86,13 @@ src_install() { done rm "${ED}"/usr/lib/libTigrFoundation.a || die - dodir /usr/share/doc/${P} + dodir /usr/share/doc/${PF} mv "${ED}"/usr/doc/* "${ED}"/usr/share/doc/${PF} || die rmdir "${ED}"/usr/doc || die dobin "${FILESDIR}"/goBambus.pl dodoc "${DISTDIR}"/scaffolding_MIRA_BAMBUS.pdf - rm -rf "${ED}"/usr/lib || die + rm -r "${ED}"/usr/lib || die } pkg_postinst(){ diff --git a/sci-biology/bamql/metadata.xml b/sci-biology/bamql/metadata.xml index 138cb7705..927a160ba 100644 --- a/sci-biology/bamql/metadata.xml +++ b/sci-biology/bamql/metadata.xml @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">BoutrosLaboratory/bamql</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/barrnap/barrnap-0.9.ebuild b/sci-biology/barrnap/barrnap-0.9.ebuild index 999f065c1..6b7176e14 100644 --- a/sci-biology/barrnap/barrnap-0.9.ebuild +++ b/sci-biology/barrnap/barrnap-0.9.ebuild @@ -6,7 +6,7 @@ EAPI=7 inherit perl-module DESCRIPTION="Predict Bacterial and Archaeal rRNA genes and output in GFF3 format" -HOMEPAGE="https://vicbioinformatics.com/software.barrnap.shtml" +HOMEPAGE="https://github.com/tseemann/barrnap" SRC_URI="https://github.com/tseemann/barrnap/archive/${PV}.tar.gz -> ${P}.tar.gz" LICENSE="GPL-3" diff --git a/sci-biology/barrnap/metadata.xml b/sci-biology/barrnap/metadata.xml index 138cb7705..9183ef1ec 100644 --- a/sci-biology/barrnap/metadata.xml +++ b/sci-biology/barrnap/metadata.xml @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">tseemann/barrnap</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/behaviopy/Manifest b/sci-biology/behaviopy/Manifest deleted file mode 100644 index e5e6f36cd..000000000 --- a/sci-biology/behaviopy/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST behaviopy-0.1.tar.gz 32986 BLAKE2B f0de67a59591f266906d0b21c8fedf1e847df47128f0cb45e10fca849c674cb95d1ef586f407c9775ccaad8a7300aa4d6a67f1a4cc77fa18af28ec0848b77605 SHA512 8cead97a6bf06b31b817999377e5460ec7b05b58a997bcad9c8947f6cd1ab48d2525600c0c6e18bd6e52fccd8a9358b5f36c9911d1fab0fb974dc6581a63949b diff --git a/sci-biology/behaviopy/behaviopy-0.1.ebuild b/sci-biology/behaviopy/behaviopy-0.1.ebuild deleted file mode 100644 index 35bcaab6b..000000000 --- a/sci-biology/behaviopy/behaviopy-0.1.ebuild +++ /dev/null @@ -1,44 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7,8} ) - -inherit distutils-r1 - -DESCRIPTION="Neuroimaging tools for Python" -HOMEPAGE="https://github.com/TheChymera/behaviopy" -SRC_URI="https://github.com/TheChymera/behaviopy/archive/${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="GPL-3" -SLOT="0" -IUSE="evaluation test" -KEYWORDS="~amd64 ~x86" -RESTRICT="!test? ( test )" - -DEPEND="dev-python/setuptools[${PYTHON_USEDEP}]" -RDEPEND=" - dev-python/matplotlib[${PYTHON_USEDEP}] - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/pandas[${PYTHON_USEDEP}] - dev-python/seaborn[${PYTHON_USEDEP}] - dev-python/statsmodels[${PYTHON_USEDEP}] - dev-python/scipy[${PYTHON_USEDEP}] - " - -src_prepare() { - if ! use evaluation; then - rm behaviopy/evaluation.py || die - fi - default -} - -python_test() { - cd behaviopy/examples - echo "backend : Agg" > matplotlibrc || die - for i in *py; do - echo "Executing $i" - ${EPYTHON} $i || die - done -} diff --git a/sci-biology/behaviopy/behaviopy-9999.ebuild b/sci-biology/behaviopy/behaviopy-9999.ebuild deleted file mode 100644 index a4c087764..000000000 --- a/sci-biology/behaviopy/behaviopy-9999.ebuild +++ /dev/null @@ -1,46 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7,8} ) - -inherit distutils-r1 git-r3 - -DESCRIPTION="Neuroimaging tools for Python" -HOMEPAGE="https://github.com/TheChymera/behaviopy" -SRC_URI="" -EGIT_REPO_URI="https://github.com/TheChymera/behaviopy" - -LICENSE="GPL-3" -SLOT="0" -IUSE="evaluation test" -KEYWORDS="" -RESTRICT="!test? ( test )" - -DEPEND="dev-python/setuptools[${PYTHON_USEDEP}]" -RDEPEND=" - dev-python/matplotlib[${PYTHON_USEDEP}] - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/pandas[${PYTHON_USEDEP}] - dev-python/seaborn[${PYTHON_USEDEP}] - dev-python/statsmodels[${PYTHON_USEDEP}] - dev-python/scipy[${PYTHON_USEDEP}] - " - #evaluation? ( sci-biology/psychopy[${PYTHON_USEDEP}] ) - -src_prepare() { - if ! use evaluation; then - rm behaviopy/evaluation.py || die - fi - default -} - -python_test() { - cd behaviopy/examples - echo "backend : Agg" > matplotlibrc || die - for i in *py; do - echo "Executing $i" - ${EPYTHON} $i || die - done -} diff --git a/sci-biology/behaviopy/metadata.xml b/sci-biology/behaviopy/metadata.xml deleted file mode 100644 index a33886a68..000000000 --- a/sci-biology/behaviopy/metadata.xml +++ /dev/null @@ -1,26 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>gentoo@chymera.eu</email> - <name>Horea Christian</name> - </maintainer> - <maintainer type="project"> - <email>sci@gentoo.org</email> - <name>Gentoo Science Project</name> - </maintainer> - <longdescription lang="en"> - BehavioPy is a Python toolkit providing evaluation (e.g. event - tracking) and plotting functions for behavioural data. Manual event - tracking is done via a simple and configurable PsychoPy-based - interface. Plotting functions are designed to work with preformatted - data in CSV format (e.g. as exported by pandas), and use Seaborn and - custom BehavioPy styles for maximum beautification. - </longdescription> - <upstream> - <remote-id type="github">TheChymera/behaviopy</remote-id> - </upstream> - <use> - <flag name="evaluation">Installs evaluation submodule.</flag> - </use> -</pkgmetadata> diff --git a/sci-biology/bidsschematools/Manifest b/sci-biology/bidsschematools/Manifest new file mode 100644 index 000000000..283f2cedf --- /dev/null +++ b/sci-biology/bidsschematools/Manifest @@ -0,0 +1,3 @@ +DIST bidsschematools-0.6.0.tar.gz 1162053 BLAKE2B b46ae2c19b96416908786347890db33aded14c0656b2af3f8396395a7decd9e74808b1ba54df3d049473eda038b706d7b0561f2e21c97ab5e9534f57c41a560a SHA512 32e2a679b85cb8c57e2a91783f315092b3e976e8cadc661a67822b499685b128a9f5abda70d2124ddcee42163a9357665474de6c3f96cf369c33cefe1586b7f1 +DIST bidsschematools-0.7.0.tar.gz 1227313 BLAKE2B 350621d8052ca8ee45be970c4f8973c34d5c7dfd9da0777758009d8f725691efaa665926d9f97723e2331f5511aedf3601fd1df520746b6ec4aebd6ef27a2cf6 SHA512 391e3ed1a96202bada1486de377ea4d96e8622cced132cbb014a697578dbd1c5fdfa3eb2ce6f44b5031136c987e2298a5bc702c1c5751e35479512cfe57a383b +DIST bidsschematools-0.7.1.tar.gz 1226794 BLAKE2B 6bbc672ac047bd1475b5b79f5cb74b61f190207531be810018768a6cf62e2cae36ccef4893bee041a53ed546f8ae6f104bb64d2f0b89550c80c911d6a48fcee5 SHA512 8cf9e94496108c15360bcc25a1c8e5900350e1fb3da9886c2d089481ae69c94a634ea0cf67e2a1120a93c2982c07061cda8d0d8ecba9715f848c01388108517e diff --git a/sci-biology/bidsschematools/bidsschematools-0.6.0.ebuild b/sci-biology/bidsschematools/bidsschematools-0.6.0.ebuild new file mode 100644 index 000000000..96b6cd57f --- /dev/null +++ b/sci-biology/bidsschematools/bidsschematools-0.6.0.ebuild @@ -0,0 +1,37 @@ +# Copyright 2022-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..11} ) + +inherit distutils-r1 pypi + +DESCRIPTION="A Python library for working with the BIDS schema" +HOMEPAGE="https://github.com/bids-standard/bids-specification" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="render" + +RDEPEND=" + dev-python/pyyaml[${PYTHON_USEDEP}] + render? ( + dev-python/markdown-it-py[${PYTHON_USEDEP}] + dev-python/pandas[${PYTHON_USEDEP}] + dev-python/tabulate[${PYTHON_USEDEP}] + ) +" +DEPEND="" + +distutils_enable_tests pytest + +src_prepare() { + if ! use render; then + rm "${S}/bidsschematools/render.py" + rm "${S}/bidsschematools/tests/test_render.py" + fi + default +} diff --git a/sci-biology/bidsschematools/bidsschematools-0.7.0.ebuild b/sci-biology/bidsschematools/bidsschematools-0.7.0.ebuild new file mode 100644 index 000000000..98b773243 --- /dev/null +++ b/sci-biology/bidsschematools/bidsschematools-0.7.0.ebuild @@ -0,0 +1,46 @@ +# Copyright 2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..11} ) + +inherit distutils-r1 pypi + +DESCRIPTION="A Python library for working with the BIDS schema" +HOMEPAGE="https://github.com/bids-standard/bids-specification" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="render" +# Documented upstream: +# https://github.com/conda-forge/bidsschematools-feedstock/pull/2 +#RESTRICT="test" + +RDEPEND=" + dev-python/pyyaml[${PYTHON_USEDEP}] + render? ( + dev-python/markdown-it-py[${PYTHON_USEDEP}] + dev-python/pandas[${PYTHON_USEDEP}] + dev-python/tabulate[${PYTHON_USEDEP}] + ) +" +DEPEND="" + +distutils_enable_tests pytest + +# Reported upstream: +# https://github.com/bids-standard/bids-specification/issues/1500 +EPYTEST_DESELECT=( + "bidsschematools/tests/test_validator.py::test_bids_datasets[ds000248]" +) + +src_prepare() { + if ! use render; then + rm "${S}/bidsschematools/render.py" + rm "${S}/bidsschematools/tests/test_render.py" + fi + default +} diff --git a/sci-biology/bidsschematools/bidsschematools-0.7.1.ebuild b/sci-biology/bidsschematools/bidsschematools-0.7.1.ebuild new file mode 100644 index 000000000..b5b12165d --- /dev/null +++ b/sci-biology/bidsschematools/bidsschematools-0.7.1.ebuild @@ -0,0 +1,37 @@ +# Copyright 2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..11} ) + +inherit distutils-r1 pypi + +DESCRIPTION="A Python library for working with the BIDS schema" +HOMEPAGE="https://github.com/bids-standard/bids-specification" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="render" + +RDEPEND=" + dev-python/pyyaml[${PYTHON_USEDEP}] + render? ( + dev-python/markdown-it-py[${PYTHON_USEDEP}] + dev-python/pandas[${PYTHON_USEDEP}] + dev-python/tabulate[${PYTHON_USEDEP}] + ) +" +DEPEND="" + +distutils_enable_tests pytest + +src_prepare() { + if ! use render; then + rm "${S}/bidsschematools/render.py" + rm "${S}/bidsschematools/tests/test_render.py" + fi + default +} diff --git a/sci-biology/bidsschematools/metadata.xml b/sci-biology/bidsschematools/metadata.xml new file mode 100644 index 000000000..3fac5f14b --- /dev/null +++ b/sci-biology/bidsschematools/metadata.xml @@ -0,0 +1,19 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>gentoo@chymera.eu</email> + <name>Horea Christian</name> + </maintainer> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <upstream> + <remote-id type="github">bids-standard/bids-specification</remote-id> + <remote-id type="pypi">bidsschematools</remote-id> + </upstream> + <use> + <flag name="render">Support for schema table rendering</flag> + </use> +</pkgmetadata> diff --git a/sci-biology/bismark/metadata.xml b/sci-biology/bismark/metadata.xml index 4c433a8ca..4ee13c559 100644 --- a/sci-biology/bismark/metadata.xml +++ b/sci-biology/bismark/metadata.xml @@ -20,4 +20,7 @@ and gapped alignments; (4) Alignment seed length, number of mismatches etc. are adjustable; (5) Output discriminates between cytosine methylation in CpG, CHG and CHH context. </longdescription> + <upstream> + <remote-id type="github">FelixKrueger/Bismark</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/blasr/Manifest b/sci-biology/blasr/Manifest deleted file mode 100644 index 7819d5a37..000000000 --- a/sci-biology/blasr/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST blasr-5.3.5.tar.gz 2709986 BLAKE2B 48a8d12e4a47159c00d5febab4222dec5e2f4e5ce4d7a481243b4b62e0ba693eb9e1aa2a11b5de36606ec977db3947178cfdd0a1a09ccfea213e1a1567402e74 SHA512 79155f29076e4a9fe1d66d9e8310d38d3b6690fe1959be923627607ed4d7dfe97c020ff9f9134a3cffcb8e1cd5eb1b3a861d10cb476f9c3866c87e85e6ae93e7 diff --git a/sci-biology/blasr/blasr-5.3.5.ebuild b/sci-biology/blasr/blasr-5.3.5.ebuild deleted file mode 100644 index 8552bff9e..000000000 --- a/sci-biology/blasr/blasr-5.3.5.ebuild +++ /dev/null @@ -1,24 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -inherit meson - -DESCRIPTION="The PacBio long read aligner" -HOMEPAGE="http://www.smrtcommunity.com/SMRT-Analysis/Algorithms/BLASR" -SRC_URI="https://github.com/PacificBiosciences/blasr/tarball/${PV} -> ${P}.tar.gz" - -LICENSE="blasr" -SLOT="0" -KEYWORDS="~amd64" - -BDEPEND=" - dev-util/cmake - virtual/pkgconfig -" -DEPEND=" - sci-biology/libblasr - dev-libs/boost:= -" -RDEPEND="${DEPEND}" diff --git a/sci-biology/blasr/metadata.xml b/sci-biology/blasr/metadata.xml deleted file mode 100644 index 8417d1580..000000000 --- a/sci-biology/blasr/metadata.xml +++ /dev/null @@ -1,8 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-biology/brkraw/Manifest b/sci-biology/brkraw/Manifest new file mode 100644 index 000000000..6bc79d823 --- /dev/null +++ b/sci-biology/brkraw/Manifest @@ -0,0 +1 @@ +DIST brkraw-0.3.11.gh.tar.gz 3919122 BLAKE2B 9881f53bb3fef038385eab4043f76d21c2e5391131c80daa49c909e7882359ed9d0b41b84fc82acd0432f4bac820a75061842de85b75cceff6f33d6f14988aea SHA512 a1e2725b6f50ff82ea6c4f9eacbd044ccb1c966aa26f2753c0872e3ee5e6469821dad336c9ef221dc6e15df2bed537ed9d31d5b09ff432694b757ab30af53631 diff --git a/sci-biology/brkraw/brkraw-0.3.11.ebuild b/sci-biology/brkraw/brkraw-0.3.11.ebuild new file mode 100644 index 000000000..60a7767b1 --- /dev/null +++ b/sci-biology/brkraw/brkraw-0.3.11.ebuild @@ -0,0 +1,36 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) + +DISTUTILS_USE_PEP517=setuptools + +inherit distutils-r1 pypi + +DESCRIPTION="Fast and easy statistical learning on NeuroImaging data" +HOMEPAGE="https://github.com/BrkRaw/brkraw" +SRC_URI="https://github.com/BrkRaw/brkraw/archive/refs/tags/${PV}.tar.gz -> ${P}.gh.tar.gz" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="test" +# Strange test infrastructure involving dynamic download via make: +# https://github.com/BrkRaw/brkraw/blob/main/.github/workflows/test.yml +RESTRICT="test" + +RDEPEND=" + >=dev-python/numpy-1.18[${PYTHON_USEDEP}] + >=dev-python/pillow-7.1.1[${PYTHON_USEDEP}] + >=dev-python/tqdm-4.45.0[${PYTHON_USEDEP}] + >=dev-python/openpyxl-3.0.3[${PYTHON_USEDEP}] + >=dev-python/xlrd-1.1.0[${PYTHON_USEDEP}] + >=dev-python/pandas-1[${PYTHON_USEDEP}] + >=sci-libs/nibabel-3.0.2[${PYTHON_USEDEP}] +" + +PATCHES=( "${FILESDIR}/${P}-testexclusion.patch" ) + +distutils_enable_tests pytest diff --git a/sci-biology/brkraw/files/brkraw-0.3.11-testexclusion.patch b/sci-biology/brkraw/files/brkraw-0.3.11-testexclusion.patch new file mode 100644 index 000000000..40cc8fc4a --- /dev/null +++ b/sci-biology/brkraw/files/brkraw-0.3.11-testexclusion.patch @@ -0,0 +1,11 @@ +--- a/setup.py 2023-07-05 17:09:42.000000000 -0400 ++++ b/setup.py 2023-11-28 12:38:07.726369571 -0500 +@@ -24,7 +24,7 @@ + author_email=__email__, + url=__url__, + license='GNLv3', +- packages=find_packages(), ++ packages=find_packages(exclude=["tests", "tests.*"]), + install_requires=['nibabel>=3.0.2', + 'numpy>=1.18.0', + 'pandas>=1.0.0', diff --git a/sci-biology/mouse-brain-atlases/metadata.xml b/sci-biology/brkraw/metadata.xml index 16fcf156a..5c436db45 100644 --- a/sci-biology/mouse-brain-atlases/metadata.xml +++ b/sci-biology/brkraw/metadata.xml @@ -9,7 +9,8 @@ <email>sci@gentoo.org</email> <name>Gentoo Science Project</name> </maintainer> - <use> - <flag name="hires">Also install high-resolution atlases.</flag> - </use> + <upstream> + <remote-id type="github">BrkRaw/brkraw</remote-id> + <remote-id type="pypi">brkraw</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/bruker2nifti/bruker2nifti-1.0.4.ebuild b/sci-biology/bruker2nifti/bruker2nifti-1.0.4.ebuild index 7a9c238ce..dc0c49e6f 100644 --- a/sci-biology/bruker2nifti/bruker2nifti-1.0.4.ebuild +++ b/sci-biology/bruker2nifti/bruker2nifti-1.0.4.ebuild @@ -1,10 +1,10 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 DISTUTILS_USE_SETUPTOOLS="rdepend" -PYTHON_COMPAT=( python3_{7,8,9} ) +PYTHON_COMPAT=( python3_{10..11} ) inherit distutils-r1 diff --git a/sci-biology/btl_bloomfilter/metadata.xml b/sci-biology/btl_bloomfilter/metadata.xml index 138cb7705..1e02bb596 100644 --- a/sci-biology/btl_bloomfilter/metadata.xml +++ b/sci-biology/btl_bloomfilter/metadata.xml @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">bcgsc/btl_bloomfilter</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/bx-python/Manifest b/sci-biology/bx-python/Manifest index 80552af85..90147dff7 100644 --- a/sci-biology/bx-python/Manifest +++ b/sci-biology/bx-python/Manifest @@ -1 +1,2 @@ -DIST bx-python-0.8.9.tar.gz 1651514 BLAKE2B ee75d08aaae8102c2af5be0175c75200382e157abc0c0c723a67b55d5542ab2d4b6ccd4e256975b0a2d00b39b2249d73df0c6f4324b3a74757c3e18e2aeb6c1a SHA512 37863c92258dc06a12b566b02697502f68bbf7e4d9decd8fc63af10ee58b614dd0e7cff35e9977ba1ddf913f176c49e7969728d8e64a9f78ac7100da4a3d70ea +DIST bx-python-0.8.9.gh.tar.gz 1651514 BLAKE2B ee75d08aaae8102c2af5be0175c75200382e157abc0c0c723a67b55d5542ab2d4b6ccd4e256975b0a2d00b39b2249d73df0c6f4324b3a74757c3e18e2aeb6c1a SHA512 37863c92258dc06a12b566b02697502f68bbf7e4d9decd8fc63af10ee58b614dd0e7cff35e9977ba1ddf913f176c49e7969728d8e64a9f78ac7100da4a3d70ea +DIST bx-python-0.9.0.gh.tar.gz 1667445 BLAKE2B 0814792a2af8bfb7af5ef5fe1ddc184ed14a68df060a8286f4eba334388497363dc002f6c0de72836b5654452fe28f4cef67cd31b765a4a121c84f3af0634ea0 SHA512 955f396614d8e6d19a74e94a6612f7752a45f752a4a59c95853474dd363ed1960d20a340f17eb1815fda3aaf26d907dc30d37aa8c23608d718742b68864ca1bc diff --git a/sci-biology/bx-python/bx-python-0.8.9.ebuild b/sci-biology/bx-python/bx-python-0.8.9.ebuild index a0d3ae3df..6cffba1be 100644 --- a/sci-biology/bx-python/bx-python-0.8.9.ebuild +++ b/sci-biology/bx-python/bx-python-0.8.9.ebuild @@ -1,28 +1,35 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 -PYTHON_COMPAT=( python3_{7..9} ) +PYTHON_COMPAT=( python3_{10..10} ) inherit distutils-r1 DESCRIPTION="Library for rapid implementation of genome scale analyses" HOMEPAGE="https://github.com/bxlab/bx-python" -SRC_URI="https://github.com/bxlab/bx-python/archive/v${PV}.tar.gz -> ${P}.tar.gz" +SRC_URI="https://github.com/bxlab/bx-python/archive/v${PV}.tar.gz -> ${P}.gh.tar.gz" LICENSE="MIT" SLOT="0" KEYWORDS="~amd64 ~x86" +# Tests require dev-python/pytest-cython (currently not in ::gentoo or ::science) +# (and might need some more work beyond that) +RESTRICT=test RDEPEND=" dev-python/numpy[${PYTHON_USEDEP}] dev-python/six[${PYTHON_USEDEP}] " -BDEPEND="dev-python/cython[${PYTHON_USEDEP}]" +BDEPEND=" + dev-python/cython[${PYTHON_USEDEP}] +" # has file collision with sci-biology/RSeQC # ToDo: fix doc building: # Reason: TemplateNotFound('i') #distutils_enable_sphinx doc/source + +distutils_enable_tests pytest diff --git a/sci-biology/bx-python/bx-python-0.9.0.ebuild b/sci-biology/bx-python/bx-python-0.9.0.ebuild new file mode 100644 index 000000000..6cffba1be --- /dev/null +++ b/sci-biology/bx-python/bx-python-0.9.0.ebuild @@ -0,0 +1,35 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..10} ) + +inherit distutils-r1 + +DESCRIPTION="Library for rapid implementation of genome scale analyses" +HOMEPAGE="https://github.com/bxlab/bx-python" +SRC_URI="https://github.com/bxlab/bx-python/archive/v${PV}.tar.gz -> ${P}.gh.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86" +# Tests require dev-python/pytest-cython (currently not in ::gentoo or ::science) +# (and might need some more work beyond that) +RESTRICT=test + +RDEPEND=" + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/six[${PYTHON_USEDEP}] +" +BDEPEND=" + dev-python/cython[${PYTHON_USEDEP}] +" + +# has file collision with sci-biology/RSeQC + +# ToDo: fix doc building: +# Reason: TemplateNotFound('i') +#distutils_enable_sphinx doc/source + +distutils_enable_tests pytest diff --git a/sci-biology/bx-python/bx-python-9999.ebuild b/sci-biology/bx-python/bx-python-9999.ebuild index 6f0b1c9ca..b29975b58 100644 --- a/sci-biology/bx-python/bx-python-9999.ebuild +++ b/sci-biology/bx-python/bx-python-9999.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 -PYTHON_COMPAT=( python3_{7..9} ) +PYTHON_COMPAT=( python3_{10..10} ) inherit distutils-r1 git-r3 @@ -14,15 +14,22 @@ EGIT_REPO_URI="https://github.com/bxlab/bx-python" LICENSE="MIT" SLOT="0" KEYWORDS="" +# Tests require dev-python/pytest-cython (currently not in ::gentoo or ::science) +# (and might need some more work beyond that) +RESTRICT=test RDEPEND=" dev-python/numpy[${PYTHON_USEDEP}] dev-python/six[${PYTHON_USEDEP}] " -BDEPEND="dev-python/cython[${PYTHON_USEDEP}]" +BDEPEND=" + dev-python/cython[${PYTHON_USEDEP}] +" # has file collision with sci-biology/RSeQC # ToDo: fix doc building: # Reason: TemplateNotFound('i') #distutils_enable_sphinx doc/source + +distutils_enable_tests pytest diff --git a/sci-biology/bx-python/metadata.xml b/sci-biology/bx-python/metadata.xml index 3e13342e3..f1fc4360e 100644 --- a/sci-biology/bx-python/metadata.xml +++ b/sci-biology/bx-python/metadata.xml @@ -10,7 +10,7 @@ <name>Gentoo Biology Project</name> </maintainer> <upstream> - <remote-id type="bitbucket">james_taylor/bx-python</remote-id> + <remote-id type="github">bxlab/bx-python</remote-id> <remote-id type="pypi">bx-python</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/caftools/Manifest b/sci-biology/caftools/Manifest deleted file mode 100644 index 761665281..000000000 --- a/sci-biology/caftools/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -DIST caftools-2.0.2.tar.gz 2645554 BLAKE2B a48d8fb71500b5dc07da37467a9dc8d5972dfd7f63ae19cf7ca016774c3a23c4a9cd0f4caa1bde8efe5ef74c2576b8143f8b7375f9bf34414edcb14ed34a17d2 SHA512 0c1a7f2127538ef932139cfee6bc6acb2411765d1006d508e65647ec74d1677a6ecd25b98cc37075bd8e5b0b1a245c11c1029cbbc51eefb46023bd121fdb2f1d -DIST caftools-2.0.tar.gz 2644892 BLAKE2B 76aa90bf18d7543eb8f39de3e3be5fbca9a549e47341b032dd569394865ae02e269ea54a607acca2d88d404d271f78e1b97399bc8bdc1a107937163c89642323 SHA512 0b2b5d09d503b900b275efd61dfa1c5b01259e53c392d68626d9c5081add27ca87b324b5702ec18293415b788208c547eb31e461861f1244b759e28221244417 diff --git a/sci-biology/caftools/caftools-2.0.2.ebuild b/sci-biology/caftools/caftools-2.0.2.ebuild deleted file mode 100644 index 7d58f3375..000000000 --- a/sci-biology/caftools/caftools-2.0.2.ebuild +++ /dev/null @@ -1,45 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -DESCRIPTION="Manipulate CAF files and convert to GAP4 format (not GAP5), ACE, PHRAP" -HOMEPAGE="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC310697/" -SRC_URI=" - ftp://ftp.sanger.ac.uk/pub/PRODUCTION_SOFTWARE/src/${P}.tar.gz - ftp://ftp.sanger.ac.uk/pub/PRODUCTION_SOFTWARE/src/${PN}-2.0.tar.gz" - -LICENSE="GRL" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -DEPEND=" - sci-libs/io_lib - dev-lang/perl" -RDEPEND="${DEPEND}" - -PATCHES=( - "${FILESDIR}"/Makefile.in-"${PV}".patch -) - -src_prepare(){ - default - mv "${WORKDIR}"/caftools-2.0/man/*.{1,5} "${S}"/man/ || die -} - -src_configure(){ - default - sed \ - -e 's:prefix = /usr:prefix = $(DESTDIR)/usr:' \ - -i Makefile src/Makefile || die -} - -# TODO: the 2.0.2 archive lacks manpages compared to 2.0, FIXME -# The man/Makefile.in is screwed in 2.0.2 so we cannot use it to install the manpage files, -# not even copying over whole caftools-2.0/man/ to caftools-2.0.2/man does not help. -src_install(){ - default - doman man/*.[1-5] || die - elog "Some usage info is at http://sarton.imb-jena.de/software/consed2gap/" - elog "for some reason caf_find_misassemblies is gone from 2.0.2 version" -} diff --git a/sci-biology/caftools/files/Makefile.in-2.0.2.patch b/sci-biology/caftools/files/Makefile.in-2.0.2.patch deleted file mode 100644 index 1e5160487..000000000 --- a/sci-biology/caftools/files/Makefile.in-2.0.2.patch +++ /dev/null @@ -1,43 +0,0 @@ ---- src/Makefile.in.ori 2010-12-05 22:59:40.000000000 +0100 -+++ src/Makefile.in 2010-12-05 23:01:19.000000000 +0100 -@@ -32,8 +32,6 @@ - includedir = @includedir@ - oldincludedir = /usr/include - --DESTDIR = -- - pkgdatadir = $(datadir)/@PACKAGE@ - pkglibdir = $(libdir)/@PACKAGE@ - pkgincludedir = $(includedir)/@PACKAGE@ -@@ -323,18 +321,18 @@ - - install-binPROGRAMS: $(bin_PROGRAMS) - @$(NORMAL_INSTALL) -- $(mkinstalldirs) $(DESTDIR)$(bindir) -+ $(mkinstalldirs) $(bindir) - @list='$(bin_PROGRAMS)'; for p in $$list; do \ - if test -f $$p; then \ -- echo " $(INSTALL_PROGRAM) $$p $(DESTDIR)$(bindir)/`echo $$p|sed 's/$(EXEEXT)$$//'|sed '$(transform)'|sed 's/$$/$(EXEEXT)/'`"; \ -- $(INSTALL_PROGRAM) $$p $(DESTDIR)$(bindir)/`echo $$p|sed 's/$(EXEEXT)$$//'|sed '$(transform)'|sed 's/$$/$(EXEEXT)/'`; \ -+ echo " $(INSTALL_PROGRAM) $$p $(bindir)/`echo $$p|sed 's/$(EXEEXT)$$//'|sed '$(transform)'|sed 's/$$/$(EXEEXT)/'`"; \ -+ $(INSTALL_PROGRAM) $$p $(bindir)/`echo $$p|sed 's/$(EXEEXT)$$//'|sed '$(transform)'|sed 's/$$/$(EXEEXT)/'`; \ - else :; fi; \ - done - - uninstall-binPROGRAMS: - @$(NORMAL_UNINSTALL) - list='$(bin_PROGRAMS)'; for p in $$list; do \ -- rm -f $(DESTDIR)$(bindir)/`echo $$p|sed 's/$(EXEEXT)$$//'|sed '$(transform)'|sed 's/$$/$(EXEEXT)/'`; \ -+ rm -f $(bindir)/`echo $$p|sed 's/$(EXEEXT)$$//'|sed '$(transform)'|sed 's/$$/$(EXEEXT)/'`; \ - done - - .c.o: -@@ -579,7 +577,7 @@ - $(MAKE) $(AM_MAKEFLAGS) AM_INSTALL_PROGRAM_FLAGS=-s install - installdirs: installdirs-recursive - installdirs-am: -- $(mkinstalldirs) $(DESTDIR)$(bindir) -+ $(mkinstalldirs) $(bindir) - - - mostlyclean-generic: diff --git a/sci-biology/caftools/files/Makefile.in.patch b/sci-biology/caftools/files/Makefile.in.patch deleted file mode 100644 index 4ddd9f628..000000000 --- a/sci-biology/caftools/files/Makefile.in.patch +++ /dev/null @@ -1,49 +0,0 @@ ---- src/Makefile.in.ori 2010-12-05 22:08:50.000000000 +0100 -+++ src/Makefile.in 2010-12-05 22:10:07.000000000 +0100 -@@ -18,7 +18,7 @@ - srcdir = @srcdir@ - top_srcdir = @top_srcdir@ - VPATH = @srcdir@ --prefix = @prefix@ -+prefix = $(DESTDIR)/@prefix@ - exec_prefix = @exec_prefix@ - - bindir = @bindir@ -@@ -394,14 +394,14 @@ - binPROGRAMS_INSTALL = $(INSTALL_PROGRAM) - install-binPROGRAMS: $(bin_PROGRAMS) - @$(NORMAL_INSTALL) -- $(mkinstalldirs) $(DESTDIR)$(bindir) -+ $(mkinstalldirs) $(bindir) - @list='$(bin_PROGRAMS)'; for p in $$list; do \ - p1=`echo $$p|sed 's/$(EXEEXT)$$//'`; \ - if test -f $$p \ - ; then \ - f=`echo "$$p1" | sed 's,^.*/,,;$(transform);s/$$/$(EXEEXT)/'`; \ -- echo " $(INSTALL_PROGRAM_ENV) $(binPROGRAMS_INSTALL) $$p $(DESTDIR)$(bindir)/$$f"; \ -- $(INSTALL_PROGRAM_ENV) $(binPROGRAMS_INSTALL) $$p $(DESTDIR)$(bindir)/$$f; \ -+ echo " $(INSTALL_PROGRAM_ENV) $(binPROGRAMS_INSTALL) $$p $(bindir)/$$f"; \ -+ $(INSTALL_PROGRAM_ENV) $(binPROGRAMS_INSTALL) $$p $(bindir)/$$f; \ - else :; fi; \ - done - -@@ -409,8 +409,8 @@ - @$(NORMAL_UNINSTALL) - @list='$(bin_PROGRAMS)'; for p in $$list; do \ - f=`echo "$$p" | sed 's,^.*/,,;s/$(EXEEXT)$$//;$(transform);s/$$/$(EXEEXT)/'`; \ -- echo " rm -f $(DESTDIR)$(bindir)/$$f"; \ -- rm -f $(DESTDIR)$(bindir)/$$f; \ -+ echo " rm -f $(bindir)/$$f"; \ -+ rm -f $(bindir)/$$f; \ - done - - clean-binPROGRAMS: -@@ -663,7 +663,7 @@ - all-am: Makefile $(PROGRAMS) config.h - installdirs: installdirs-recursive - installdirs-am: -- $(mkinstalldirs) $(DESTDIR)$(bindir) -+ $(mkinstalldirs) $(bindir) - - install: install-recursive - install-exec: install-exec-recursive diff --git a/sci-biology/caftools/metadata.xml b/sci-biology/caftools/metadata.xml deleted file mode 100644 index 224641279..000000000 --- a/sci-biology/caftools/metadata.xml +++ /dev/null @@ -1,17 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <longdescription> -CAF is a text format for describing sequence assemblies. It is acedb-compliant -and is an extension of the ace-file format used earlier, but with support for -base quality measures and a more extensive description of the Sequence data. -</longdescription> -</pkgmetadata> diff --git a/sci-biology/canu/Manifest b/sci-biology/canu/Manifest deleted file mode 100644 index f7859b395..000000000 --- a/sci-biology/canu/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST canu-2.1.1.tar.xz 2281796 BLAKE2B ada9326054e0455fac824545baa0ed86d5e53325256a388b9a1bdfa393a2b9ad8926f64b5c871bc10acc9b2d8bac96bcb80682e6ed7c19d01d6ed3b7764111af SHA512 9be64df3c46c6eb98dde915959df346292ac033e650b428b16187e700637b91a87e67ccdf23a241dfbcef7bdb3df289e412d38a2233831eba855fd84dc6ea7c0 diff --git a/sci-biology/canu/canu-2.1.1.ebuild b/sci-biology/canu/canu-2.1.1.ebuild deleted file mode 100644 index e14efe3af..000000000 --- a/sci-biology/canu/canu-2.1.1.ebuild +++ /dev/null @@ -1,71 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7,8,9} ) - -inherit java-pkg-2 perl-module python-r1 - -DESCRIPTION="Fork of a wgs-assembler for Oxfordnanopore and PacBio sequences" -HOMEPAGE="https://canu.readthedocs.io/en/latest" -SRC_URI="https://github.com/marbl/canu/releases/download/v${PV}/${P}.tar.xz" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="~amd64" - -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -RDEPEND="${PYTHON_DEPS} - >=virtual/jre-1.8:* - dev-lang/perl - virtual/perl-File-Path - sci-visualization/gnuplot - sci-biology/minimap2 -" -# =sci-biology/mhap-2.1.3 if we unbundle it -DEPEND="${RDEPEND} - >=virtual/jdk-1.8:* - dev-java/ant-core - !sci-biology/wgs-assembler - " - -# Detected file collision(s): -# * sci-biology/wgs-assembler-8.3_rc2:0::science -# * /usr/bin/bogart -# * /usr/bin/bogus -# * /usr/bin/fastqAnalyze -# * /usr/bin/fastqSample -# * /usr/bin/fastqSimulate -# * /usr/bin/fastqSimulate-sort -# * /usr/bin/meryl -# * /usr/bin/overlapInCore -# * /usr/bin/utgcns - -# Perl 5.12.0, or File::Path 2.08 -# Java SE 8 -# https://github.com/marbl/MHAP uses Apache maven - -# contains bundled mhap-2.1.3.jar, kmer, pbutgcns, FALCON - -src_compile(){ - cd src || die - emake -} - -src_install(){ - # installs - # /usr/bin - # /usr/lib/libcanu.a - # /usr/lib64/perl5/vendor_perl/5.28.0/lib/site_perl/canu - # /usr/share/java/classes/mhap-2.1.3.jar - rm -rf Linux-amd64/obj - insinto /usr - doins -r Linux-amd64/{bin,share} - insinto /usr/$(get_libdir) - dolib.a Linux-amd64/lib/libcanu.a - rm Linux-amd64/lib/libcanu.a || die - perl_set_version - perl_domodule -r Linux-amd64/lib -} diff --git a/sci-biology/chiron/Manifest b/sci-biology/chiron/Manifest deleted file mode 100644 index 2cde5a081..000000000 --- a/sci-biology/chiron/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST chiron-0.6.1.1.tar.gz 53281188 BLAKE2B 56c623ec0d2f8970cd03d892d321362145b44890a0384d5209a2bd8c19b22509ec0557e539f021240a447e836ca6cd3531f3c9ac827b6ece715b086fca73d9f3 SHA512 b74e7f3cea9d206bc0c456189ec643de684a866bdb2dd6fd9d05ac11efd2b980d1aa09f7fc2a2aa3d5df56ca60e7a57c23d63e20df3df10f3ab82c5289d8a52f diff --git a/sci-biology/chiron/chiron-0.6.1.1.ebuild b/sci-biology/chiron/chiron-0.6.1.1.ebuild deleted file mode 100644 index 645e4ed30..000000000 --- a/sci-biology/chiron/chiron-0.6.1.1.ebuild +++ /dev/null @@ -1,29 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7,8} ) -DISTUTILS_USE_SETUPTOOLS=rdepend - -inherit distutils-r1 - -DESCRIPTION="A deep neural network basecaller for nanopore sequencing" -HOMEPAGE="https://github.com/haotianteng/chiron - https://www.biorxiv.org/content/early/2017/09/12/179531" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -LICENSE="MPL-2.0" -SLOT="0" -KEYWORDS="~amd64" - -RDEPEND=" - dev-python/h5py[${PYTHON_USEDEP}] - sci-biology/mappy[${PYTHON_USEDEP}] - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/statsmodels[${PYTHON_USEDEP}] - dev-python/tqdm[${PYTHON_USEDEP}] - sci-biology/biopython[${PYTHON_USEDEP}] - dev-python/packaging[${PYTHON_USEDEP}] - sci-libs/tensorflow[${PYTHON_USEDEP}] -" diff --git a/sci-biology/chiron/metadata.xml b/sci-biology/chiron/metadata.xml deleted file mode 100644 index 138cb7705..000000000 --- a/sci-biology/chiron/metadata.xml +++ /dev/null @@ -1,12 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-biology/cluster/files/cluster-1.38-helpmenu-fix.patch b/sci-biology/cluster/files/cluster-1.38-helpmenu-fix.patch deleted file mode 100644 index 69f3a963e..000000000 --- a/sci-biology/cluster/files/cluster-1.38-helpmenu-fix.patch +++ /dev/null @@ -1,30 +0,0 @@ ---- X11/gui.c 2007-05-05 00:21:30.000000000 -0500 -+++ X11/gui.c-new 2007-08-09 04:25:53.000000000 -0500 -@@ -1786,15 +1786,15 @@ - { int item_no = (int) client_data; - switch (item_no) - { case CMD_HELP_HTMLHELP: -- { system("netscape "PREFIX"/cluster/html/index.html &"); -+ { system("xdg-open "PREFIX"/share/doc/cluster-1.36/html/index.html &"); - break; - } - case CMD_HELP_MANUAL: -- { system("acroread "PREFIX"/cluster/doc/cluster3.pdf &"); -+ { system("xpdf "PREFIX"/share/doc/cluster-1.36/cluster3.pdf &"); - break; - } - case CMD_HELP_DOWNLOAD: -- { system("netscape http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster/manual/index.html &"); -+ { system("xdg-open http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster/manual/index.html &"); - break; - } - case CMD_HELP_FILEFORMAT: -@@ -1852,7 +1852,7 @@ - XtManageChild(widget); - free(helptext); - n = 0; -- pixmap = XmGetPixmap(XtScreen(dialog),PREFIX"/cluster/format.xpm",0,0); -+ pixmap = XmGetPixmap(XtScreen(dialog),PREFIX"/share/doc/cluster-1.36/format.xpm",0,0); - XtSetArg(args[n], XmNx, 10); n++; - XtSetArg(args[n], XmNy, 410); n++; - XtSetArg(args[n],XmNlabelType, XmPIXMAP); n++; diff --git a/sci-biology/clview/Manifest b/sci-biology/clview/Manifest deleted file mode 100644 index 271e4eb76..000000000 --- a/sci-biology/clview/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -DIST clview_linux_i386.tar.gz 1050318 BLAKE2B c5c52662df29a0f70a5355c0f2f563e8fef0ec473a707aed0c51d79bd1f1d7e9555139a21bb0c83c509fbac549d8c532d2af8d9ecb9af77b329be581f255493f SHA512 2fbd5ed5ef7bb96a715537a1b1d8f0957e5733d2603aacc5a0dba5a5002a27483ca57dd53780204a98d5ce05ac1090e3d04a3b2784cec021f0afc545e98b35b1 -DIST clview_src.tar.gz 62178 BLAKE2B b116a03c6ddba0caf77168fdd9e39bb86f4b1eccc0535dcd9f81a1e7c2a9b81c1219a4786ae37944abeb4913633acd9cf6b94824adba9851359a955440d9f21f SHA512 24c115b76041981d6dba731180485108d92cccc4719fe6982a135d73c3d18deed2e89ebb6d7daeb8d79941084ec912be2c3333369ec0bf403f96a156932909b9 diff --git a/sci-biology/clview/clview-0.1.ebuild b/sci-biology/clview/clview-0.1.ebuild deleted file mode 100644 index 2f200426d..000000000 --- a/sci-biology/clview/clview-0.1.ebuild +++ /dev/null @@ -1,108 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -DESCRIPTION="clview is an assembly .ace file viewer from TIGR Gene Indices project tools" -HOMEPAGE="https://sourceforge.net/projects/clview" -SRC_URI=" - https://sourceforge.net/projects/clview/files/source%20code/clview_src.tar.gz - ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/clview/clview_src.tar.gz - ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/clview/clview_linux_i386.tar.gz" - -# the ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/tgi_cpp_library.tar.gz -# contain maybe an older but definitely larger set of .cpp files compared to clview/gcl/ -# contents. clview compiles against both versions with same warning messages from g++. -# -# mokrejs@vrapenec$ ls -la /var/tmp/portage/sci-biology/clview-0.1/work/gclib/ -# total 188 -# drwxr-xr-x 2 mmokrejs mmokrejs 4096 Dec 2 22:23 . -# drwx------ 5 mmokrejs portage 4096 Dec 2 22:23 .. -# -rw-r--r-- 1 mmokrejs mmokrejs 11632 Sep 17 2008 AceParser.cpp -# -rw-r--r-- 1 mmokrejs mmokrejs 906 Sep 14 2008 AceParser.h -# -rw-r--r-- 1 mmokrejs mmokrejs 32276 Dec 2 22:23 AceParser.o -# -rw-r--r-- 1 mmokrejs mmokrejs 11012 Jan 22 2009 GBase.cpp -# -rw-r--r-- 1 mmokrejs mmokrejs 9200 Dec 16 2008 GBase.h -# -rw-r--r-- 1 mmokrejs mmokrejs 8844 Dec 2 22:23 GBase.o -# -rw-r--r-- 1 mmokrejs mmokrejs 16813 Jul 29 2008 GHash.hh -# -rw-r--r-- 1 mmokrejs mmokrejs 16516 Sep 10 2008 GList.hh -# -rw-r--r-- 1 mmokrejs mmokrejs 11221 Jan 22 2009 LayoutParser.cpp -# -rw-r--r-- 1 mmokrejs mmokrejs 6246 Sep 14 2008 LayoutParser.h -# -rw-r--r-- 1 mmokrejs mmokrejs 32956 Dec 2 22:23 LayoutParser.o -# mokrejs@vrapenec$ ls -la /var/tmp/portage/sci-biology/clview-0.1/work/tgi_cl/gcl/ -# total 268 -# drwxr-xr-x 2 mmokrejs mmokrejs 4096 Nov 18 2008 . -# drwxr-xr-x 3 mmokrejs mmokrejs 4096 Oct 18 2006 .. -# -rw-r--r-- 1 mmokrejs mmokrejs 9515 Nov 7 2005 AceParser.cpp -# -rw-r--r-- 1 mmokrejs mmokrejs 886 Nov 7 2005 AceParser.h -# -rw-r--r-- 1 mmokrejs mmokrejs 10768 Nov 7 2005 BitHash.hh -# -rw-r--r-- 1 mmokrejs mmokrejs 7250 Nov 7 2005 GArgs.cpp -# -rw-r--r-- 1 mmokrejs mmokrejs 2507 Nov 7 2005 GArgs.h -# -rw-r--r-- 1 mmokrejs mmokrejs 10156 Nov 18 2008 GBase.cpp -# -rw-r--r-- 1 mmokrejs mmokrejs 8142 Nov 18 2008 GBase.h -# -rw-r--r-- 1 mmokrejs mmokrejs 14742 Nov 7 2005 GCdbYank.cpp -# -rw-r--r-- 1 mmokrejs mmokrejs 1831 Nov 7 2005 GCdbYank.h -# -rw-r--r-- 1 mmokrejs mmokrejs 16723 Nov 7 2005 GFastaFile.h -# -rw-r--r-- 1 mmokrejs mmokrejs 16245 Nov 7 2005 GHash.hh -# -rw-r--r-- 1 mmokrejs mmokrejs 15561 Nov 7 2005 GList.hh -# -rw-r--r-- 1 mmokrejs mmokrejs 28 Nov 7 2005 GReadBuf.cpp -# -rw-r--r-- 1 mmokrejs mmokrejs 4022 Nov 7 2005 GReadBuf.h -# -rw-r--r-- 1 mmokrejs mmokrejs 48 Nov 7 2005 GShMem.cpp -# -rw-r--r-- 1 mmokrejs mmokrejs 4012 Nov 7 2005 GShMem.h -# -rw-r--r-- 1 mmokrejs mmokrejs 32875 Nov 7 2005 GString.cpp -# -rw-r--r-- 1 mmokrejs mmokrejs 8453 Nov 7 2005 GString.h -# -rw-r--r-- 1 mmokrejs mmokrejs 11157 Nov 7 2005 LayoutParser.cpp -# -rw-r--r-- 1 mmokrejs mmokrejs 6063 Nov 7 2005 LayoutParser.h -# -rw-r--r-- 1 mmokrejs mmokrejs 20253 Nov 7 2005 gcdb.cpp -# -rw-r--r-- 1 mmokrejs mmokrejs 6941 Nov 7 2005 gcdb.h -# -rw-r--r-- 1 mmokrejs mmokrejs 8998 Nov 7 2005 gcompress.cpp -# -rw-r--r-- 1 mmokrejs mmokrejs 3670 Nov 7 2005 gcompress.h -# - -LICENSE="Artistic" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -DEPEND="=x11-libs/fox-1.6*" -RDEPEND="${DEPEND}" - -S=${WORKDIR} - -src_unpack() { - unpack clview_src.tar.gz -} - -src_prepare() { - default - # FIXME: we have to run `/usr/bin/fox-config --cflags' to yield - # `-I/usr/include/fox-1.6' - # similarly `fox-config --libs' to yield e.g. - # `-lFOX-1.6 -lXext -lX11 -lXft -lXrender -lfontconfig -lfreetype -lz -lX11 - # -lXcursor -lXrandr -ldl -lpthread -lrt -ljpeg -lpng -ltiff -lz -lbz2 -lm - # -lcups -lnsl -lGLU -lGL' - FOXVERSION=`WANT_FOX="1.6" fox-config --version` - FOXPREFIX=`WANT_FOX="1.6" fox-config --prefix` - FOXINCPATH=`WANT_FOX="1.6" fox-config --cflags` - FOXLIBS=`WANT_FOX="1.6" fox-config --libs` - einfo "Discovered path to fox ${FOXVERSION} files: ${FOXINCPATH}\n${FOXLIBS}" - - sed -i "s#FOXPREFIX = /mylocal/geo#FOXPREFIX = ${FOXPREFIX}#" clview/Makefile || die "Failed to hack FOXPREFIX in clview/Makefile" - sed -i "s#FOXINCDIR := .*#FOXINCDIR := ${FOXINCPATH}#" clview/Makefile || die "Failed to hack FOXINCDIR in clview/Makefile" - sed -i "s#-I\${FOXINCDIR}#\${FOXINCDIR}#" clview/Makefile || die "Failed to revert the extra -I we introduced on a previous line to clview/Makefile" - sed -i "s#FOXLIBDIR := .*#FOXLIBDIR := ${FOXPREFIX}/lib#" clview/Makefile || die "Failed to hack FOXLIBDIR in clview/Makefile" - sed -i "s#LOADLIBS :=.*#LOADLIBS := ${FOXLIBS}#" clview/Makefile || die "Failed to hack LOADLIBS in clview/Makefile" - sed -i "s#-I-#-I #" clview/Makefile || die - - # see tgi_cl/gcl/ - sed -i "s#TGICLASSDIR := /tucan/geo/src/tgi_cl#TGICLASSDIR := ../gcl#" clview/Makefile || die -} - -src_compile(){ - cd "${S}"/clview || die - default -} - -src_install() { - # install at least the binaries for clview when we cannot compile it - dobin clview/clview -} diff --git a/sci-biology/clview/metadata.xml b/sci-biology/clview/metadata.xml deleted file mode 100644 index 7adf609cd..000000000 --- a/sci-biology/clview/metadata.xml +++ /dev/null @@ -1,15 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="sourceforge">clview</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-biology/codonw/codonw-1.4.4-r2.ebuild b/sci-biology/codonw/codonw-1.4.4-r2.ebuild index 6478e9169..49bf65452 100644 --- a/sci-biology/codonw/codonw-1.4.4-r2.ebuild +++ b/sci-biology/codonw/codonw-1.4.4-r2.ebuild @@ -6,9 +6,9 @@ EAPI=7 inherit toolchain-funcs DESCRIPTION="Multivariate statistical analysis of codon and amino acid usage" -HOMEPAGE="http://codonw.sourceforge.net/" +HOMEPAGE="https://codonw.sourceforge.net/" SRC_URI="mirror://sourceforge/${PN}/CodonWSourceCode_${PV//./_}.tar.gz - http://codonw.sourceforge.net/JohnPedenThesisPressOpt_water.pdf" + https://codonw.sourceforge.net/JohnPedenThesisPressOpt_water.pdf" LICENSE="GPL-2" SLOT="0" diff --git a/sci-biology/coral/coral-1.4.1.ebuild b/sci-biology/coral/coral-1.4.1.ebuild index bfa2fc85a..0481e5e80 100644 --- a/sci-biology/coral/coral-1.4.1.ebuild +++ b/sci-biology/coral/coral-1.4.1.ebuild @@ -6,8 +6,8 @@ EAPI=7 inherit toolchain-funcs DESCRIPTION="Error corrector for Illumina and Roche/454 reads using multiple alignment info" -HOMEPAGE="http://www.cs.helsinki.fi/u/lmsalmel/coral" -SRC_URI="http://www.cs.helsinki.fi/u/lmsalmel/coral/${P}.tar.gz" +HOMEPAGE="https://www.cs.helsinki.fi/u/lmsalmel/coral" +SRC_URI="https://www.cs.helsinki.fi/u/lmsalmel/coral/${P}.tar.gz" LICENSE="GPL-3" SLOT="0" diff --git a/sci-biology/cortex_var/Manifest b/sci-biology/cortex_var/Manifest deleted file mode 100644 index 969e60d0a..000000000 --- a/sci-biology/cortex_var/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -DIST CORTEX_release_v1.0.5.21.tgz 26902149 BLAKE2B 397d309fa941fd76ca51f58f20e036dd51548455ae2831738f03fed2293bb3f8dac7443282bba900b3f264a14e6bdacc23ff5460e713c05d4c5e5f11de021080 SHA512 92200cc1e886e519a8e54c9054a2901a03001091654a0534c7a92a5fa7a0ac43aba782b59731d588525902adf749cabca64cdb9cdb25c215be9afb01690215e3 -DIST cortex_var_user_manual.pdf 265899 BLAKE2B 83797183e88f0c17fe3a114c2912263bb84b4c2dca1a0a2a563c82fe377111d24a8ad726581f62b3e44a6cc714bcf58ffd8c18f9f5bd0eb9df6130bd49b296ee SHA512 e4ff442f9280e9eee384c2b82c75493bdb90589b354333fc8b2bee8cf9c9baa432ec09dce5325b2e12c1e1930971616065713858565d56f9a361c573ac0c4f65 diff --git a/sci-biology/cortex_var/cortex_var-1.0.5.21.ebuild b/sci-biology/cortex_var/cortex_var-1.0.5.21.ebuild deleted file mode 100644 index d368f5db3..000000000 --- a/sci-biology/cortex_var/cortex_var-1.0.5.21.ebuild +++ /dev/null @@ -1,51 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit perl-functions - -DESCRIPTION="Genotype variant discovery without reference sequence" -HOMEPAGE="http://cortexassembler.sourceforge.net/index_cortex_var.html" # no https -SRC_URI=" - https://sourceforge.net/projects/cortexassembler/files/cortex_var/latest/CORTEX_release_v${PV}.tgz - http://cortexassembler.sourceforge.net/cortex_var_user_manual.pdf" - -LICENSE="GPL-3" -SLOT="0" -KEYWORDS="" - -# http://www.well.ox.ac.uk/project-stampy - -DEPEND=" - sci-biology/vcftools - sci-libs/gsl - sci-libs/htslib:0= - dev-lang/perl" -RDEPEND="${DEPEND}" - -S="${WORKDIR}/CORTEX_release_v${PV}" - -src_prepare(){ - default - sed -i -e "s/ -O3 / ${CFLAGS} /" Makefile || die - sed -i -e "s#libs/gsl-1.15#${EPREFIX}/usr/include/gsl#" Makefile || die -} - -src_compile(){ - rm -rf libs/htslib libs/gsl-1.15 || die - emake -C libs/string_buffer - emake STRING_BUF_PATH="${S}/libs/string_buffer" HTS_PATH="/usr/include/" -C libs/seq_file - emake NUM_COLS=1 MAXK=31 cortex_var -} - -src_install(){ - bash install.sh || die - perl_set_version - perl_domodule scripts/analyse_variants/bioinf-perl/lib/* scripts/calling/* - echo \ - "PATH=${EPREFIX}/usr/share/${PN}/scripts/analyse_variants/needleman_wunsch" \ - > "${T}/99${PN}" || die - doenvd "${T}/99${PN}" - dodoc "${DISTDIR}"/cortex_var_user_manual.pdf -} diff --git a/sci-biology/cortex_var/metadata.xml b/sci-biology/cortex_var/metadata.xml deleted file mode 100644 index a2867d6fd..000000000 --- a/sci-biology/cortex_var/metadata.xml +++ /dev/null @@ -1,15 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="sourceforge">cortexassembler</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-biology/cutadapt/Manifest b/sci-biology/cutadapt/Manifest deleted file mode 100644 index 30063661a..000000000 --- a/sci-biology/cutadapt/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -DIST cutadapt-2.10.tar.gz 282198 BLAKE2B 87784fd092d3417775f3a627d68bea1d3421f6392ae90f65e9b5f231f10a4da8cfacecc8c6fc3cd8420d0255ffc44ec72188bc901d1768f18f3b78077a165314 SHA512 afefb101a25daa071e5945e442de46cd594a6f4ba5915e9d11943280039223ff5d686b358de44f11b6367f203767d97b76fc529eae70b072139e55831189e594 -DIST cutadapt-3.3.tar.gz 294579 BLAKE2B 1cf833d65a9611e50d747b6ce544dbf639ccc8eab8c5e83425d47bfe5526a0a25faab10cec7b41fad5b012ccf0552948a778b81dac3d5768674326d210dd4540 SHA512 d8895453455aff31c613a4e031559c08646ce2bf072d85ed7b195e5863700a02a1ed44bfb409b63849aadf1db7cf40dea33d0ead4f056307365dc91aa6c93234 diff --git a/sci-biology/cutadapt/cutadapt-2.10.ebuild b/sci-biology/cutadapt/cutadapt-2.10.ebuild deleted file mode 100644 index c0c263469..000000000 --- a/sci-biology/cutadapt/cutadapt-2.10.ebuild +++ /dev/null @@ -1,42 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7..9} ) - -inherit distutils-r1 - -DESCRIPTION="Remove adapter sequences from high-throughput sequencing data" -HOMEPAGE="https://github.com/marcelm/cutadapt" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -DEPEND=" - dev-python/dnaio[${PYTHON_USEDEP}] - dev-python/xopen[${PYTHON_USEDEP}] -" -RDEPEND=" - ${PYTHON_DEPS} - ${DEPEND} -" -BDEPEND=" - test? ( - dev-python/cython - dev-python/pytest-mock - dev-python/pytest-timeout - dev-python/sphinx - dev-python/sphinx-issues - ) -" - -distutils_enable_tests pytest - -# needs call to installed cutadapt executable -python_test() { - distutils_install_for_testing - pytest -vv || die "pytest failed with ${EPYTHON}" -} diff --git a/sci-biology/cutadapt/cutadapt-3.3.ebuild b/sci-biology/cutadapt/cutadapt-3.3.ebuild deleted file mode 100644 index e1990f222..000000000 --- a/sci-biology/cutadapt/cutadapt-3.3.ebuild +++ /dev/null @@ -1,42 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7..9} ) - -inherit distutils-r1 - -DESCRIPTION="Remove adapter sequences from high-throughput sequencing data" -HOMEPAGE="https://github.com/marcelm/cutadapt" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -DEPEND=" - dev-python/dnaio[${PYTHON_USEDEP}] - dev-python/xopen[${PYTHON_USEDEP}] -" -RDEPEND=" - ${PYTHON_DEPS} - ${DEPEND} -" -BDEPEND=" - test? ( - dev-python/cython - dev-python/pytest-mock - dev-python/pytest-timeout - ) -" - -PATCHES=( "${FILESDIR}"/${PN}-3.3-skiptest.patch ) - -distutils_enable_tests pytest - -# needs call to installed cutadapt executable -python_test() { - distutils_install_for_testing - pytest -vv || die "pytest failed with ${EPYTHON}" -} diff --git a/sci-biology/cutadapt/files/cutadapt-3.3-skiptest.patch b/sci-biology/cutadapt/files/cutadapt-3.3-skiptest.patch deleted file mode 100644 index c2dc2a741..000000000 --- a/sci-biology/cutadapt/files/cutadapt-3.3-skiptest.patch +++ /dev/null @@ -1,13 +0,0 @@ -diff --git a/tests/test_command.py b/tests/test_command.py -index a81b04a..cf40233 100644 ---- a/tests/test_command.py -+++ b/tests/test_command.py -@@ -76,7 +76,7 @@ def test_force_fasta_output(tmpdir, cores): - assert_files_equal(cutpath("small.fasta"), out_path) - - --@pytest.mark.skipif(sys.platform == "win32", reason="Maybe this can be made to work") -+@pytest.mark.skipif(reason="Maybe this can be made to work") - def test_non_utf8_locale(): - subprocess.check_call( - [sys.executable, "-m", "cutadapt", "-o", os.devnull, datapath("small.fastq")], diff --git a/sci-biology/cutadapt/metadata.xml b/sci-biology/cutadapt/metadata.xml deleted file mode 100644 index 6a2aeb852..000000000 --- a/sci-biology/cutadapt/metadata.xml +++ /dev/null @@ -1,20 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="person"> - <email>gentoo@aisha.cc</email> - <name>Aisha Tammy</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="github">marcelm/cutadapt</remote-id> - <remote-id type="pypi">cutadapt</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-biology/dargcc_bidsdata/dargcc_bidsdata-1.0.ebuild b/sci-biology/dargcc_bidsdata/dargcc_bidsdata-1.0.ebuild index df7ba43bb..0312eda29 100644 --- a/sci-biology/dargcc_bidsdata/dargcc_bidsdata-1.0.ebuild +++ b/sci-biology/dargcc_bidsdata/dargcc_bidsdata-1.0.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2020 Gentoo Authors +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=7 @@ -7,7 +7,6 @@ DESCRIPTION="BIDS data selection of wildtype animals from DARGCC article" HOMEPAGE="https://academic.oup.com/cercor/article/28/7/2495/4975475" SRC_URI=" https://zenodo.org/record/3885733/files/${P}.tar.xz - http://chymera.eu/distfiles/${P}.tar.xz " LICENSE="GPL-3" diff --git a/sci-biology/dcm2niix/metadata.xml b/sci-biology/dcm2niix/metadata.xml index 9c9e19081..773e706a6 100644 --- a/sci-biology/dcm2niix/metadata.xml +++ b/sci-biology/dcm2niix/metadata.xml @@ -19,4 +19,7 @@ format to the NIfTI format. ICOM provides many ways to store/compress image data, known as transfer syntaxes. </longdescription> + <upstream> + <remote-id type="github">rordenlab/dcm2niix</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/dcmstack/Manifest b/sci-biology/dcmstack/Manifest index ca8d74137..ab8414c4e 100644 --- a/sci-biology/dcmstack/Manifest +++ b/sci-biology/dcmstack/Manifest @@ -1 +1 @@ -DIST dcmstack-0.8.tar.gz 1740289 BLAKE2B d57276c02db3f6a64874635528cb98d874cbc4f64464cfe47aa7217db96caddd46465e9275fced32363a22076b0b75e8c27649aac2fc15133d1354d7dd3b039e SHA512 c6ba0933e173f63426af60fb34fe671c9b49d3cf958628c15920f99925368a14f40c7821c1972c247e7f91c73be3bba288bf8794f334f32fef1feba4c5d5e7c1 +DIST dcmstack-0.9.gh.tar.gz 1739820 BLAKE2B 08b65589b1317ab7ac16a5ac126cf6fba7933941b0b929baa689fb72425f590fb98ae967908b358d5316f5009aa6443787e7077c13f22f156d3fae67a9b8396c SHA512 8061f55c0fa467c3fae94f8790f01331d377d8552cf7a896d705b3cf895340051aad7a4a79237cc225f587d2411be23255635970ab4067d1e5a37f82407b4b39 diff --git a/sci-biology/dcmstack/dcmstack-0.8.ebuild b/sci-biology/dcmstack/dcmstack-0.9.ebuild index de4dfde54..d207526c0 100644 --- a/sci-biology/dcmstack/dcmstack-0.8.ebuild +++ b/sci-biology/dcmstack/dcmstack-0.9.ebuild @@ -1,16 +1,16 @@ -# Copyright 1999-2020 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 -PYTHON_COMPAT=( python3_{7..9} ) +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..11} ) inherit distutils-r1 DESCRIPTION="DICOM to Nifti coversion" HOMEPAGE="https://dcmstack.readthedocs.org/en/latest/" -SRC_URI="https://github.com/moloney/dcmstack/archive/v${PV}.tar.gz -> ${P}.tar.gz" -EGIT_REPO_URI="https://github.com/moloney/dcmstack" +SRC_URI="https://github.com/moloney/dcmstack/archive/v${PV}.tar.gz -> ${P}.gh.tar.gz" LICENSE="MIT" SLOT="0" @@ -22,4 +22,4 @@ RDEPEND=" sci-libs/pydicom[${PYTHON_USEDEP}] " -distutils_enable_tests setup.py +distutils_enable_tests pytest diff --git a/sci-biology/dcmstack/metadata.xml b/sci-biology/dcmstack/metadata.xml index ae9640ffb..0272cf14e 100644 --- a/sci-biology/dcmstack/metadata.xml +++ b/sci-biology/dcmstack/metadata.xml @@ -5,4 +5,7 @@ <email>sci@gentoo.org</email> <name>Gentoo Science Project</name> </maintainer> + <upstream> + <remote-id type="github">moloney/dcmstack</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/deeptools-intervals/deeptools-intervals-0.1.9.ebuild b/sci-biology/deeptools-intervals/deeptools-intervals-0.1.9.ebuild index 1eecdd1b9..38f9aea0f 100644 --- a/sci-biology/deeptools-intervals/deeptools-intervals-0.1.9.ebuild +++ b/sci-biology/deeptools-intervals/deeptools-intervals-0.1.9.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 -PYTHON_COMPAT=( python3_{7,8,9} ) +PYTHON_COMPAT=( python3_{10..11} ) inherit distutils-r1 diff --git a/sci-biology/deeptools-intervals/metadata.xml b/sci-biology/deeptools-intervals/metadata.xml index 08881e6e4..853bd539c 100644 --- a/sci-biology/deeptools-intervals/metadata.xml +++ b/sci-biology/deeptools-intervals/metadata.xml @@ -6,6 +6,6 @@ <name>Gentoo Biology Project</name> </maintainer> <upstream> - <remote-id type="github">fidelram/deepTools_intervals</remote-id> + <remote-id type="github">deeptools/deeptools_intervals</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/deeptools/Manifest b/sci-biology/deeptools/Manifest index 31a5bdb90..649a31cdf 100644 --- a/sci-biology/deeptools/Manifest +++ b/sci-biology/deeptools/Manifest @@ -1 +1,2 @@ DIST deeptools-3.5.0.tar.gz 62553343 BLAKE2B a8cd1520b96c50ad36667405677cf422a74376d88f0716f83cc0c6f58d01aefcf47ac1b862aa98b8801e61445d59831dbc9246660e2f41a5b3e0ed3d6573ad50 SHA512 699734c8a863ec76dfead728e3227bbe3ec04d62e91f447269a6aa8406d627ff618837b85ab2e31cc635c671e1d62230c4db0992106bbe921281b81164387b38 +DIST deeptools-3.5.1.tar.gz 62552044 BLAKE2B 3c785ba478b88fbbe7ba2617e2d05984b8a897f787e85d6f8f144f596af07b9e16ba920c8adee35efc4b1b067f255e81f66cf746aaea43e5ee61c23c4d15c9c3 SHA512 f7618f1a51b975d42712a38e13e9ab2ddfeafffe24d81fdab41f1ef7c2e44fd09da0351210670b0036bf72e7af11b679417275adce300ae9fabe4b5339ee9810 diff --git a/sci-biology/deeptools/deeptools-3.5.0.ebuild b/sci-biology/deeptools/deeptools-3.5.0.ebuild index f53a19bcb..7c2eaa739 100644 --- a/sci-biology/deeptools/deeptools-3.5.0.ebuild +++ b/sci-biology/deeptools/deeptools-3.5.0.ebuild @@ -1,9 +1,10 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 -PYTHON_COMPAT=( python3_{7,8,9} ) +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..11} ) inherit distutils-r1 @@ -13,7 +14,7 @@ SRC_URI="https://github.com/deeptools/deepTools/archive/${PV}.tar.gz -> ${P}.tar LICENSE="BSD" SLOT="0" -KEYWORDS="~amd64 ~x86" +KEYWORDS="~amd64" # TODO: fix this RESTRICT="test" @@ -23,7 +24,7 @@ RDEPEND=" >=dev-python/numpy-1.9.0[${PYTHON_USEDEP}] >=dev-python/numpydoc-0.5[${PYTHON_USEDEP}] >=dev-python/scipy-0.17.0[${PYTHON_USEDEP}] - >=dev-python/plotly-2.0.0[${PYTHON_USEDEP}] + dev-python/plotly[${PYTHON_USEDEP}] >=dev-python/py2bit-0.2.0[${PYTHON_USEDEP}] >=dev-python/pyBigWig-0.2.1[${PYTHON_USEDEP}] >=sci-biology/pysam-0.14.0[${PYTHON_USEDEP}] @@ -32,5 +33,5 @@ RDEPEND=" S="${WORKDIR}/deepTools-${PV}" -distutils_enable_sphinx docs dev-python/sphinx_rtd_theme dev-python/sphinx-argparse -distutils_enable_tests nose +distutils_enable_sphinx docs dev-python/sphinx-rtd-theme dev-python/sphinx-argparse +#distutils_enable_tests nose diff --git a/sci-biology/deeptools/deeptools-3.5.1.ebuild b/sci-biology/deeptools/deeptools-3.5.1.ebuild new file mode 100644 index 000000000..7c2eaa739 --- /dev/null +++ b/sci-biology/deeptools/deeptools-3.5.1.ebuild @@ -0,0 +1,37 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..11} ) + +inherit distutils-r1 + +DESCRIPTION="Extract reads from BAM files, normalize, draw figures, convert BAM to bigWig" +HOMEPAGE="https://github.com/deeptools/deepTools" +SRC_URI="https://github.com/deeptools/deepTools/archive/${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64" + +# TODO: fix this +RESTRICT="test" + +RDEPEND=" + >=sci-biology/deeptools-intervals-0.1.8[${PYTHON_USEDEP}] + >=dev-python/numpy-1.9.0[${PYTHON_USEDEP}] + >=dev-python/numpydoc-0.5[${PYTHON_USEDEP}] + >=dev-python/scipy-0.17.0[${PYTHON_USEDEP}] + dev-python/plotly[${PYTHON_USEDEP}] + >=dev-python/py2bit-0.2.0[${PYTHON_USEDEP}] + >=dev-python/pyBigWig-0.2.1[${PYTHON_USEDEP}] + >=sci-biology/pysam-0.14.0[${PYTHON_USEDEP}] + >=dev-python/matplotlib-3.1.0[${PYTHON_USEDEP}] +" + +S="${WORKDIR}/deepTools-${PV}" + +distutils_enable_sphinx docs dev-python/sphinx-rtd-theme dev-python/sphinx-argparse +#distutils_enable_tests nose diff --git a/sci-biology/diamond/metadata.xml b/sci-biology/diamond/metadata.xml index 138cb7705..ac7dfc24a 100644 --- a/sci-biology/diamond/metadata.xml +++ b/sci-biology/diamond/metadata.xml @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">bbuchfink/diamond</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/dipy/dipy-1.1.1.ebuild b/sci-biology/dipy/dipy-1.1.1.ebuild index c2c9f724e..3656d6dc8 100644 --- a/sci-biology/dipy/dipy-1.1.1.ebuild +++ b/sci-biology/dipy/dipy-1.1.1.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 -PYTHON_COMPAT=( python3_{7..9} ) +PYTHON_COMPAT=( python3_10 ) inherit distutils-r1 diff --git a/sci-biology/dipy/dipy-9999.ebuild b/sci-biology/dipy/dipy-9999.ebuild deleted file mode 100644 index a1b162df6..000000000 --- a/sci-biology/dipy/dipy-9999.ebuild +++ /dev/null @@ -1,37 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7..9} ) - -inherit distutils-r1 git-r3 - -DESCRIPTION="Computational neuroanatomy project focusing on diffusion MRI" -HOMEPAGE="https://github.com/nipy/dipy" -SRC_URI="" -EGIT_REPO_URI="https://github.com/nipy/dipy" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="" -IUSE="test" -RESTRICT="!test? ( test )" - -RDEPEND=" - sci-libs/nibabel[${PYTHON_USEDEP}] - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/scipy[${PYTHON_USEDEP}] -" -DEPEND=" - dev-python/cython[${PYTHON_USEDEP}] - dev-python/h5py[${PYTHON_USEDEP}] - dev-python/setuptools[${PYTHON_USEDEP}] - test? ( dev-python/nose[${PYTHON_USEDEP}] ) -" - -python_test() { - distutils_install_for_testing - cd "${TEST_DIR}"/lib || die - nosetests || die -} diff --git a/sci-biology/drlfom_bidsdata/drlfom_bidsdata-1.1.ebuild b/sci-biology/drlfom_bidsdata/drlfom_bidsdata-1.1.ebuild index 6385db093..8ddd4007e 100644 --- a/sci-biology/drlfom_bidsdata/drlfom_bidsdata-1.1.ebuild +++ b/sci-biology/drlfom_bidsdata/drlfom_bidsdata-1.1.ebuild @@ -1,24 +1,20 @@ -# Copyright 1999-2020 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 inherit check-reqs DESCRIPTION="BIDS data files released with the DRLFOM publication" -HOMEPAGE="http://www.aic-fmi.ethz.ch/" +HOMEPAGE="https://chymera.eu/docs/focus/open-science/" SRC_URI=" https://zenodo.org/record/3598424/files/${P}.tar.xz - http://chymera.eu/distfiles/${P}.tar.xz " LICENSE="CC-BY-SA-4.0" SLOT="0" KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -RDEPEND="" -DEPEND="" - pkg_pretend() { CHECKREQS_DISK_BUILD="21G" check-reqs_pkg_pretend diff --git a/sci-biology/estscan/Manifest b/sci-biology/estscan/Manifest deleted file mode 100644 index 79281bc74..000000000 --- a/sci-biology/estscan/Manifest +++ /dev/null @@ -1,9 +0,0 @@ -DIST At.smat.gz 32314 BLAKE2B c48c043fa7e7e26e406a677587380e0ade911aafb5878988668da9b9f09a978a369e636c931d2d4d65b6efc65398723e1a78c032805cfc71f2927a42d87788c4 SHA512 aeb3dec65b730570d70e8f49930bf85cc73fe39696d2ccc08e6a804cfe435ea43423f1f4a02b192c68da03727b628bb43ec0ba27bb4549e59f743eccd203df09 -DIST BTLib-0.19.tar.gz 36283 BLAKE2B 53d26fdc7fee3325104a7f2041617bbde464421c540b29c7d47381c60d8f837601e7274d9f0ef5694d1b86b3e2cc7e9a0b289090c3c957a343542e3e7305cd50 SHA512 00261daa7fab4d16dec9e9d4f9e382cc804a10c0ed6b813d6223902b53f6b260dc0a242acfab93897afa750e949ab3f21ecae537206d81eb712f06289387f7d2 -DIST Dm.smat.gz 31711 BLAKE2B 5e8da0668d0788ce2e70535605cb85ced4ec052c4e736b11d838919c0328c6978170aed8e6102d62c6f8770a99a7f49aad373492ddc79328df3238486b7ee703 SHA512 fe141598291fd1bead1f0918c2e52533db1f5c5f60d4c71838a16298ccf60a8a1857a02379f58979dbab3cfad4e0ac64556cf629fcb65d9a0e6861fe4ca163a4 -DIST Dr.smat.gz 8813 BLAKE2B 465d980cc9c1d61f8a83e4c3dd203852b2cfa4bde5730de268655d7a05db9d018f6cff6357246bbfc42002f3993aebf44c9fc27c2d31fa6657194600e5a364b0 SHA512 1880981db252ed08a762fdc8a321b27063ea2341cde56c40146cc7eeed0fdfa620e9b4c71c245fffee6521ae1efbc89b52e6558cd84aef89138e8b26b60460de -DIST Hs.smat.gz 62935 BLAKE2B 4089dbcc54af5544071d9fc270a9048c758fef15e4846f92dc9c61abd5c60ba9d8ba4a25b9064f4d418cbe1a8a277c5bba49af9a85f51dd9f3bcaac30a7b568d SHA512 7ac3af9b018992014643fbbd83abc4128df4c8b9c516fb1b6b16e1fdc65b23df07811fa5b23ecec5ef2993de71e3efaec5bee3fc1626bcf2984794f13e343447 -DIST Mm.smat.gz 62711 BLAKE2B c65aeb6f8833e4effb360de29e3c25985184e4a9822272f370fc292ec2142843b78ac66485ec98b017aac3a18b7936fc45b510f58cb2db909d5230291573bdf3 SHA512 4ee5fac326bee7e4fe17ad9eab608a90007485a90b479557a181eb49628ff5fee22d04a3ef360b6bc29a76709723faa0a9df8ef1cdb40421d772a0b2dc9f3fc5 -DIST Rn.smat.gz 32388 BLAKE2B 06144cce26cd35eeb15d94db5f169a9cf6c6ab02b4c4f213e42140b2fe864473e7c107c910092620f255384eadd1e07a366e58a21d3df570e63e2843e537aaa3 SHA512 e517d95aa4d1928f766ac9cc885f277d9f980d27265dcc7a2c5d747b1023a5606bccb2dbce2fa9ff76fc0f0333fadd3bc0b7abe9ea4aa82396b57bb06b8dcf43 -DIST estscan-3.0.3.tar.gz 46412 BLAKE2B 998f4f117503e044492495d52e5b064fcb62c3800adb4ec4b357042ea90d8c6ce86902257e5b28ee119c2b332044389c8775101bad6875cba069db6961f73931 SHA512 d3ddb91a71a700a67807a63f7b9c9e2a1c45af847a7808afd757f60f276f7410e22adde6e0ffadbfef8e579890b79fe785b8a05e28cb3d67345464cd2035f69c -DIST user_guide_fev_07.pdf 327005 BLAKE2B 5d66466c122c12618c5aadb2f12a404159b553b57e80fa421d707d8c3e70d795da7285a6976beacd67b7c6462297fde7843b89b48ed773752cdc0e00bfd1c36c SHA512 de1f046656c3e01a9b3e3930aadc7a91cb10d907a9d6af8fc1c2b0abe6ef0d1305baaeee463c80df0c700951a03b1c26a211fdd14e76fbf41ac5fca3467e49c1 diff --git a/sci-biology/estscan/estscan-3.0.3.ebuild b/sci-biology/estscan/estscan-3.0.3.ebuild deleted file mode 100644 index a0992b76b..000000000 --- a/sci-biology/estscan/estscan-3.0.3.ebuild +++ /dev/null @@ -1,124 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit fortran-2 perl-module toolchain-funcs - -DESCRIPTION="Prediction of coding regions in DNA/RNA sequences" -HOMEPAGE="https://sourceforge.net/projects/estscan/" -SRC_URI=" - https://downloads.sourceforge.net/${PN}/${P}.tar.gz - https://downloads.sourceforge.net/${PN}/At.smat.gz - https://downloads.sourceforge.net/${PN}/Dm.smat.gz - https://downloads.sourceforge.net/${PN}/Dr.smat.gz - https://downloads.sourceforge.net/${PN}/Hs.smat.gz - https://downloads.sourceforge.net/${PN}/Mm.smat.gz - https://downloads.sourceforge.net/${PN}/Rn.smat.gz - https://downloads.sourceforge.net/${PN}/user_guide_fev_07.pdf - https://downloads.sourceforge.net/${PN}/BTLib-0.19.tar.gz" - -SLOT="0" -LICENSE="estscan" -KEYWORDS="~amd64 ~x86" -IUSE="icc ifc" - -DEPEND=" - dev-perl/BTLib - icc? ( dev-lang/icc ) - ifc? ( dev-lang/ifc )" -RDEPEND="${DEPEND}" - -S="${WORKDIR}" - -src_prepare() { - default - sed \ - -e 's/\\rm -f/rm -rf/' \ - -e 's/^ LDFLAGS = -lm/LDFLAGS = -lm/' \ - -i "${P}"/Makefile || die "failed to edit Makefile" - - # fix hard-coded paths - sed -e 's+/usr/molbio/share/ESTScan+/usr/share/ESTscan+' -i "${P}"/${PN}.c || die - sed -e 's+/usr/molbio/share/ESTScan+/usr/share/ESTscan+' -i "${P}"/${PN}.spec || die - - if ! use icc; then - sed \ - -e 's/^ CFLAGS = -O2/#CFLAGS = ${CFLAGS}/' -i "${P}"/Makefile || die - fi - - if ! use ifc; then - sed \ - -e 's/^ FFLAGS = -O2/#FFLAGS = ${FFLAGS}/' \ - -e "s/^ F77 = g77/F77 = $(tc-getF77)/" -i "${P}"/Makefile \ - || die - fi - - if use icc; then - # FIXME: I would use $(tc-getCC) instead of hard-coded icc but it gives - # me gcc instead, same for $(tc-getF77) - # Moreover, the if/else logic here should separate users having only icc - # while not ifort (and vice-versa) from those having only - # gcc/gfortran/g77 - # - # FIXME: below as a dirty hack I force gfortran instead of ifort for - # my testing purposes. Didn't ebuild contain "PROVIDES" line? - # Same for FFLAGS. - sed \ - -e "s:^# CC = icc:CC = icc:" \ - -e "s:^# CFLAGS = -O3 -ipo -axP:#CFLAGS = -O3 -ipo -axP:" \ - -e "s/^ CFLAGS = -O2/#CFLAGS = -O2/" \ - -e "s/^ CC = gcc/# CC = gcc/" \ - -i "${P}"/Makefile || die "sed failed to fix CFLAGS and CC" - - fi - - if use ifc; then - sed \ - -e "s:^# FFLAGS = -O3 -ipo -axP:#FFLAGS = -O3 -ipo -axP:" \ - -e "s/^# F77 = ifort/F77 = gfortran/" \ - -e "s/^ FFLAGS = -O2/#FFLAGS = -O2/" \ - -e "s/^ F77 = g77/# F77 = g77/" \ - -i "${P}"/Makefile || die "sed failed to fix FFLAGS and F77" - fi -} - -src_compile() { - emake -C ${P} -} - -src_install() { - # FIXME: Some kind of documentation is in {P}/${PN}.spec - cd ${P} || die "Failed to chdir to ${P}" - dobin \ - build_model ${PN} evaluate_model extract_EST extract_UG_EST \ - extract_mRNA makesmat maskred prepare_data winsegshuffle - # the file build_model_utils.pl should go into some PERL site-packages dir - # see {P}/${PN}.spec - - # install the doc (but is not in ${WORKDIR} because src_unpack() failed on it as it has .pdf extension - insinto /usr/share/doc/${PN} - # grab the file directly from ../distdir/ - doins "${DISTDIR}"/user_guide_fev_07.pdf - - # install the default precomputed matrices - cd "${WORKDIR}" || die "Failed to chdir to ${WORKDIR}" - insinto /usr/share/${PN} - doins *.smat - - # install BTlib (in perl) - # dobin fetch indexer netfetch - insinto /usr/share/${PN}/ - # install the config file which is packed inside the BTLib tarball while is not - # being installed by dev-perl/BTLib - doins "${WORKDIR}"/BTLib-0.19/fetch.conf - - # FIXME: install the *.pm files from BTLib-0.19 - # cd "${WORKDIR}"/BTLib-0.19 || die "Failed to chdir to "${WORKDIR}"/BTLib-0.19 - # myinst="DESTDIR=${D}" - # perl-module_src_install - - einfo "Please edit /usr/share/${PN}/fetch.conf to fit your local database layout." - einfo "Also create your own scoring matrices and place them into /usr/share/${PN}/." - einfo "You may follow the hints from http://${PN}.sourceforge.net/" -} diff --git a/sci-biology/estscan/metadata.xml b/sci-biology/estscan/metadata.xml deleted file mode 100644 index c79c2d1b5..000000000 --- a/sci-biology/estscan/metadata.xml +++ /dev/null @@ -1,19 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <use> - <flag name="icc">Undocumented USE</flag> - <flag name="ifc">Undocumented USE</flag> - </use> - <upstream> - <remote-id type="sourceforge">downloads</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-biology/fastp/Manifest b/sci-biology/fastp/Manifest new file mode 100644 index 000000000..c158050fa --- /dev/null +++ b/sci-biology/fastp/Manifest @@ -0,0 +1 @@ +DIST fastp-0.23.4.tar.gz 164071 BLAKE2B 58745d494b83bbf9ae34593159228dbef5c854ab856af91fea8770fef171ed7b3053a4cac8c31053af3dcd91d4298fddb7594670a32963f53f75bd5fa1ec3a68 SHA512 2c929e974708f8cd2d8cab95d59c0a5fd01bea912f6ba5d08841fd929f0f5019ef89e506c771057bd02b879836ae30564b8417271866b6bbcb4917fbeb387e76 diff --git a/sci-biology/fastp/fastp-0.23.4.ebuild b/sci-biology/fastp/fastp-0.23.4.ebuild new file mode 100644 index 000000000..70d5ce330 --- /dev/null +++ b/sci-biology/fastp/fastp-0.23.4.ebuild @@ -0,0 +1,20 @@ +# Copyright 1999-2023 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DESCRIPTION="An ultra-fast all-in-one FASTQ preprocessor" +HOMEPAGE="https://github.com/OpenGene/fastp" +SRC_URI="https://github.com/OpenGene/fastp/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz" +KEYWORDS="~amd64" + +LICENSE="MIT" +SLOT="0" + +DEPEND="app-arch/libdeflate + dev-libs/isa-l" + +src_install() { + dodir /usr/bin + emake PREFIX="${ED}"/usr install +} diff --git a/sci-biology/ncbi-genome-download/metadata.xml b/sci-biology/fastp/metadata.xml index a394f7ee4..d51d87c5a 100644 --- a/sci-biology/ncbi-genome-download/metadata.xml +++ b/sci-biology/fastp/metadata.xml @@ -2,10 +2,10 @@ <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> - <email>freeh4cker@gmail.com</email> - <name>Bertrand Néron</name> + <email>mschu.dev@gmail.com</email> + <name>Michael Schubert</name> </maintainer> <upstream> - <remote-id type="github">kblin/ncbi-genome-download</remote-id> + <remote-id type="github">OpenGene/fastp</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/fastqc/metadata.xml b/sci-biology/fastqc/metadata.xml index 7c86089a2..f13c6ccba 100644 --- a/sci-biology/fastqc/metadata.xml +++ b/sci-biology/fastqc/metadata.xml @@ -13,4 +13,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">s-andrews/FastQC</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/ffindex/metadata.xml b/sci-biology/ffindex/metadata.xml index 138cb7705..a9577a9c3 100644 --- a/sci-biology/ffindex/metadata.xml +++ b/sci-biology/ffindex/metadata.xml @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">ahcm/ffindex</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/fsa/fsa-1.15.9.ebuild b/sci-biology/fsa/fsa-1.15.9.ebuild index 44e1d5cff..f77ae61aa 100644 --- a/sci-biology/fsa/fsa-1.15.9.ebuild +++ b/sci-biology/fsa/fsa-1.15.9.ebuild @@ -1,10 +1,10 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 DESCRIPTION="Distance-based probabilistic multiple sequence alignment algo for DNA/RNA/prot" -HOMEPAGE="http://fsa.sourceforge.net" +HOMEPAGE="https://fsa.sourceforge.net" SRC_URI="https://downloads.sourceforge.net/project/fsa/${P}.tar.gz" LICENSE="GPL-3+" diff --git a/sci-biology/fsa/metadata.xml b/sci-biology/fsa/metadata.xml index 0f267b755..e8c9d160f 100644 --- a/sci-biology/fsa/metadata.xml +++ b/sci-biology/fsa/metadata.xml @@ -10,6 +10,6 @@ <name>Gentoo Biology Project</name> </maintainer> <upstream> - <remote-id type="sourceforge">downloads</remote-id> + <remote-id type="sourceforge">fsa</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/fsl/files/fsl-6.0.2-cuda_buildsettings.patch b/sci-biology/fsl/files/fsl-6.0.2-cuda_buildsettings.patch deleted file mode 100644 index a3872acf0..000000000 --- a/sci-biology/fsl/files/fsl-6.0.2-cuda_buildsettings.patch +++ /dev/null @@ -1,12 +0,0 @@ -diff -Naur fsl.orig/config/buildSettings.mk fsl/config/buildSettings.mk ---- fsl.orig/config/buildSettings.mk 2020-07-23 15:43:42.277064365 -0400 -+++ fsl/config/buildSettings.mk 2020-07-23 15:45:17.705069496 -0400 -@@ -141,7 +141,7 @@ - # CUDA development environment - CUDAVER := $(or $(CUDAVER),9.1) - #$(info $$CUDAVER is [${CUDAVER}]) --CUDA_INSTALLATION = /opt/cuda-${CUDAVER} -+CUDA_INSTALLATION = /opt/cuda - GENCODE_FLAGS = $(shell ${FSLDIR}/config/common/supportedGencodes.sh ${CUDA_INSTALLATION}) - LIB_CUDA = ${CUDA_INSTALLATION}/lib64 - INC_CUDA = ${CUDA_INSTALLATION}/include diff --git a/sci-biology/fsl/files/fsl-6.0.2-eddy_cuda.patch b/sci-biology/fsl/files/fsl-6.0.2-eddy_cuda.patch deleted file mode 100644 index 40409ec08..000000000 --- a/sci-biology/fsl/files/fsl-6.0.2-eddy_cuda.patch +++ /dev/null @@ -1,21 +0,0 @@ -diff -Naur fsl.orig/src/eddy/Makefile fsl/src/eddy/Makefile ---- fsl.orig/src/eddy/Makefile 2020-07-30 14:30:06.414884410 -0400 -+++ fsl/src/eddy/Makefile 2020-07-30 14:33:03.400889914 -0400 -@@ -29,6 +29,8 @@ - TMPCXXFLAGS_2= - TMPNAME_1= - TMPNAME_2= -+cuda=1 -+cpu=1 - - ifndef cuda - ifndef cpu #Default single cpu, no threading -@@ -74,7 +75,7 @@ - ifdef NVCC11 - NVCC=${NVCC11} - endif --NVCCFLAGS=-c -DCOMPILE_GPU -O3 -m 64 -std=c++11 -+NVCCFLAGS=-c -DCOMPILE_GPU -O3 -m 64 -std=c++11 @@GENTOO_NVCC_FLAGS@@ - ifeq ($(CLOBBER_CLANG),1) - NVCCFLAGS+= -DCLOBBER_CLANG - endif diff --git a/sci-biology/fsl/files/fsl-6.0.2-fsldir_redux-p1.patch b/sci-biology/fsl/files/fsl-6.0.2-fsldir_redux-p1.patch deleted file mode 100644 index ca3945442..000000000 --- a/sci-biology/fsl/files/fsl-6.0.2-fsldir_redux-p1.patch +++ /dev/null @@ -1,240 +0,0 @@ -From 2bc4be1f55b27a733e1e624b34bc570187ba95e1 Mon Sep 17 00:00:00 2001 -From: François Bissey <frp.bissey@gmail.com> -Date: Mon, 20 Jan 2020 11:40:53 +1300 -Subject: [PATCH] Making sure fsl code and executable can find other executable - and data in standard location. - ---- - src/fast4/fast_two.cc | 8 ++++---- - src/feat5/feat_model.cc | 8 +++----- - src/feat5/tsplot.cc | 7 +++---- - src/first/first_utils.cc | 4 ++-- - src/fnirt/fnirtfns.cpp | 11 ++++------- - src/fslsurface/fslsurface_first.cc | 6 ++---- - src/fslsurface/fslsurfacemaths.cpp | 12 ------------ - src/libvis/miscpic.h | 7 +------ - src/melodic/meldata.cc | 4 ++-- - src/melodic/meloptions.cc | 8 -------- - src/melodic/meloptions.h | 1 - - src/melodic/melreport.cc | 12 ++++++------ - src/melodic/melreport.h | 20 ++++++++++---------- - src/mm/mixture_model.cc | 4 ++-- - src/siena/siena_diff.cc | 28 +++++++++++++--------------- - src/topup/topupfns.cpp | 3 +-- - 16 files changed, 53 insertions(+), 90 deletions(-) - -diff --git a/src/fast4/fast_two.cc b/src/fast4/fast_two.cc -index 592b5df..b525444 100644 ---- a/src/fast4/fast_two.cc -+++ b/src/fast4/fast_two.cc -@@ -166,7 +166,7 @@ int prior_registration(string inname, string main_prior_vol, NEWIMAGE::volume<fl - string csfPriorName, grayPriorName, whitePriorName; - if(alternatePriors.unset()) - { -- string priorRootName=string(getenv("FSLDIR")) + "/data/standard/tissuepriors/avg152T1_"; -+ string priorRootName="@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/tissuepriors/avg152T1_"; - csfPriorName = priorRootName+"csf"; - grayPriorName = priorRootName+"gray"; - whitePriorName = priorRootName+"white"; -@@ -215,15 +215,15 @@ string csfPriorName, grayPriorName, whitePriorName; - if(bapused>0) - { - char reg[1024]; -- sprintf(reg, "%s/bin/flirt -ref %s -in %s -out %s -applyxfm -init %s", getenv("FSLDIR"), inname.c_str(), csfPriorName.c_str(), (main_prior_vol+"_csf_stdspace").c_str(), bapriori.value().c_str()); -+ sprintf(reg, "flirt -ref %s -in %s -out %s -applyxfm -init %s", inname.c_str(), csfPriorName.c_str(), (main_prior_vol+"_csf_stdspace").c_str(), bapriori.value().c_str()); - if(verbose.value()) - cout<<reg<<endl; - system(reg); -- sprintf(reg, "%s/bin/flirt -ref %s -in %s -out %s -applyxfm -init %s", getenv("FSLDIR"), inname.c_str(), grayPriorName.c_str(), (main_prior_vol+"_gm_stdspace").c_str(), bapriori.value().c_str()); -+ sprintf(reg, "flirt -ref %s -in %s -out %s -applyxfm -init %s", inname.c_str(), grayPriorName.c_str(), (main_prior_vol+"_gm_stdspace").c_str(), bapriori.value().c_str()); - if(verbose.value()) - cout<<reg<<endl; - system(reg); -- sprintf(reg, "%s/bin/flirt -ref %s -in %s -out %s -applyxfm -init %s", getenv("FSLDIR"), inname.c_str(), whitePriorName.c_str(), (main_prior_vol+"_wm_stdspace").c_str(), bapriori.value().c_str()); -+ sprintf(reg, "flirt -ref %s -in %s -out %s -applyxfm -init %s", inname.c_str(), whitePriorName.c_str(), (main_prior_vol+"_wm_stdspace").c_str(), bapriori.value().c_str()); - if(verbose.value()) - cout << reg << endl; - system(reg); -diff --git a/src/feat5/feat_model.cc b/src/feat5/feat_model.cc -index 399a13e..e15e43c 100644 ---- a/src/feat5/feat_model.cc -+++ b/src/feat5/feat_model.cc -@@ -744,7 +744,7 @@ int main(int argc, char **argv) - vector<int> G; - vector<string> titles; - float tr, mult, trmult, nltffwhm=0, maxconvwin=0; -- char fl[10000], *FSLDIR; -+ char fl[10000]; - string fn, filename; - FONT_DATA *font_data = new FONT_DATA[1]; - -@@ -763,8 +763,6 @@ int main(int argc, char **argv) - if (argc==3) - motionparams=remmean(read_ascii_matrix(argv[2])); - -- FSLDIR=getenv("FSLDIR"); -- - fn = string(argv[1])+".fsf"; - - level = atoi(find_line(fn, "fmri(level)", fl)); -@@ -1510,7 +1508,7 @@ int main(int argc, char **argv) - writeCovarianceImage(string(argv[1])+"_cov.ppm", contrasts, F, nftests, realDesign, level, evs.eigenvals, font_data, contrasts.RE); - writeImagePreview(string(argv[1])+".ppm", contrasts, F, nftests, realDesign, level, evs, font_data, titles, tr, nltffwhm, nTimepoints, G); - -- filename=string(getenv("FSLDIR"))+"/bin/wpng -q -overwrite "+string(argv[1])+".ppm "; -+ filename="wpng -q -overwrite "+string(argv[1])+".ppm "; - system(filename.c_str()); - - return(0); -@@ -2161,6 +2159,6 @@ char the_string[10000]; - - fclose(outputfile); - -- filename=string(getenv("FSLDIR")) + "/bin/wpng -q -overwrite " + filename; -+ filename="wpng -q -overwrite " + filename; - system(filename.c_str()); - } -diff --git a/src/feat5/tsplot.cc b/src/feat5/tsplot.cc -index ae191fd..3a02b55 100644 ---- a/src/feat5/tsplot.cc -+++ b/src/feat5/tsplot.cc -@@ -293,7 +293,7 @@ int main(int argc, char **argv) - ofstream outputFile; - int numEVs, npts, numContrasts=1, nftests=0, GRPHSIZE(600), PSSIZE(600); - vector<double> normalisedContrasts, model, triggers; -- string fmriFileName, fslPath, featdir, vType, indexText; -+ string fmriFileName, featdir, vType, indexText; - ColumnVector NewimageVoxCoord(4),NiftiVoxCoord(4); - bool outputText(true), useCoordinate(false), prewhiten(false), useTriggers(false), customMask(false), modelFree(false), isHigherLevel(false), outputDataOnly(false); - bool zWeightClusters(true); -@@ -307,7 +307,6 @@ volume<float> immask; - if (argc<2) usage(""); - featdir=string(argv[1]); - fmriFileName=featdir+"/filtered_func_data"; -- fslPath=string(getenv("FSLDIR")); - - string outputName(featdir); - -@@ -753,7 +752,7 @@ volume4D<float> acs; - cerr << "Can't open output report file " << outputName << endl; - exit(1); - } -- outputFile << "<HTML>\n<TITLE>"<< statType << num2str(i) <<"</TITLE>\n<BODY BACKGROUND=\"file:"<< fslPath <<"/doc/images/fsl-bg.jpg\">\n<hr><CENTER>\n<H1>FEAT Time Series Report - "<< statType << num2str(i) <<"</H1>\n</CENTER>\n<hr><b>Full plots</b><p>\n"<< graphText; -+ outputFile << "<HTML>\n<TITLE>"<< statType << num2str(i) <<"</TITLE>\n<BODY BACKGROUND=\"file:"<< "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-bg.jpg\">\n<hr><CENTER>\n<H1>FEAT Time Series Report - "<< statType << num2str(i) <<"</H1>\n</CENTER>\n<hr><b>Full plots</b><p>\n"<< graphText; - if (useTriggers) outputFile << "\n<hr><b>Peristimulus plots</b><p>\n"<< peristimulusText <<"\n<HR></BODY></HTML>\n\n"; - else outputFile << "\n</BODY></HTML>\n\n"; - outputFile.close(); -@@ -768,7 +767,7 @@ volume4D<float> acs; - cerr << "Can't open output report file " << outputName << endl; - exit(1); - } -- outputFile << "<HTML>\n<TITLE>FEAT Time Series Report</TITLE>\n<BODY BACKGROUND=\"file:" << fslPath << "/doc/images/fsl-bg.jpg\">\n<hr><CENTER>\n<H1>FEAT Time Series Report</H1>\n</CENTER>\n<hr>" << indexText << "<HR></BODY></HTML>" << endl << endl; -+ outputFile << "<HTML>\n<TITLE>FEAT Time Series Report</TITLE>\n<BODY BACKGROUND=\"file:" << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-bg.jpg\">\n<hr><CENTER>\n<H1>FEAT Time Series Report</H1>\n</CENTER>\n<hr>" << indexText << "<HR></BODY></HTML>" << endl << endl; - outputFile.close(); - - /* now output same thing without start and end, for inclusion in feat report */ -diff --git a/src/first/first_utils.cc b/src/first/first_utils.cc -index 68be44b..85960f4 100644 ---- a/src/first/first_utils.cc -+++ b/src/first/first_utils.cc -@@ -1954,8 +1954,8 @@ void do_work_bvars(){ - if (!surfaceVAout.value()) { - // do not output on the surface, instead do the new default of outputting a volume with the scalar normal dot product values (for use with randomise) - volume<float> refim; -- if (useReconMNI.value()) { read_volume(refim,string(getenv("FSLDIR")) + "/data/standard/MNI152_T1_1mm"); } -- else { read_volume(refim,string(getenv("FSLDIR")) + "/data/standard/MNI152_T1_1mm"); } -+ if (useReconMNI.value()) { read_volume(refim,"@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/MNI152_T1_1mm"); } -+ else { read_volume(refim,"@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/MNI152_T1_1mm"); } - volume<float> maskvol(refim); - maskvol=0.0f; - volume4D<float> volnormals; -diff --git a/src/fnirt/fnirtfns.cpp b/src/fnirt/fnirtfns.cpp -index 24e26fd..77899e7 100644 ---- a/src/fnirt/fnirtfns.cpp -+++ b/src/fnirt/fnirtfns.cpp -@@ -1203,8 +1203,7 @@ string existing_ref_fname(const string& ref_fname) - return(string(ref_fname)); - } - else { -- const char *fsldir_ptr = getenv("FSLDIR"); -- string eref_fname = string(fsldir_ptr) + string("/data/standard/") + ref_fname; -+ string eref_fname = string("@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/") + ref_fname; - if (NEWIMAGE::FslFileExists(eref_fname)) return(eref_fname); - else return(string("")); - } -@@ -1230,9 +1229,8 @@ string existing_ref_fname(const string& ref_fname) - NEWIMAGE::read_volume_hdr_only(vref,ref_fname); // Throws if file dont exist - eref_fname = ref_fname; - } -- catch(...) { // Didn't exist in current directory, try in ${FSLDIR}/data/standard -- const char *fsldir_ptr = getenv("FSLDIR"); -- eref_fname = string(fsldir_ptr) + string("/data/standard/") + ref_fname; -+ catch(...) { // Didn't exist in current directory, try in .../data/standard -+ eref_fname = string("@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/") + ref_fname; - try { - cout << "Could not find " << ref_fname << ", now checking " << eref_fname << endl; - NEWIMAGE::read_volume_hdr_only(vref,eref_fname); // Throws if file dont exist -@@ -1267,8 +1265,7 @@ string existing_conf_file(const string& cfname) - if (check_exist(ecfname)) return(ecfname); - } - if (!FNIRT::path(cfname).length()) { // If no path explicitly given -- const char *fsldir_ptr = getenv("FSLDIR"); -- ecfname = string(fsldir_ptr) + string("/etc/flirtsch/") + cfname; -+ ecfname = string("@GENTOO_PORTAGE_EPREFIX@/etc/flirtsch/") + cfname; - if (check_exist(ecfname)) return(ecfname); - else if (!FNIRT::extension(ecfname).length()) { // If no path _and_ no extension given - ecfname += string(".cnf"); -diff --git a/src/fslsurface/fslsurface_first.cc b/src/fslsurface/fslsurface_first.cc -index faec642..b2ef794 100644 ---- a/src/fslsurface/fslsurface_first.cc -+++ b/src/fslsurface/fslsurface_first.cc -@@ -500,8 +500,7 @@ namespace fslsurface_name { - - volume<float>* immni = new volume<float>(); - -- char* fsldir = getenv("FSLDIR"); -- read_volume_hdr_only(*immni, string(fsldir) + "/data/standard/MNI152_T1_1mm"); -+ read_volume_hdr_only(*immni, "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/MNI152_T1_1mm"); - - //read_volume_hdr_only(*immni, template_name); - -@@ -699,8 +698,7 @@ namespace fslsurface_name { - - volume<float>* immni = new volume<float>(); - -- char* fsldir = getenv("FSLDIR"); -- read_volume_hdr_only(*immni, string(fsldir) + "/data/standard/MNI152_T1_1mm"); -+ read_volume_hdr_only(*immni, "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/MNI152_T1_1mm"); - - //read_volume_hdr_only(*immni, template_name); - -diff --git a/src/fslsurface/fslsurfacemaths.cpp b/src/fslsurface/fslsurfacemaths.cpp -index eaf55eb..3dc184d 100644 ---- a/src/fslsurface/fslsurfacemaths.cpp -+++ b/src/fslsurface/fslsurfacemaths.cpp -@@ -598,12 +598,6 @@ int main (int argc, char * argv[]) - - }else if (command == "-reconFromBvars"){ - cout<<"do recon "<<endl; -- char* fsldir = getenv("FSLDIR"); -- if (fsldir == NULL) -- { -- cerr<<"FSLDIR has not been set. "<<endl; -- exit(EXIT_FAILURE); -- } - //file.bvars,mni_template.nii.gz - // string mni = string(fsldir)+"/data/standard/MNI152_T1_1mm"; - reconSurface_from_bvars( surf, string(argv[i_arg+1])); -@@ -612,12 +606,6 @@ int main (int argc, char * argv[]) - - }else if (command == "-reconAllFromBvarsAndSave"){ - cout<<"do recon+save "<<argc<<" "<<i_arg<<endl; -- char* fsldir = getenv("FSLDIR"); -- if (fsldir == NULL) -- { -- cerr<<"FSLDIR has not been set. "<<endl; -- exit(EXIT_FAILURE); -- } - //file.bvars,mni_template.nii.gz - // string mni = string(fsldir)+"/data/standard/MNI152_T1_1mm"; - cout<<"recon "<< string(argv[i_arg+1])<<endl; diff --git a/sci-biology/fsl/files/fsl-6.0.2-fsldir_redux-p2.patch b/sci-biology/fsl/files/fsl-6.0.2-fsldir_redux-p2.patch deleted file mode 100644 index 74bf19169..000000000 --- a/sci-biology/fsl/files/fsl-6.0.2-fsldir_redux-p2.patch +++ /dev/null @@ -1,255 +0,0 @@ -diff --git a/src/libvis/miscpic.h b/src/libvis/miscpic.h -index a2f3855..5f440f2 100644 ---- a/src/libvis/miscpic.h -+++ b/src/libvis/miscpic.h -@@ -90,12 +90,7 @@ namespace MISCPIC{ - markRight=false; - trans= -10; - edgethresh = 0.0; -- if(getenv("FSLDIR")!=0){ -- lutbase = string(getenv("FSLDIR")) + "/etc/luts/"; -- } -- else{ -- lutbase = string("/"); -- } -+ lutbase = "@GENTOO_PORTAGE_EPREFIX@/etc/luts/"; - title = string(""); - cbartype = string(""); - cbarptr = NULL; -diff --git a/src/melodic/meldata.cc b/src/melodic/meldata.cc -index 1749a45..c4ad234 100644 ---- a/src/melodic/meldata.cc -+++ b/src/melodic/meldata.cc -@@ -992,7 +992,7 @@ namespace Melodic{ - void MelodicData::est_smoothness() - { - if(Resels == 0){ -- string SM_path = opts.binpath + "smoothest"; -+ string SM_path = "smoothest"; - string Mask_fname = logger.appendDir("mask"); - - if(opts.segment.value().length()>0){ -@@ -1157,7 +1157,7 @@ namespace Melodic{ - // set up all strings - string BET_outputfname = string(Mean_fname)+"_brain"; - -- string BET_path = opts.binpath + "bet"; -+ string BET_path = "bet"; - string BET_optarg = "-m -f 0.4"; // see man bet - string Mask_fname = BET_outputfname+"_mask"; - -diff --git a/src/melodic/meloptions.cc b/src/melodic/meloptions.cc -index 08170c7..252e72b 100644 ---- a/src/melodic/meloptions.cc -+++ b/src/melodic/meloptions.cc -@@ -93,14 +93,6 @@ MelodicOptions* MelodicOptions::gopt = NULL; - explicitnums = false; - logfname = string("log.txt"); - -- // work out the path to the $FSLDIR/bin directory -- if(getenv("FSLDIR")!=0){ -- binpath = (string) getenv("FSLDIR") + "/bin/"; -- } else{ -- binpath = argv[0]; -- binpath = binpath.substr(0,binpath.length()-7); -- } -- - // parse once to establish log directory name - for(int a = options.parse_command_line(argc, argv); a < argc; a++); - -diff --git a/src/melodic/meloptions.h b/src/melodic/meloptions.h -index f546125..b964b7d 100644 ---- a/src/melodic/meloptions.h -+++ b/src/melodic/meloptions.h -@@ -93,7 +93,6 @@ class MelodicOptions { - ~MelodicOptions() { delete gopt; } - - string version; -- string binpath; - string logfname; - bool filtermode; - bool explicitnums; -diff --git a/src/melodic/melreport.cc b/src/melodic/melreport.cc -index 141b6c2..2625059 100644 ---- a/src/melodic/melreport.cc -+++ b/src/melodic/melreport.cc -@@ -84,8 +84,8 @@ namespace Melodic{ - IChtml.setDir(report.getDir(),mmodel.get_prefix()+".html"); - - {//start IC page -- IChtml << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" + -- (string) getenv("FSLDIR") +"/doc/fsl.css>" << endl -+ IChtml << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" -+ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" << endl - << "<style type=\"text/css\">OBJECT { width: 100% }</style>" - << "<TITLE>FSL</TITLE></HEAD>" << endl - << "<IFRAME height=" << int(melodat.get_numfiles()/30 + 1)*50 -@@ -486,8 +486,8 @@ namespace Melodic{ - - {//start IC2 page - IChtml2.setDir(report.getDir(),mmodel.get_prefix()+"_MM.html"); -- IChtml2 << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" + -- (string) getenv("FSLDIR") +"/doc/fsl.css>" << endl -+ IChtml2 << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" -+ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" << endl - << "<style type=\"text/css\">OBJECT { width: 100% }</style>" - << "<TITLE>FSL</TITLE></HEAD>" << endl - << "<IFRAME height="<< int(melodat.get_numfiles()/30 + 1)*50 -@@ -665,8 +665,8 @@ namespace Melodic{ - IChtml << "<HTML> " << endl - << "<TITLE>MELODIC Component " << num2str(cnum) - << "</TITLE>" << endl -- << "<BODY BACKGROUND=\"file:" << getenv("FSLDIR") -- << "/doc/images/fsl-bg.jpg\">" << endl -+ << "<BODY BACKGROUND=\"file:" -+ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-bg.jpg\">" << endl - << "<hr><CENTER><H1>MELODIC Component " << num2str(cnum) - << "</H1>"<< endl; - -diff --git a/src/melodic/melreport.h b/src/melodic/melreport.h -index 574fc4c..e444681 100644 ---- a/src/melodic/melreport.h -+++ b/src/melodic/melreport.h -@@ -104,21 +104,21 @@ namespace Melodic{ - const time_t tmptime = time(NULL); - system(("mkdir "+ logger.appendDir("report") + " 2>/dev/null").c_str()); - report.setDir(logger.appendDir("report"),"00index.html",true,false,ios::out); -- report << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" + -- (string) getenv("FSLDIR") +"/doc/fsl.css>" -+ report << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" -+ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" - << "<TITLE>MELODIC report</TITLE></HEAD><BODY>" - << endl <<endl; - loghtml.setDir(report.getDir(),"log.html"); -- loghtml << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" + -- (string) getenv("FSLDIR") +"/doc/fsl.css>" -+ loghtml << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" -+ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" - << "<TITLE>MELODIC report</TITLE></HEAD><BODY>" - << endl <<endl; - navigator.setDir(report.getDir(),"nav.html"); - head.setDir(report.getDir(),"head.html"); -- navigator << "<link REL=stylesheet TYPE=text/css href=file:"+ -- (string) getenv("FSLDIR") +"/doc/fsl.css>" << endl; -- head << "<link REL=stylesheet TYPE=text/css href=file:"+ -- (string) getenv("FSLDIR") +"/doc/fsl.css>" << endl; -+ navigator << "<link REL=stylesheet TYPE=text/css href=file:" -+ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" << endl; -+ head << "<link REL=stylesheet TYPE=text/css href=file:" -+ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" << endl; - head <<"<TABLE BORDER=0><TR>" << endl - <<" <TD ALIGN=CENTER WIDTH=100%>"<< endl - <<"<TABLE BORDER=0>"<< endl -@@ -130,8 +130,8 @@ namespace Melodic{ - << "</tr></table>" << endl - << "<TD ALIGN=RIGHT>" << endl - << "<a href=http://www.fmrib.ox.ac.uk/fsl target=_top>" << endl -- << "<IMG BORDER=0 SRC=file:"<< getenv("FSLDIR") -- << "/doc/images/fsl-logo-big.jpg WIDTH=165></a>" << endl -+ << "<IMG BORDER=0 SRC=file:" -+ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-logo-big.jpg WIDTH=165></a>" << endl - << "</TD>"<<endl<<"</TR></TABLE> <hr>"<<endl; - if(opts.guireport.value()==""){ - report <<"<OBJECT data=head.html></OBJECT>" << endl; -diff --git a/src/mm/mixture_model.cc b/src/mm/mixture_model.cc -index b8e6167..5f00693 100644 ---- a/src/mm/mixture_model.cc -+++ b/src/mm/mixture_model.cc -@@ -2224,8 +2224,8 @@ namespace Mm { - - htmllog << "<HTML> " << endl - << "<TITLE>Mixture Model fit for" << data_name << "</TITLE>" << endl -- << "<BODY BACKGROUND=\"file:" << getenv("FSLDIR") -- << "/doc/images/fsl-bg.jpg\">" << endl -+ << "<BODY BACKGROUND=\"file:" -+ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-bg.jpg\">" << endl - << "<hr><CENTER><H1>Mixture Model fit for<br>" << data_name << " </H1>"<< endl; - - htmllog << "<hr><p>" << endl; -diff --git a/src/siena/siena_diff.cc b/src/siena/siena_diff.cc -index e19193a..17d8701 100644 ---- a/src/siena/siena_diff.cc -+++ b/src/siena/siena_diff.cc -@@ -107,7 +107,7 @@ int main(int argc,char *argv[]) - { - // {{{ vars - --char thestring[10000], segoptions[10000], fsldir[10000]; -+char thestring[10000], segoptions[10000]; - int x_size, y_size, z_size, size, x, y, z, i, count, - seg2=0, ignore_z=0, ignore_top_slices=0, //erode_mask=0, - ignore_bottom_slices=0, debug=0, flow_output=1, edge_masking=0; -@@ -124,8 +124,6 @@ if (argc<3) - - string argv1(argv[1]), argv2(argv[2]); - --sprintf(fsldir,"%s",getenv("FSLDIR")); -- - for (i = 3; i < argc; i++) { - if (!strcmp(argv[i], "-i")) - ignore_z=1; -@@ -209,26 +207,26 @@ for (i = 3; i < argc; i++) { - // }}} - // {{{ transform images and masks - --sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s", -- fsldir,argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]); -+sprintf(thestring,"flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s", -+ argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]); - printf("%s\n",thestring); system(thestring); - --sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s", -- fsldir,argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]); -+sprintf(thestring,"flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s", -+ argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]); - printf("%s\n",thestring); system(thestring); - --sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask", -- fsldir,argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]); -+sprintf(thestring,"flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask", -+ argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]); - printf("%s\n",thestring); system(thestring); - --sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask", -- fsldir,argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]); -+sprintf(thestring,"flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask", -+ argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]); - printf("%s\n",thestring); system(thestring); - - if (edge_masking) - { -- sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s_valid_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_valid_mask_with_%s", -- fsldir,argv[1],argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]); -+ sprintf(thestring,"flirt -o %s_halfwayto_%s_valid_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_valid_mask_with_%s", -+ argv[1],argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]); - printf("%s\n",thestring); system(thestring); - } - -@@ -287,8 +285,8 @@ if(1) // always done unless the above uncommented and used instead of this test - cout << "saving image 1 to disk prior to segmentation" << endl; - save_volume(in1,argv1+"_halfwayto_"+argv2+"_brain"); - in1.destroy(); -- sprintf(thestring,"%s/bin/fast %s %s %s_halfwayto_%s_brain > %s_halfwayto_%s_brain.vol 2>&1", -- fsldir,segtype,segoptions,argv[1],argv[2],argv[1],argv[2]); -+ sprintf(thestring,"fast %s %s %s_halfwayto_%s_brain > %s_halfwayto_%s_brain.vol 2>&1", -+ segtype,segoptions,argv[1],argv[2],argv[1],argv[2]); - cout << thestring << endl; - system(thestring); - } -diff --git a/src/topup/topupfns.cpp b/src/topup/topupfns.cpp -index 6873758..9e8b956 100644 ---- a/src/topup/topupfns.cpp -+++ b/src/topup/topupfns.cpp -@@ -463,8 +463,7 @@ string existing_conf_file(const string& cfname) - if (TOPUP::check_exist(ecfname)) return(ecfname); - } - if (!TOPUP::path(cfname).length()) { // If no path explicitly given -- const char *fsldir_ptr = getenv("FSLDIR"); -- ecfname = string(fsldir_ptr) + string("/etc/flirtsch/") + cfname; -+ ecfname = string("@GENTOO_PORTAGE_EPREFIX@/etc/flirtsch/") + cfname; - if (TOPUP::check_exist(ecfname)) return(ecfname); - else if (!TOPUP::extension(ecfname).length()) { // If no path _and_ no extension given - ecfname += string(".cnf"); --- -2.24.1 - diff --git a/sci-biology/fsl/files/fsl-6.0.2-gcc10_include.patch b/sci-biology/fsl/files/fsl-6.0.2-gcc10_include.patch deleted file mode 100644 index 9ddb11a2b..000000000 --- a/sci-biology/fsl/files/fsl-6.0.2-gcc10_include.patch +++ /dev/null @@ -1,10 +0,0 @@ ---- a/src/newimage/newimageio.h 2020-06-18 06:05:51.287864975 -0400 -+++ b/src/newimage/newimageio.h 2020-06-18 06:06:27.535129711 -0400 -@@ -75,6 +75,7 @@ - #include <iostream> - #include <fstream> - #include <sstream> -+#include <stdexcept> - #include "NewNifti/NewNifti.h" - #include "newmatio.h" - #include "newimage.h" diff --git a/sci-biology/fsl/files/fsl-6.0.2-setup.patch b/sci-biology/fsl/files/fsl-6.0.2-setup.patch deleted file mode 100644 index 39737fd85..000000000 --- a/sci-biology/fsl/files/fsl-6.0.2-setup.patch +++ /dev/null @@ -1,198 +0,0 @@ -From baae97cc3c8d0cadcabb7ed16559f4e4de26ddbe Mon Sep 17 00:00:00 2001 -From: François Bissey <frp.bissey@gmail.com> -Date: Mon, 20 Jan 2020 11:54:37 +1300 -Subject: [PATCH] Adjust the build system so it doesnt build packages - externally provided by portage. Make the compilation flags more generic and - easily adjustable. Make the build system stop at the first fault. - ---- - build | 6 +++--- - config/buildSettings.mk | 20 ++++++++++---------- - config/common/buildproj | 8 +++++--- - config/common/vars.mk | 10 +++++----- - extras/build | 8 ++++---- - src/mist-clean/Makefile | 2 +- - 6 files changed, 28 insertions(+), 26 deletions(-) - -diff --git a/build b/build -index 05dac06c..d90e407b 100755 ---- a/build -+++ b/build -@@ -3,7 +3,7 @@ - if [ $# -ge 1 ] ; then - PROJECTS="$@"; - else -- MASTERPROJECTS="CiftiLib-master utils znzlib NewNifti niftiio fslio giftiio miscmaths newimage libhfunc libvis first_lib \ -+ MASTERPROJECTS="utils znzlib NewNifti niftiio fslio giftiio miscmaths newimage libhfunc libvis first_lib \ - meshclass fslvtkio misc_tcl basisfield warpfns bint shapeModel MVdisc fslvtkconv fslsurface libmeshutils newmesh \ - DiscreteOpt FastPDlib MSMRegLib misc_c dpm topup \ - asl_mfree \ -@@ -80,8 +80,8 @@ xtract"; - done - fi - --echo "Building projects - see build.log file for progress..." --./config/common/buildproj $PROJECTS > ./build.log 2>&1 -+echo "Building projects" -+./config/common/buildproj $PROJECTS - finalStatus=$? - if [ $finalStatus -eq 0 ]; then - echo "Build completed successfully."; -diff --git a/config/buildSettings.mk b/config/buildSettings.mk -index b2e1f150..04532fc2 100644 ---- a/config/buildSettings.mk -+++ b/config/buildSettings.mk -@@ -18,7 +18,7 @@ MV = /bin/mv - CHMOD = /bin/chmod - MKDIR = /bin/mkdir - INSTALL = install -p --TCLSH = ${FSLDIR}/bin/fsltclsh -+TCLSH = tclsh - DEPENDFLAGS = -MM - MACHDBGFLAGS = -g - ##################################################################### -@@ -124,19 +124,19 @@ endif # if Darwin - ##################################################################### - ifeq ($(SYSTYPE), Linux) - ############### System Vars ##################################### --CC = gcc --CXX = c++ --CXX11 = c++ -+CC = @@GENTOO_CC@@ -+CXX = @@GENTOO_CXX@@ -+CXX11 = @@GENTOO_CXX@@ - CSTATICFLAGS = -static - CXXSTATICFLAGS = -static --ARCHFLAGS = -m64 --ARCHLDFLAGS = -Wl,-rpath,'$$ORIGIN/../lib' -+ARCHFLAGS = -+ARCHLDFLAGS = - PARALLELFLAGS = -fopenmp --OPTFLAGS = -g -O3 -fexpensive-optimizations ${ARCHFLAGS} -+OPTFLAGS = - GNU_ANSI_FLAGS = -Wall -ansi -pedantic -Wno-long-long - SGI_ANSI_FLAGS = -ansi -fullwarn - ANSI_FLAGS = ${GNU_ANSI_FLAGS} --RANLIB = echo -+RANLIB = @@GENTOO_RANLIB@@ - FSLML = ${FSLDIR}/bin/fslml - # CUDA development environment - CUDAVER := $(or $(CUDAVER),9.1) -@@ -148,8 +148,8 @@ INC_CUDA = ${CUDA_INSTALLATION}/include - NVCC = ${CUDA_INSTALLATION}/bin/nvcc - ############### External Libs ##################################### - # ZLIB library --LIB_ZLIB = /lib64 --INC_ZLIB = /usr/include -+#LIB_ZLIB = /lib64 -+#INC_ZLIB = /usr/include - # QT library - QTDIR = /usr/lib/qt3 - LIB_QT = ${QTDIR}/lib -diff --git a/config/common/buildproj b/config/common/buildproj -index 2f0f2b8f..48624a1f 100755 ---- a/config/common/buildproj -+++ b/config/common/buildproj -@@ -11,10 +11,10 @@ if [ X$1 = X-strict ] ; then - fi - PROJECTS="$@" ; export PROJECTS ; - --FSLDIR=`pwd` -+#FSLDIR=`pwd` - FSLDEVDIR=${FSLDIR} - FSLCONFDIR=${FSLDIR}/config --FSLMACHTYPE=`${FSLDIR}/etc/fslconf/fslmachtype.sh` -+#FSLMACHTYPE=`${FSLDIR}/etc/fslconf/fslmachtype.sh` - FSLMASTERBUILD=1 - export FSLDIR FSLDEVDIR FSLCONFDIR FSLMACHTYPE FSLMASTERBUILD - -@@ -67,7 +67,7 @@ for projname in $PROJECTS; do - if [ -x ./fslconfig ] ; then - . ./fslconfig ; - fi -- if ${MAKE} -k ${MAKEOPTIONS} ; then -+ if ${MAKE} ${MAKEOPTIONS} ; then - if ${MAKE} ${MAKEOPTIONS} install ; then - installok=true; - # Clean up after ourselves -@@ -82,6 +82,7 @@ for projname in $PROJECTS; do - if [ $installok = false ] ; then - echo " " - echo "ERROR::Could not install $projname successfully" ; -+ exit 1 - fi - else - echo " " -@@ -90,6 +91,7 @@ for projname in $PROJECTS; do - echo " " - echo " " - errorprojs="$errorprojs $projname" ; export errorprojs ; -+ exit 1 - fi - fi - done -diff --git a/config/common/vars.mk b/config/common/vars.mk -index b027b010..aeeae67c 100755 ---- a/config/common/vars.mk -+++ b/config/common/vars.mk -@@ -24,15 +24,15 @@ USRINCFLAGS = - USRCFLAGS = - USRCXXFLAGS = - --LDFLAGS = ${ARCHLDFLAGS} ${USRLDFLAGS} -L. -L${DEVLIBDIR} -L${LIBDIR} -+LDFLAGS = ${ARCHLDFLAGS} ${USRLDFLAGS} -L. -L${DEVLIBDIR} -L${LIBDIR} ${USERLDFLAGS} - --AccumulatedIncFlags = -I${INC_BOOST} ${USRINCFLAGS} -I. -I${DEVINCDIR} -I${INCDIR} -+AccumulatedIncFlags = ${USRINCFLAGS} -I. -I${DEVINCDIR} -I${INCDIR} ${CPPFLAGS} - - CFLAGS = ${ANSI_FLAGS} ${ANSI_CFLAGS} ${DBGFLAGS} ${USEDCSTATICFLAGS} ${USRCFLAGS} ${ARCHFLAGS} ${OPTFLAGS} \ -- ${AccumulatedIncFlags} -+ ${AccumulatedIncFlags} ${USERCFLAGS} - --CXXFLAGS = ${ANSI_FLAGS} ${ANSI_CXXFLAGS} ${DBGFLAGS} ${USEDCXXSTATICFLAGS} ${USRCXXFLAGS} ${ARCHFLAGS} ${OPTFLAGS} \ -- ${AccumulatedIncFlags} -+CXXFLAGS = ${ANSI_CXXFLAGS} ${DBGFLAGS} ${USEDCXXSTATICFLAGS} ${USRCXXFLAGS} ${ARCHFLAGS} ${OPTFLAGS} \ -+ ${AccumulatedIncFlags} ${USERCXXFLAGS} - - HFILES = *.h - AFILES = *.a -diff --git a/extras/build b/extras/build -index 59e7a2ed..0d68232e 100755 ---- a/extras/build -+++ b/extras/build -@@ -96,16 +96,16 @@ if [ X"${OS}" = "XDarwin" ]; then - BUILDICONV=1 - fi - fi --PROJECTS="tcl tk" -+#PROJECTS="tcl tk" - if [ ${BUILDZLIB} -eq 1 ]; then - PROJECTS="${PROJECTS} zlib" - fi --PROJECTS="${PROJECTS} libpng" -+#PROJECTS="${PROJECTS} libpng" - if [ ${BUILDICONV} -eq 1 ]; then - PROJECTS="${PROJECTS} libiconv" - fi --PROJECTS="${PROJECTS} libgd libgdc libprob libcprob newmat cprob newran fftw" --PROJECTS="${PROJECTS} boost libxml2-2.9.2 libxmlpp libsqlite libnlopt ../include/armawrap/dummy_newmat" -+PROJECTS="${PROJECTS} libgdc libprob libcprob newmat cprob newran" -+PROJECTS="${PROJECTS} ../include/armawrap/dummy_newmat" - for projname in $PROJECTS; do - if [ -d $FSLESRCDIR/$projname ] ; then - buildIt $FSLESRCDIR $projname 1 -diff --git a/src/mist-clean/Makefile b/src/mist-clean/Makefile -index 20402cca..6918bee4 100755 ---- a/src/mist-clean/Makefile -+++ b/src/mist-clean/Makefile -@@ -52,6 +52,6 @@ installpython: - cp -r python/* ${DESTDIR}/python/mist - - clean: -- rm -f ${OBJS} mist/mist.o mist/mist -+ rm -f ${OBJS} mist/mist.o mist/mist || echo "CLEAN could not locate some files scheduled for deletion." - - .PHONY: all clean installdata --- -2.24.1 - diff --git a/sci-biology/fsl/fsl-6.0.4.ebuild b/sci-biology/fsl/fsl-6.0.4.ebuild index 4797c1298..6e5d6e779 100644 --- a/sci-biology/fsl/fsl-6.0.4.ebuild +++ b/sci-biology/fsl/fsl-6.0.4.ebuild @@ -28,12 +28,8 @@ DEPEND=" dev-lang/tk:0= >=virtual/lapack-3.8 >=virtual/blas-3.8 - cuda? ( - || ( - ( =dev-util/nvidia-cuda-toolkit-10* =sys-devel/gcc-8*:* ) - ( =dev-util/nvidia-cuda-toolkit-11* =sys-devel/gcc-9*:* ) - ) + =dev-util/nvidia-cuda-toolkit-11* =sys-devel/gcc-9*:* ) " RDEPEND="${DEPEND}" @@ -155,8 +151,8 @@ src_compile() { # define the default build system to match upstream official standard # -> individual projects may overwrite the '-std=' flag - export ANSI_CFLAGS="-std=c99" - export ANSI_CXXFLAGS="-std=c++98" + export ANSI_CFLAGS="-std=c11" + export ANSI_CXXFLAGS="-std=c++11" export USERLDFLAGS="${LDFLAGS}" export USERCFLAGS="${CFLAGS}" diff --git a/sci-biology/fsl/fsl-6.0.5.ebuild b/sci-biology/fsl/fsl-6.0.5.ebuild index c51a9d30e..d3ec1de1d 100644 --- a/sci-biology/fsl/fsl-6.0.5.ebuild +++ b/sci-biology/fsl/fsl-6.0.5.ebuild @@ -39,9 +39,7 @@ DEPEND=" >=virtual/lapack-3.8 >=virtual/blas-3.8 cuda? ( - || ( - ( =dev-util/nvidia-cuda-toolkit-11* =sys-devel/gcc-9*:* ) - ) + =dev-util/nvidia-cuda-toolkit-11* =sys-devel/gcc-9*:* ) " RDEPEND="${DEPEND}" diff --git a/sci-biology/gemini/Manifest b/sci-biology/gemini/Manifest deleted file mode 100644 index e85205a03..000000000 --- a/sci-biology/gemini/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST gemini-0.30.2.tar.gz 1629220 BLAKE2B cbcbcb367817550d39f5385617fa577895d13a084ef2f7e8be2aa3895f9f22e9df2d453673993962819cdfa1705b1a8fa5f7f899d836f055eff753a7f6c5ae2f SHA512 08f88cc54631bc6f9fca72eaa996457dff1f19e4a5791b5ce11a2c2983e3ca23101aa572d2dcbd2fb1340d4e3ed1ea87d99e88530b25f2bfc533f879ac584b6d diff --git a/sci-biology/gemini/gemini-0.30.2.ebuild b/sci-biology/gemini/gemini-0.30.2.ebuild deleted file mode 100644 index f041c2c48..000000000 --- a/sci-biology/gemini/gemini-0.30.2.ebuild +++ /dev/null @@ -1,45 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7,8,9} ) - -inherit distutils-r1 - -DESCRIPTION="Lightweight VCF to DB framework for disease and population genetics" -HOMEPAGE="https://github.com/arq5x/gemini - http://gemini.readthedocs.org/en/latest" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -RDEPEND=" - dev-python/bottle[${PYTHON_USEDEP}] - dev-python/cython[${PYTHON_USEDEP}] - dev-python/ipyparallel[${PYTHON_USEDEP}] - dev-python/jinja[${PYTHON_USEDEP}] - dev-python/networkx[${PYTHON_USEDEP}] - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/numexpr[${PYTHON_USEDEP}] - dev-python/openpyxl[${PYTHON_USEDEP}] - dev-python/pandas[${PYTHON_USEDEP}] - dev-python/pyyaml[${PYTHON_USEDEP}] - dev-python/unidecode[${PYTHON_USEDEP}] - dev-python/sqlalchemy[${PYTHON_USEDEP}] - sci-biology/bx-python[${PYTHON_USEDEP}] - sci-libs/htslib - sci-biology/pybedtools[${PYTHON_USEDEP}] - sci-biology/pysam[${PYTHON_USEDEP}] -" - -distutils_enable_sphinx docs - -python_prepare_all() { - # this has been renamed in newer versions of sphinx - sed -i -e 's/sphinx.ext.pngmath/sphinx.ext.imgmath/g' docs/conf.py || die - - distutils-r1_python_prepare_all -} diff --git a/sci-biology/gemini/metadata.xml b/sci-biology/gemini/metadata.xml deleted file mode 100644 index 260a8b4ae..000000000 --- a/sci-biology/gemini/metadata.xml +++ /dev/null @@ -1,15 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="github">arq5x/gemini</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-biology/genomeview-bin/genomeview-bin-2450.ebuild b/sci-biology/genomeview-bin/genomeview-bin-2450.ebuild index 8de34c9fa..9d4480272 100644 --- a/sci-biology/genomeview-bin/genomeview-bin-2450.ebuild +++ b/sci-biology/genomeview-bin/genomeview-bin-2450.ebuild @@ -6,7 +6,7 @@ EAPI=7 inherit java-pkg-opt-2 java-ant-2 DESCRIPTION="Genome browser and annotation tool" -HOMEPAGE="http://genomeview.sourceforge.net" +HOMEPAGE="https://genomeview.sourceforge.net" SRC_URI="https://downloads.sourceforge.net/project/genomeview/GenomeView/genomeview-2450.zip" LICENSE="GPL-2" diff --git a/sci-biology/genomeview-bin/metadata.xml b/sci-biology/genomeview-bin/metadata.xml index 0f267b755..b6476ca7b 100644 --- a/sci-biology/genomeview-bin/metadata.xml +++ b/sci-biology/genomeview-bin/metadata.xml @@ -10,6 +10,6 @@ <name>Gentoo Biology Project</name> </maintainer> <upstream> - <remote-id type="sourceforge">downloads</remote-id> + <remote-id type="sourceforge">genomeview</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/gffcompare/files/Makefile.patch b/sci-biology/gffcompare/files/Makefile.patch deleted file mode 100644 index afb52b2e1..000000000 --- a/sci-biology/gffcompare/files/Makefile.patch +++ /dev/null @@ -1,79 +0,0 @@ ---- gffcompare-0.10.5/Makefile 2018-06-26 09:24:06.058542487 +0200 -+++ gffcompare-0.10.5/Makefile 2018-06-26 09:28:08.045119603 +0200 -@@ -16,7 +16,7 @@ - endif - - # CVS checked in --CC := g++ -+CXX ?= g++ - BASEFLAGS = -Wall -Wextra ${INCDIRS} $(MARCH) \ - -fno-exceptions -fno-rtti -D_REENTRANT - -@@ -24,7 +24,8 @@ - - ifneq (,$(filter %release %static, $(MAKECMDGOALS))) - # -- release build -- CFLAGS = -O3 -DNDEBUG $(BASEFLAGS) -+ CXXFLAGS ?= -O3 -g -+ CXXFLAGS += -DNDEBUG $(BASEFLAGS) - LDFLAGS = - LIBS = - ifneq (,$(findstring static,$(MAKECMDGOALS))) -@@ -37,16 +38,16 @@ - ifeq "$(GCCVER49)" "0" - $(error gcc version 4.9 or greater is required for this build target) - endif -- CFLAGS := -fno-omit-frame-pointer -fsanitize=undefined -fsanitize=address -+ CXXFLAGS += -fno-omit-frame-pointer -fsanitize=undefined -fsanitize=address - GCCVER5 := $(shell expr `g++ -dumpversion | cut -f1 -d.` \>= 5) - ifeq "$(GCCVER5)" "1" -- CFLAGS += -fsanitize=bounds -fsanitize=float-divide-by-zero -fsanitize=vptr -- CFLAGS += -fsanitize=float-cast-overflow -fsanitize=object-size -- #CFLAGS += -fcheck-pointer-bounds -mmpx -+ CXXFLAGS += -fsanitize=bounds -fsanitize=float-divide-by-zero -fsanitize=vptr -+ CXXFLAGS += -fsanitize=float-cast-overflow -fsanitize=object-size -+ #CXXFLAGS += -fcheck-pointer-bounds -mmpx - endif -- CFLAGS += $(BASEFLAGS) -- CFLAGS := -g -DDEBUG -D_DEBUG -DGDEBUG -fno-common -fstack-protector $(CFLAGS) -- LDFLAGS := -g -+ CXXFLAGS += $(BASEFLAGS) -+ CXXFLAGS += -DDEBUG -D_DEBUG -DGDEBUG -fno-common -fstack-protector -+ LDFLAGS ?= -g - #LIBS := -Wl,-Bstatic -lasan -lubsan -Wl,-Bdynamic -ldl $(LIBS) - LIBS := -lasan -lubsan -ldl $(LIBS) - else -@@ -55,26 +56,26 @@ - # GMEMTRACE=1 - #endif - #--- just plain debug build --- -- CFLAGS = -g -DDEBUG -D_DEBUG -DGDEBUG $(BASEFLAGS) -- LDFLAGS = -g -+ CXXFLAGS += -DDEBUG -D_DEBUG -DGDEBUG $(BASEFLAGS) -+ LDFLAGS += -g - LIBS = - endif - endif - - %.o : %.c -- ${CC} ${CFLAGS} -c $< -o $@ -+ ${CXX} ${CXXFLAGS} -c $< -o $@ - - %.o : %.cc -- ${CC} ${CFLAGS} -c $< -o $@ -+ ${CXX} ${CXXFLAGS} -c $< -o $@ - - %.o : %.C -- ${CC} ${CFLAGS} -c $< -o $@ -+ ${CXX} ${CXXFLAGS} -c $< -o $@ - - %.o : %.cpp -- ${CC} ${CFLAGS} -c $< -o $@ -+ ${CXX} ${CXXFLAGS} -c $< -o $@ - - %.o : %.cxx -- ${CC} ${CFLAGS} -c $< -o $@ -+ ${CXX} ${CXXFLAGS} -c $< -o $@ - - # C/C++ linker - diff --git a/sci-biology/gffread/Manifest b/sci-biology/gffread/Manifest index ea0f27b53..999049e10 100644 --- a/sci-biology/gffread/Manifest +++ b/sci-biology/gffread/Manifest @@ -1,2 +1,2 @@ -DIST gclib-0.11.0.tar.gz 184895 BLAKE2B ea8434c8a68fc7d032341271ed55eab3dcc8618da0ea823f7e1588598275a775369d1b7e7ce38eba02437272c28b56543ac50a50f5b0a03d01f37e24e85bb53e SHA512 ec773a805141e8f0f98774760e0608aac6c66c7541d4777c8cb0edcf2172a4bc86a0f0c1f6f7459858b408f47d8b1f6eeb35c871668991424f74d55a9c19bce2 -DIST gffread-0.11.0.tar.gz 28887 BLAKE2B 0d9e89666770c64713d0edb256aa9f18b8d33cba941afbb14a82e26359bfa96044a1655678095a8468e1d1d651406fb0250b20696b4026c4a47892cc45785935 SHA512 79d8a376c892c1567c80a045b08b8f4c97d8778a46b89bcce0372e2e3d6b4bcfe746b64b2101fd8411d02a2d157585eb39d0e067a2aaeb5e8c1e1f7da21bc834 +DIST gclib-0.12.7.tar.gz 259314 BLAKE2B 9e3d4b535a7bbeb4b03360801a4ce4c81055d49525857cce306009e18f78709808732e24cb3dc3efa050b293c863d6f045f5fc3a5d3c14f3c6a2566acbc1f6f4 SHA512 2ff7be21f8ae002afdd7e34b6200e308f87077331c174dbea863972a01a0b6758062accda431bb73ef45ae91db44871f9eb0f5ae4bd564252599236282e57f90 +DIST gffread-0.12.7.tar.gz 403734 BLAKE2B e925518fad8e1047d7e4a785338e51cd0317d8e26545587024ee2617a2e432426e80172c62b9d4103ec9da0d33d758105d8803cc82b4f74cf5dba07009aab477 SHA512 33a2308caecd3e891788a76c6b68b79569afd8d0d749bf57a8c528550d26f7a7b61b8ca77e8a37e05a7dfaeac600470c255a22314ea94f63e2b2cac45674f97b diff --git a/sci-biology/gffread/gffread-0.11.0.ebuild b/sci-biology/gffread/gffread-0.12.7.ebuild index 871d38d03..9758ccef0 100644 --- a/sci-biology/gffread/gffread-0.11.0.ebuild +++ b/sci-biology/gffread/gffread-0.12.7.ebuild @@ -1,7 +1,7 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 DESCRIPTION="GFF/GTF utility providing format conversions, filter/extract regions from FASTA" HOMEPAGE="http://ccb.jhu.edu/software/stringtie/gff.shtml @@ -12,13 +12,8 @@ SRC_URI="https://github.com/gpertea/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz LICENSE="MIT" SLOT="0" KEYWORDS="~amd64 ~x86" -IUSE="" - -DEPEND="" -RDEPEND="${DEPEND}" src_prepare(){ - src_unpack "${DISTDIR}"/gclib-${PV}.tar.gz default sed -e "s/-g -O3/${CXXFLAGS}/" -i Makefile || die cd .. && ln -s gclib-"${PV}" gclib || die @@ -30,4 +25,5 @@ src_compile(){ src_install(){ dobin gffread + einstalldocs } diff --git a/sci-biology/gffutils/Manifest b/sci-biology/gffutils/Manifest index a697f0784..e8b006cbf 100644 --- a/sci-biology/gffutils/Manifest +++ b/sci-biology/gffutils/Manifest @@ -1,2 +1 @@ -DIST gffutils-0.10.1.tar.gz 1636628 BLAKE2B ca539bdcf2a2e199d264194e23c3d1b52e1f4b141d2a43a1346024c008020ff531d5b642c63bd4c3a34cd97de2a399975eea430163f16218f5a1d671521e69b6 SHA512 21f56e013abdf1368756db97afcea0be6d0edc56cb0636e9e796603959570c7c3ba0cecf1bf90a69ab7afd2c4c831d3d42b92960a8c34f9b645be7e47d42190a -DIST gffutils-0.8.7.1.tar.gz 1541112 BLAKE2B 65676cf0b910ad0fee478315409dba808a13d11922d0ab254694939ebd01f10b62c2237ae517d941999c6cf9bcb08d903bde8b9055bcf7a67116e14439ec4cca SHA512 4739dd402963d402f34a5e3da9cca7ba9586dcbbe62efbad89bf85c5dbb0feff0e260eea20563340911756e6817289c1556c261ef973a61f4e66e50efdfc8aa8 +DIST gffutils-0.11.1.tar.gz 1646787 BLAKE2B 96e573cf366844c8a348aff062362aeaea1a46360c74ae75a2d8d730d37cd69f0e6c658d1d0f348ca8f8e8c49d9a7c923c52619341e8d2dabd92a329fb43b677 SHA512 1844e9d7626a800549def2ba09b4d97e60c8a1a0fce2da60d7841cf4c4347da50aea850e8c1a67b07de08d4e6cf737b0d5c2bf8eb5fc87900427866282e82bdb diff --git a/sci-biology/gffutils/gffutils-0.10.1.ebuild b/sci-biology/gffutils/gffutils-0.11.1.ebuild index c7a437264..8ee8fd4b5 100644 --- a/sci-biology/gffutils/gffutils-0.10.1.ebuild +++ b/sci-biology/gffutils/gffutils-0.11.1.ebuild @@ -1,19 +1,23 @@ -# Copyright 1999-2020 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 -PYTHON_COMPAT=( python3_{7..9} ) +PYTHON_COMPAT=( python3_{10..11} ) inherit distutils-r1 DESCRIPTION="GFF and GTF file manipulation and interconversion" -HOMEPAGE="https://pythonhosted.org/gffutils/" +HOMEPAGE="https://gffutils.readthedocs.io/en/latest/" SRC_URI="https://github.com/daler/gffutils/archive/v${PV}.tar.gz -> ${P}.tar.gz" LICENSE="MIT" SLOT="0" KEYWORDS="~amd64 ~x86" +IUSE="test" +# Nose tests no longer supported, migration on next release +#RESTRICT="test" +RESTRICT="!test? ( test )" RDEPEND=" dev-python/simplejson[${PYTHON_USEDEP}] @@ -32,7 +36,6 @@ python_prepare_all() { distutils-r1_python_prepare_all } -distutils_enable_tests nose python_test() { distutils_install_for_testing nosetests -v -x --with-doctest -a '!slow' || die diff --git a/sci-biology/gffutils/gffutils-0.8.7.1.ebuild b/sci-biology/gffutils/gffutils-0.8.7.1.ebuild deleted file mode 100644 index c6b304fb1..000000000 --- a/sci-biology/gffutils/gffutils-0.8.7.1.ebuild +++ /dev/null @@ -1,23 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7..9} ) - -inherit distutils-r1 - -DESCRIPTION="GFF and GTF file manipulation and interconversion" -HOMEPAGE="https://pythonhosted.org/gffutils/" -SRC_URI="https://github.com/daler/gffutils/archive/v${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -RDEPEND=" - sci-biology/pyfaidx[${PYTHON_USEDEP}] - dev-python/simplejson[${PYTHON_USEDEP}] - dev-python/argh[${PYTHON_USEDEP}] - dev-python/argcomplete[${PYTHON_USEDEP}]" -DEPEND="${RDEPEND}" diff --git a/sci-biology/glean/glean-1.0.1.ebuild b/sci-biology/glean/glean-1.0.1.ebuild index d459d664b..507f76900 100644 --- a/sci-biology/glean/glean-1.0.1.ebuild +++ b/sci-biology/glean/glean-1.0.1.ebuild @@ -6,7 +6,7 @@ EAPI=7 inherit perl-module DESCRIPTION="Merge various gene prediction into one (unsupervised learning system)" -HOMEPAGE="https://sourceforge.net/projects/glean-gene" +HOMEPAGE="https://sourceforge.net/projects/glean-gene/" SRC_URI="https://downloads.sourceforge.net/project/glean-gene/GLEAN/glean-${PV//./-}/glean-${PV//./-}.tar.gz" LICENSE="Artistic" diff --git a/sci-biology/glean/metadata.xml b/sci-biology/glean/metadata.xml index 0f267b755..26831499b 100644 --- a/sci-biology/glean/metadata.xml +++ b/sci-biology/glean/metadata.xml @@ -10,6 +10,6 @@ <name>Gentoo Biology Project</name> </maintainer> <upstream> - <remote-id type="sourceforge">downloads</remote-id> + <remote-id type="sourceforge">glean-gene</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/hisat2/hisat2-2.2.1.ebuild b/sci-biology/hisat2/hisat2-2.2.1.ebuild index 8841bd445..9a30d7aef 100644 --- a/sci-biology/hisat2/hisat2-2.2.1.ebuild +++ b/sci-biology/hisat2/hisat2-2.2.1.ebuild @@ -1,15 +1,15 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 -PYTHON_COMPAT=( python3_{7,8,9} ) +PYTHON_COMPAT=( python3_{10..11} ) inherit python-r1 DESCRIPTION="Align DNA reads to a population of genomes" HOMEPAGE=" - https://ccb.jhu.edu/software/hisat2 + https://daehwankimlab.github.io/hisat2 https://github.com/DaehwanKimLab/hisat2" SRC_URI="https://github.com/DaehwanKimLab/hisat2/archive/v${PV}.tar.gz -> ${P}.tar.gz" diff --git a/sci-biology/hisat2/metadata.xml b/sci-biology/hisat2/metadata.xml index 2a70cba7e..7954bc741 100644 --- a/sci-biology/hisat2/metadata.xml +++ b/sci-biology/hisat2/metadata.xml @@ -10,6 +10,6 @@ <name>Gentoo Biology Project</name> </maintainer> <upstream> - <remote-id type="github">infphilo/hisat2</remote-id> + <remote-id type="github">DaehwanKimLab/hisat2</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/imagej/Manifest b/sci-biology/imagej/Manifest index 1d4db507e..4c5068f0a 100644 --- a/sci-biology/imagej/Manifest +++ b/sci-biology/imagej/Manifest @@ -1,3 +1,3 @@ DIST ImageJ.png 13012 BLAKE2B b42ee855e6214b275cbdcc722f6c7b095fe83de477a151714c4afec8e23abe12b2d0bf62ae81a4f9c4ccefc9245a9e144085b844ee3f92121a88f7d27106acf5 SHA512 60c2ff73bcfc668931c59b0dfb299723a369b741601bdd591a407302e30fc58c6c626525b3f08b955a5dab37729d3f704db689317b42a94e7a3ccbfb72abc9b3 -DIST ij153.zip 6394791 BLAKE2B 1b942f808e600fee95f0442f7ec6439164585276b130c295845f6d3c4cf6bcaba1befafc12394fb59a289aab3263d684c89f6c3b1d3be04f443a3a39396baad0 SHA512 3c367a502d3fd46272756228c6cefba2e94e635db74edbd117ca083a8c8dc68a2eef4da6deefcdcece5d68c7c03b67233de8ff7a6c33aad0c30a58abd0f0786a -DIST ij153g-src.zip 1498513 BLAKE2B d1ab359b061896644ed003ec5c331418bd89445c90e792b127b88f000cea5a20e621d18b5a1912d541668a33dcaf02a857f9a0cb5c5e354dd12daddfd521ef2a SHA512 5be0e6e53139f8954983f5f7a9c48f911e71849832b6915e8ae02aabc6fc274ef886523285bc90590a23a767ab8aa51aa2837e147da0005d9b83c88f540848f7 +DIST ij154.zip 6677151 BLAKE2B acd99e95c8123461710e3565a31121e475ac9bd1bb993649dc9569c1e17a055e6e0aad9a3fa482b4a021f39cd3467e779529a1512be557a370277c6091fa7b08 SHA512 92c9f13335e9d2cc111bf08851a6fb747d1d1eac8f3088563f42669e225cff6fd2ffbfd4ea474e7baaa266656c4a433107a3264539f9744412aa6400094cb2c9 +DIST imagej-1.54h.gh.tar.gz 5822723 BLAKE2B a293a4b3c2f5f998822c61e67586124491c0b902c5c91538d7ab7eb7d84f6f8ce79759eaa5f4e5de60731566923cc4b837277539c9522c2efe7bc079c6c13455 SHA512 6061fad8c11b26cdf7537f945abc26f9e4a10f34ed151701f6f89e794028be646dc8013437605c6889073acf803ea6784457f47e3cd645c54265fef24bfeb615 diff --git a/sci-biology/imagej/imagej-1.53g.ebuild b/sci-biology/imagej/imagej-1.54h-r1.ebuild index 6c9fdf736..0252d6613 100644 --- a/sci-biology/imagej/imagej-1.53g.ebuild +++ b/sci-biology/imagej/imagej-1.54h-r1.ebuild @@ -1,27 +1,41 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 inherit java-pkg-2 java-ant-2 desktop MY_PN="ij" -MY_PV=${PV//.} -IJ_PV=${MY_PV::-1} +IJ_PV="154" #plugins now available for 154 DESCRIPTION="Image Processing and Analysis in Java" -HOMEPAGE="https://imagej.nih.gov/ij/" -SRC_URI="https://imagej.nih.gov/ij/download/src/${MY_PN}${MY_PV}-src.zip - https://rsb.info.nih.gov/ij/images/ImageJ.png +HOMEPAGE=" + https://imagej.nih.gov/ij/ + https://github.com/imagej +" + +SRC_URI=" + https://imagej.nih.gov/ij/images/ImageJ.png plugins? ( https://wsr.imagej.net/distros/cross-platform/${MY_PN}${IJ_PV}.zip )" # plugins are under a different licenses and can be installed into user's $IJ_HOME/plugins -# plugins? ( http://rsb.info.nih.gov/ij/download/zips/${MY_PN}${IJ_PV}.zip )" -LICENSE="public-domain" # http://imagej.net/disclaimer.html -SLOT="0" +if [[ ${PV} == 9999 ]]; then + inherit git-r3 + EGIT_REPO_URI="https://github.com/imagej/ImageJ" + IJ_S="${S}/ImageJ" +else + SRC_URI+=" + https://github.com/imagej/ImageJ/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz + " + S="${WORKDIR}/ImageJ-${PV}" + IJ_S="${WORKDIR}/ImageJ" + KEYWORDS="~amd64" +fi + +LICENSE="public-domain" -KEYWORDS="~amd64" +SLOT="0" IUSE="doc plugins debug" @@ -29,18 +43,26 @@ RDEPEND=" >=virtual/jre-1.7:* dev-java/java-config " -DEPEND="${RDEPEND} + +DEPEND=" + ${RDEPEND} >=virtual/jdk-1.7:* +" + +BDEPEND=" dev-java/ant-core app-arch/unzip " -S="${WORKDIR}/source" -IJ_S=${WORKDIR}/ImageJ - src_prepare() { cp "${DISTDIR}"/ImageJ.png "${WORKDIR}/${PN}.png" || die + if [[ ${PV} == 9999 ]]; then + if use plugins ; then + unpack "${MY_PN}${IJ_PV}.zip" + fi + fi + if ! use debug ; then sed -i 's: debug="on">: debug="off">:' "${S}"/build.xml || die fi @@ -56,9 +78,11 @@ src_compile() { # Max memory usage depends on available memory and CPU type MEM=$(grep MemTotal /proc/meminfo | cut -d':' -f2 | grep -o [0-9]*) IJ_MAX_MEM=$(expr ${MEM} / 1024) + if use x86 && $IJ_MAX_MEM -gt 2048 ; then - IJ_MAX_MEM=2048 + IJ_MAX_MEM=2048 fi + # build finished, generate startup wrapper cat <<EOF > "${T}/${PN}" #!${EPREFIX}/bin/bash diff --git a/sci-biology/imagej/imagej-9999.ebuild b/sci-biology/imagej/imagej-9999.ebuild new file mode 100644 index 000000000..0252d6613 --- /dev/null +++ b/sci-biology/imagej/imagej-9999.ebuild @@ -0,0 +1,144 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit java-pkg-2 java-ant-2 desktop + +MY_PN="ij" +IJ_PV="154" #plugins now available for 154 + +DESCRIPTION="Image Processing and Analysis in Java" + +HOMEPAGE=" + https://imagej.nih.gov/ij/ + https://github.com/imagej +" + +SRC_URI=" + https://imagej.nih.gov/ij/images/ImageJ.png + plugins? ( https://wsr.imagej.net/distros/cross-platform/${MY_PN}${IJ_PV}.zip )" +# plugins are under a different licenses and can be installed into user's $IJ_HOME/plugins + +if [[ ${PV} == 9999 ]]; then + inherit git-r3 + EGIT_REPO_URI="https://github.com/imagej/ImageJ" + IJ_S="${S}/ImageJ" +else + SRC_URI+=" + https://github.com/imagej/ImageJ/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz + " + S="${WORKDIR}/ImageJ-${PV}" + IJ_S="${WORKDIR}/ImageJ" + KEYWORDS="~amd64" +fi + +LICENSE="public-domain" + +SLOT="0" + +IUSE="doc plugins debug" + +RDEPEND=" + >=virtual/jre-1.7:* + dev-java/java-config +" + +DEPEND=" + ${RDEPEND} + >=virtual/jdk-1.7:* +" + +BDEPEND=" + dev-java/ant-core + app-arch/unzip +" + +src_prepare() { + cp "${DISTDIR}"/ImageJ.png "${WORKDIR}/${PN}.png" || die + + if [[ ${PV} == 9999 ]]; then + if use plugins ; then + unpack "${MY_PN}${IJ_PV}.zip" + fi + fi + + if ! use debug ; then + sed -i 's: debug="on">: debug="off">:' "${S}"/build.xml || die + fi + default +} + +src_compile() { + local antflags="build" + use doc && antflags="${antflags} javadocs" + + ant ${antflags} || die "ant build failed" + + # Max memory usage depends on available memory and CPU type + MEM=$(grep MemTotal /proc/meminfo | cut -d':' -f2 | grep -o [0-9]*) + IJ_MAX_MEM=$(expr ${MEM} / 1024) + + if use x86 && $IJ_MAX_MEM -gt 2048 ; then + IJ_MAX_MEM=2048 + fi + + # build finished, generate startup wrapper + cat <<EOF > "${T}/${PN}" +#!${EPREFIX}/bin/bash +IJ_LIB=${EPREFIX}/usr/share/${PN}/lib +if !([ "\${IJ_HOME}" ]) ; then + IJ_HOME=\${HOME}/.imagej +fi +if [ -d \${IJ_HOME}/plugins ] ; then + IJ_PLG=\${IJ_HOME} +else + IJ_PLG=${EPREFIX}/usr/share/${PN}/lib +fi +if !([ "\$IJ_MEM" ]) ; then + IJ_MEM=${IJ_MAX_MEM} +fi +if !([ "\$IJ_CP" ]) ; then + IJ_CP=\$(java-config -p imagej):\$(java-config -O)/lib/tools.jar +else + IJ_CP=\$(java-config -p imagej):\$(java-config -O)/lib/tools.jar:\${IJ_CP} +fi +\$(java-config --java) \\ + -Xmx\${IJ_MEM}m -Dswing.aatext=true \\ + -Dawt.useSystemAAFontSettings=on\\ + -cp \${IJ_CP} \\ + -Duser.home=\${IJ_HOME} \\ + -Dplugins.dir=\${IJ_PLG} \\ + ij.ImageJ "\$@" +EOF +} + +src_install() { + java-pkg_dojar *.jar + dobin "${T}/${PN}" + + if use plugins ; then + cp -R "${IJ_S}"/plugins "${ED}"/usr/share/"${PN}"/lib/ + cp -R "${IJ_S}"/macros "${ED}"/usr/share/"${PN}"/lib/ + fi + + use doc && java-pkg_dohtml -r "${WORKDIR}"/api + + insinto /usr/share/pixmaps + doins "${WORKDIR}/${PN}".png + make_desktop_entry "${PN}" ImageJ "${PN}" Graphics +} + +pkg_postinst() { + einfo "" + einfo "You can configure the path of a folder, which contains \"plugins\" directory and IJ_Prefs.txt," + einfo "by setting the environmental variable, \$IJ_HOME." + einfo "Default setting is \$IJ_HOME=\${HOME}/.imagej, i.e. \${HOME}/.imagej/plugins and \${HOME}/.imagej/IJ_Prefs.txt." + einfo "" + einfo "You can also configure the memory size by setting the environmental variable, \$IJ_MEM," + einfo "and the class path by setting the environmental variable, \$IJ_CP." + einfo "" + einfo "If you want to use much more plugins, please see http://rsb.info.nih.gov/ij/plugins/index.html" + einfo "and add *.class files to \$IJ_HOME/plugins folder" + einfo "" +} diff --git a/sci-biology/imagej/metadata.xml b/sci-biology/imagej/metadata.xml index ca2867d8c..8b8ebd7d9 100644 --- a/sci-biology/imagej/metadata.xml +++ b/sci-biology/imagej/metadata.xml @@ -12,4 +12,7 @@ <use> <flag name="plugins">Install additional plugins</flag> </use> + <upstream> + <remote-id type="github">imagej/ImageJ</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/irsabi_bidsdata/irsabi_bidsdata-1.4.ebuild b/sci-biology/irsabi_bidsdata/irsabi_bidsdata-1.4.ebuild index b8cc73c5a..021929bad 100644 --- a/sci-biology/irsabi_bidsdata/irsabi_bidsdata-1.4.ebuild +++ b/sci-biology/irsabi_bidsdata/irsabi_bidsdata-1.4.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2020 Gentoo Authors +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=7 @@ -6,9 +6,8 @@ EAPI=7 inherit check-reqs DESCRIPTION="BIDS data files released with the IRSABI publication" -HOMEPAGE="http://www.aic-fmi.ethz.ch/" +HOMEPAGE="https://chymera.eu/docs/focus/open-science/" SRC_URI=" - http://chymera.eu/distfiles/${P}.tar.xz https://zenodo.org/record/3601531/files/${P}.tar.xz " diff --git a/sci-biology/jellyfish/jellyfish-1.1.12.ebuild b/sci-biology/jellyfish/jellyfish-1.1.12.ebuild index b2e6ea25b..a6989c2bf 100644 --- a/sci-biology/jellyfish/jellyfish-1.1.12.ebuild +++ b/sci-biology/jellyfish/jellyfish-1.1.12.ebuild @@ -1,10 +1,10 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 DESCRIPTION="k-mer counter within reads for assemblies" -HOMEPAGE="http://www.cbcb.umd.edu/software/jellyfish" +HOMEPAGE="https://genome.umd.edu/jellyfish.html" SRC_URI="https://github.com/gmarcais/Jellyfish/releases/download/v${PV}/${P}.tar.gz" # older version is hidden in trinityrnaseq_r20140413p1/trinity-plugins/jellyfish-1.1.11 diff --git a/sci-biology/jellyfish/jellyfish-2.3.0.ebuild b/sci-biology/jellyfish/jellyfish-2.3.0.ebuild index e8e3c8fd0..2237173e0 100644 --- a/sci-biology/jellyfish/jellyfish-2.3.0.ebuild +++ b/sci-biology/jellyfish/jellyfish-2.3.0.ebuild @@ -1,10 +1,10 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 DESCRIPTION="k-mer counter within reads for assemblies" -HOMEPAGE="http://www.genome.umd.edu/jellyfish.html" +HOMEPAGE="https://genome.umd.edu/jellyfish.html" SRC_URI="https://github.com/gmarcais/Jellyfish/releases/download/v${PV}/${P}.tar.gz" # older version is hidden in trinityrnaseq_r20140413p1/trinity-plugins/jellyfish-1.1.11 diff --git a/sci-biology/jellyfish/metadata.xml b/sci-biology/jellyfish/metadata.xml index 138cb7705..f2c1cd819 100644 --- a/sci-biology/jellyfish/metadata.xml +++ b/sci-biology/jellyfish/metadata.xml @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">gmarcais/Jellyfish</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/jtreeview-bin/jtreeview-bin-1.2.0.ebuild b/sci-biology/jtreeview-bin/jtreeview-bin-1.2.0.ebuild index fe8fef44a..63ec84d2f 100644 --- a/sci-biology/jtreeview-bin/jtreeview-bin-1.2.0.ebuild +++ b/sci-biology/jtreeview-bin/jtreeview-bin-1.2.0.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=7 @@ -8,11 +8,12 @@ inherit java-pkg-2 java-ant-2 perl-module S="${WORKDIR}"/TreeView-1.1.6r4-bin DESCRIPTION="Viewer for Microarray Data in PCL or CDT formats" -HOMEPAGE="http://jtreeview.sourceforge.net/" # no https +HOMEPAGE="https://jtreeview.sourceforge.net/" SRC_URI=" https://sourceforge.net/projects/jtreeview/files/jtreeview/${PV}/TreeView-${PV}-bin.tar.gz https://sourceforge.net/projects/jtreeview/files/helper-scripts/0.0.2/helper-scripts-0.0.2.tar.gz " +S="${WORKDIR}/TreeView-${PV}-bin" LICENSE="GPL-2" SLOT="0" @@ -20,11 +21,10 @@ KEYWORDS="~amd64" DEPEND=" >virtual/jdk-1.5:* - !sci-biology/jtreeview" +" RDEPEND="${DEPEND} - >=virtual/jre-1.5:*" - -S="${WORKDIR}/TreeView-${PV}-bin" + >=virtual/jre-1.5:* +" # TODO: use xltproc to create docs following TreeView-1.1.6r4-src/doc/README diff --git a/sci-biology/kat/Manifest b/sci-biology/kat/Manifest deleted file mode 100644 index 0bdd2dd15..000000000 --- a/sci-biology/kat/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST kat-2.4.2.tar.gz 21829118 BLAKE2B 52a0056f322dfb405c005b31a0cb182c739a6af05173123dc1cef1d986f515a8318c1481f1ed0f8c247c01c6b460c951147d81f904709f4e27a7d3d1f47bda3d SHA512 696e3b9ed307ed17085790b24d617195f47fbdb7180be13ee644718c2464c429ffd964959857fc8d1317a451d57b74f6d7b2857fe3764573d9605d58a53b2a0c diff --git a/sci-biology/kat/files/kat-2.4.2-ignore-bundled-deps.patch b/sci-biology/kat/files/kat-2.4.2-ignore-bundled-deps.patch deleted file mode 100644 index 46d343294..000000000 --- a/sci-biology/kat/files/kat-2.4.2-ignore-bundled-deps.patch +++ /dev/null @@ -1,79 +0,0 @@ -diff --git a/lib/Makefile.am b/lib/Makefile.am -index ac23917..0ca4be9 100644 ---- a/lib/Makefile.am -+++ b/lib/Makefile.am -@@ -6,7 +6,6 @@ pkgconfig_DATA = kat.pc - lib_LTLIBRARIES = libkat.la - - libkat_la_LDFLAGS = \ -- -L$(top_builddir)/deps/boost/build/lib/ \ - -version-info 2:4:2 - - LIBS = \ -@@ -41,7 +40,6 @@ library_include_HEADERS = $(KI)/distance_metrics.hpp \ - - libkat_la_CPPFLAGS = \ - -I$(top_srcdir)/deps/jellyfish-2.2.0/include \ -- -I$(top_srcdir)/deps/boost/build/include \ - -I$(top_srcdir)/lib/include \ - -DKAT_SITE_PKGS='"$(prefix)/lib/python$(PYTHON_VERSION)/site-packages"' \ - @AM_CPPFLAGS@ -diff --git a/src/Makefile.am b/src/Makefile.am -index 1cdf7e0..dfa878b 100644 ---- a/src/Makefile.am -+++ b/src/Makefile.am -@@ -14,7 +14,6 @@ kat_CXXFLAGS = \ - kat_CPPFLAGS = \ - -I$(top_srcdir)/deps/seqan-library-2.0.0/include \ - -I$(top_srcdir)/deps/jellyfish-2.2.0/include \ -- -I$(top_srcdir)/deps/boost/build/include \ - -I$(top_srcdir)/lib/include \ - -DKAT_SCRIPTS='"$(datarootdir)/scripts"' \ - -DKAT_SITE_PKGS='"$(prefix)/lib/python$(PYTHON_VERSION)/site-packages"' \ -@@ -25,13 +24,13 @@ kat_LDFLAGS = \ - @AM_LDFLAGS@ - - kat_LDADD = \ -- $(top_builddir)/deps/boost/build/lib/libboost_timer.a \ -- $(top_builddir)/deps/boost/build/lib/libboost_chrono.a \ -- $(top_builddir)/deps/boost/build/lib/libboost_filesystem.a \ -- $(top_builddir)/deps/boost/build/lib/libboost_program_options.a \ -- $(top_builddir)/deps/boost/build/lib/libboost_system.a \ -- $(top_builddir)/deps/jellyfish-2.2.0/.libs/libkat_jellyfish.la \ - $(top_builddir)/lib/libkat.la \ -+ $(top_builddir)/deps/jellyfish-2.2.0/.libs/libkat_jellyfish.la \ -+ -lboost_timer \ -+ -lboost_chrono \ -+ -lboost_filesystem \ -+ -lboost_program_options \ -+ -lboost_system \ - @AM_LIBS@ - - noinst_HEADERS = \ -diff --git a/tests/Makefile.am b/tests/Makefile.am -index eee4e8b..dec2a5f 100644 ---- a/tests/Makefile.am -+++ b/tests/Makefile.am -@@ -31,7 +31,6 @@ AM_CPPFLAGS = \ - -I$(top_srcdir)/lib/include \ - -I$(top_srcdir)/deps/seqan-library-2.0.0/include \ - -I$(top_srcdir)/deps/jellyfish-2.2.0/include \ -- -I$(top_srcdir)/deps/boost/build/include \ - -DDATADIR=\"$(srcdir)/data\" \ - -DKAT_SITE_PKGS='"$(prefix)/lib/python$(PYTHON_VERSION)/site-packages"' \ - @AM_CPPFLAGS@ -@@ -58,13 +57,11 @@ check_unit_tests_SOURCES = \ - - check_unit_tests_LDFLAGS = \ - -static \ -- -L$(top_builddir)/deps/boost/build/lib \ -- -Wl,-rpath $(top_builddir)/deps/boost/build/lib \ - @AM_LDFLAGS@ - - check_unit_tests_LDADD = \ - libgtest.la \ -- $(top_builddir)/lib/libkat.la \ -+ $(top_builddir)/lib/libkat.la \ - -lboost_timer \ - -lboost_chrono \ - -lboost_filesystem \ diff --git a/sci-biology/kat/files/kat-2.4.2-no_static_build.patch b/sci-biology/kat/files/kat-2.4.2-no_static_build.patch deleted file mode 100644 index 48ad6d562..000000000 --- a/sci-biology/kat/files/kat-2.4.2-no_static_build.patch +++ /dev/null @@ -1,56 +0,0 @@ -diff --git a/configure.ac b/configure.ac -index 9acc141..24a4b14 100644 ---- a/configure.ac -+++ b/configure.ac -@@ -178,8 +178,6 @@ define([PC_FILE], lib/kat-2.2.pc) - - AM_CXXFLAGS="-g -O2 -std=c++11" - AC_SUBST([AM_CXXFLAGS]) --AM_LDFLAGS="-static-libstdc++" --AC_SUBST([AM_LDFLAGS]) - - if [[ "${make_pykat}" == "yes" ]]; then - AM_CPPFLAGS="${PYTHON_CPPFLAGS}" -diff --git a/deps/jellyfish-2.2.0/Makefile.am b/deps/jellyfish-2.2.0/Makefile.am -index 83192d9..e3b1694 100644 ---- a/deps/jellyfish-2.2.0/Makefile.am -+++ b/deps/jellyfish-2.2.0/Makefile.am -@@ -7,7 +7,7 @@ man1_MANS = doc/kat_jellyfish.man - pkgconfigdir = $(libdir)/pkgconfig - pkgconfig_DATA = kat_jellyfish.pc - --AM_LDFLAGS = -lz -lpthread -static-libstdc++ # $(VALGRIND_LIBS) -+AM_LDFLAGS = -lz -lpthread # $(VALGRIND_LIBS) - AM_CPPFLAGS = -I$(top_srcdir) -I$(top_srcdir)/include # $(VALGRIND_CFLAGS) - AM_CXXFLAGS = $(ALL_CXXFLAGS) -Wall -Wnon-virtual-dtor -Wno-deprecated-declarations - -diff --git a/src/Makefile.am b/src/Makefile.am -index 2d5cd72..cb5cb0e 100644 ---- a/src/Makefile.am -+++ b/src/Makefile.am -@@ -18,10 +18,6 @@ kat_CPPFLAGS = \ - -DKAT_SCRIPTS='"$(datadir)/scripts"' \ - @AM_CPPFLAGS@ - --kat_LDFLAGS = \ -- -static \ -- @AM_LDFLAGS@ -- - kat_LDADD = \ - $(top_builddir)/lib/libkat.la \ - $(top_builddir)/deps/jellyfish-2.2.0/.libs/libkat_jellyfish.la \ -diff --git a/tests/Makefile.am b/tests/Makefile.am -index d96363a..90e4f61 100644 ---- a/tests/Makefile.am -+++ b/tests/Makefile.am -@@ -54,10 +54,6 @@ check_unit_tests_SOURCES = \ - check_compcounters.cc \ - check_main.cc - --check_unit_tests_LDFLAGS = \ -- -static \ -- @AM_LDFLAGS@ -- - check_unit_tests_LDADD = \ - libgtest.la \ - $(top_builddir)/lib/libkat.la \ diff --git a/sci-biology/kat/kat-2.4.2.ebuild b/sci-biology/kat/kat-2.4.2.ebuild deleted file mode 100644 index a915d1491..000000000 --- a/sci-biology/kat/kat-2.4.2.ebuild +++ /dev/null @@ -1,83 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7,8,9} ) -DISTUTILS_USE_SETUPTOOLS=rdepend -# https://github.com/Ensembl/Bio-DB-HTS/issues/30 - -inherit autotools distutils-r1 - -DESCRIPTION="K-mer Analysis Toolkit (histogram, filter, compare sets, plot)" -HOMEPAGE="https://github.com/TGAC/KAT" -SRC_URI="https://github.com/TGAC/KAT/archive/Release-${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="GPL-3+" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="cpu_flags_x86_sse static-libs test" - -CDEPEND=" - >=dev-libs/boost-1.52[${PYTHON_USEDEP}] - sys-libs/zlib - dev-python/tabulate[${PYTHON_USEDEP}] - dev-python/matplotlib[${PYTHON_USEDEP}] - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/scipy[${PYTHON_USEDEP}] -" -DEPEND="${CDEPEND} - test? ( sys-process/time )" -RDEPEND="${CDEPEND}" -# contains bundled and *modified* version of jellyfish-2.2.0 -# (libkat_jellyfish.{a,so} and "kat_" prefixes are added to all binaries) -# https://github.com/TGAC/KAT/issues/93#issuecomment-383377666 -# contains embedded sci-biology/seqan headers - -PATCHES=( - "${FILESDIR}"/kat-2.4.2-ignore-bundled-deps.patch - "${FILESDIR}"/kat-2.4.2-no_static_build.patch - ) - -S="${WORKDIR}"/KAT-Release-"${PV}" - -distutils_enable_sphinx "${S}/doc/source" --no-autodoc -distutils_enable_tests pytest - -src_prepare(){ - default - rm -rf deps/boost || die "Failed to zap bundled boost" - eautoreconf -} - -src_configure(){ - python_setup - local myconf=() - myconf+=( - --disable-gnuplot - --disable-pykat-install - $(use_enable static-libs static) - ) # python3 does better image rendering, no need for gnuplot - # pass down to jellyfish-2.2.0/configure - use cpu_flags_x86_sse && myconf+=( $(use_with cpu_flags_x86_sse sse) ) - econf ${myconf[@]} -} - -src_compile(){ - default - pushd scripts >/dev/null || die - distutils-r1_src_compile - popd > /dev/null || die -} - -src_install(){ - default - pushd scripts >/dev/null || die - distutils-r1_src_install - popd > /dev/null || die -} - -src_test(){ - default - python_foreach_impl python_test -} diff --git a/sci-biology/kat/kat-9999.ebuild b/sci-biology/kat/kat-9999.ebuild deleted file mode 100644 index acbdac423..000000000 --- a/sci-biology/kat/kat-9999.ebuild +++ /dev/null @@ -1,84 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7,8,9} ) -DISTUTILS_USE_SETUPTOOLS=rdepend -# https://github.com/Ensembl/Bio-DB-HTS/issues/30 - -inherit autotools distutils-r1 git-r3 - -DESCRIPTION="K-mer Analysis Toolkit (histogram, filter, compare sets, plot)" -HOMEPAGE="https://github.com/TGAC/KAT" -EGIT_REPO_URI="https://github.com/TGAC/KAT.git" -EGIT_CHECKOUT_DIR="${WORKDIR}"/KAT-Release-"${PV}" - -LICENSE="GPL-3+" -SLOT="0" -KEYWORDS="" -IUSE="cpu_flags_x86_sse static-libs test" - -CDEPEND=" - >=dev-libs/boost-1.52[${PYTHON_USEDEP}] - sys-libs/zlib - dev-python/tabulate[${PYTHON_USEDEP}] - dev-python/matplotlib[${PYTHON_USEDEP}] - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/scipy[${PYTHON_USEDEP}] -" -DEPEND="${CDEPEND} - test? ( sys-process/time )" -RDEPEND="${CDEPEND}" -# contains bundled and *modified* version of jellyfish-2.2.0 -# (libkat_jellyfish.{a,so} and "kat_" prefixes are added to all binaries) -# https://github.com/TGAC/KAT/issues/93#issuecomment-383377666 -# contains embedded sci-biology/seqan headers - -PATCHES=( - "${FILESDIR}"/kat-2.4.2-ignore-bundled-deps.patch - "${FILESDIR}"/kat-2.4.2-no_static_build.patch - ) - -S="${WORKDIR}"/KAT-Release-"${PV}" - -distutils_enable_sphinx "${S}/doc/source" --no-autodoc -distutils_enable_tests pytest - -src_prepare(){ - default - rm -rf deps/boost || die "Failed to zap bundled boost" - eautoreconf -} - -src_configure(){ - python_setup - local myconf=() - myconf+=( - --disable-gnuplot - --disable-pykat-install - $(use_enable static-libs static) - ) # python3 does better image rendering, no need for gnuplot - # pass down to jellyfish-2.2.0/configure - use cpu_flags_x86_sse && myconf+=( $(use_with cpu_flags_x86_sse sse) ) - econf ${myconf[@]} -} - -src_compile(){ - default - pushd scripts >/dev/null || die - distutils-r1_src_compile - popd > /dev/null || die -} - -src_install(){ - default - pushd scripts >/dev/null || die - distutils-r1_src_install - popd > /dev/null || die -} - -src_test(){ - default - python_foreach_impl python_test -} diff --git a/sci-biology/kat/metadata.xml b/sci-biology/kat/metadata.xml deleted file mode 100644 index 6810aabae..000000000 --- a/sci-biology/kat/metadata.xml +++ /dev/null @@ -1,15 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="github">TGAC/KAT</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-biology/khmer/Manifest b/sci-biology/khmer/Manifest deleted file mode 100644 index 18a85fae6..000000000 --- a/sci-biology/khmer/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST khmer-2.1.1.tar.gz 8507798 BLAKE2B e4db949736c6d01f0878140d0d7be0a91916532bc6709845eeb8d458e145349c868bc381c35ae007716b3c9b7c7a9ca5171965cf187c838a59033b1b969bf177 SHA512 aca35d2b12812470afb271c17eb521e9d80ecaefedde60312ed676bbf73a8662a581e722ebaa4bee6572adc65021a4bc010adbfb84d5393b11c0552139614914 diff --git a/sci-biology/khmer/khmer-2.1.1.ebuild b/sci-biology/khmer/khmer-2.1.1.ebuild deleted file mode 100644 index 11c4231e8..000000000 --- a/sci-biology/khmer/khmer-2.1.1.ebuild +++ /dev/null @@ -1,34 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7,8,9} ) - -inherit distutils-r1 - -DESCRIPTION="In-memory K-mer counting in DNA/RNA/protein sequences" -HOMEPAGE="https://github.com/dib-lab/khmer" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -# ToDo: Fix this: -# ModuleNotFoundError: No module named 'khmer._khmer' -# even happens with --install option for enable_tests -RESTRICT="test" - -RDEPEND=" - sci-biology/screed[${PYTHON_USEDEP}] - dev-python/bz2file[${PYTHON_USEDEP}] -" - -distutils_enable_tests pytest - -python_prepare_all() { - # do not depend on pytest-runner - sed -i "/pytest-runner/d" setup.py || die - distutils-r1_python_prepare_all -} diff --git a/sci-biology/khmer/metadata.xml b/sci-biology/khmer/metadata.xml deleted file mode 100644 index 91ed395d8..000000000 --- a/sci-biology/khmer/metadata.xml +++ /dev/null @@ -1,16 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="github">ged-lab/khmer</remote-id> - <remote-id type="pypi">khmer</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-biology/kmergenie/Manifest b/sci-biology/kmergenie/Manifest deleted file mode 100644 index f38792478..000000000 --- a/sci-biology/kmergenie/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST kmergenie-1.7048.tar.gz 664034 BLAKE2B 1835cf7a9a360e125d1f793091b9000b106ca7816ff400caf8c79a8ae8bb304e6ab6ea3ac4c29dee3cd7cf65b45db42c11b44c606f9f5808fc068037a222a68b SHA512 7c98a329f39443b689ad6431feb7fdb36b0f0bd8a4d8d7637b7af44064d12c8949690771f50e109660ce5e598c592fe8c0ea32ded27f1055e1b1c203d60938f7 diff --git a/sci-biology/kmergenie/kmergenie-1.7048.ebuild b/sci-biology/kmergenie/kmergenie-1.7048.ebuild deleted file mode 100644 index 3a0d6a105..000000000 --- a/sci-biology/kmergenie/kmergenie-1.7048.ebuild +++ /dev/null @@ -1,22 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7,8,9} ) - -inherit distutils-r1 - -DESCRIPTION="Estimate best k-mer length to be used in novo assemblies" -HOMEPAGE="http://kmergenie.bx.psu.edu/" -SRC_URI="http://kmergenie.bx.psu.edu/${P}.tar.gz" - -LICENSE="CeCILL-1.1" -SLOT="0" -KEYWORDS="~amd64" - -DEPEND=" - dev-python/docopt[${PYTHON_USEDEP}] - dev-lang/R -" -RDEPEND="${DEPEND}" diff --git a/sci-biology/kmergenie/metadata.xml b/sci-biology/kmergenie/metadata.xml deleted file mode 100644 index 138cb7705..000000000 --- a/sci-biology/kmergenie/metadata.xml +++ /dev/null @@ -1,12 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-biology/kraken/Manifest b/sci-biology/kraken/Manifest deleted file mode 100644 index bb9fb5722..000000000 --- a/sci-biology/kraken/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -DIST kraken-1.1.1.tar.gz 76541 BLAKE2B 74a302196c9e40757981094838a4a31b24f803ce49941b11be955f7fafc1f89a0e63ab2d8661a7c099c82058959744206c057d047c852693c80df627efa66ba8 SHA512 9f4897d7738b8aed2839581b4f629eff9229ce8333e2a99aa0d2a90fee34036a9f8dd89b4aecbdaf46b785b7d1080b3a014cf89f88efa4d49acf1d36638dedcb -DIST kraken-2.1.1.tar.gz 193878 BLAKE2B d5494038f715e0bb9bd7325a7a0f5430ff3062b0589f0cbd154d671a98aadbd85ce3334f7f3c7844b6becaafdc06889893f427d2da76db71bca71cb8dd7073a5 SHA512 3b5c24955deff63d23017ee5e798648ebd2319a1ead77e85d285b6a1735d38155799f5988c6d1c69121bd7902dde1aaa03782a7d72b841b74c93e314f8a81bfe diff --git a/sci-biology/kraken/kraken-1.1.1-r2.ebuild b/sci-biology/kraken/kraken-1.1.1-r2.ebuild deleted file mode 100644 index 3dd599b83..000000000 --- a/sci-biology/kraken/kraken-1.1.1-r2.ebuild +++ /dev/null @@ -1,51 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit perl-functions - -DESCRIPTION="Detect sequencing project contaminants by mapping reads to taxonomic groups" -HOMEPAGE="https://ccb.jhu.edu/software/kraken" -SRC_URI="https://github.com/DerrickWood/kraken/archive/v${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="GPL-3" -SLOT="1" -KEYWORDS="~amd64" - -DEPEND="" -RDEPEND="${DEPEND} - dev-lang/perl - net-misc/wget - sci-biology/jellyfish:1 -" - -src_prepare(){ - default - sed -e 's/^CXX = /CXX ?= /' -e 's/^CXXFLAGS = /CXXFLAGS ?= /' -i src/Makefile || die - echo "exit 0" >> install_kraken.sh || die -} - -src_compile(){ - ./install_kraken.sh destdir || die -} - -src_install(){ - dodoc -r docs - perl_set_version - perl_domodule destdir/*.pm - dosym ../../"${VENDOR_LIB//${EPREFIX/}}/krakenlib.pm" /usr/bin/krakenlib.pm - insinto /usr/share/${PN}/util - doins destdir/*.pl - chmod -R a+rx "${ED}/usr/share/${PN}/util" - rm -f destdir/krakenlib.pm - dobin destdir/* -} - -pkg_postinst(){ - ewarn "Kraken may optionally need <=sci-biology/jellyfish-2 if you want to build your own dbs" - ewarn "Kraken needs high network bandwidth for its huge downloads, be sure to read" - ewarn "https://ccb.jhu.edu/software/kraken and prepare at least 160GB of disk space" - ewarn "Consider placing the db files in ramfs (needs root permissions) taking >75GB RAM" - ewarn "Results can be visualized with https://sourceforge.net/p/krona/home/krona" -} diff --git a/sci-biology/kraken/kraken-2.1.1.ebuild b/sci-biology/kraken/kraken-2.1.1.ebuild deleted file mode 100644 index 0991f94fa..000000000 --- a/sci-biology/kraken/kraken-2.1.1.ebuild +++ /dev/null @@ -1,55 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit perl-functions - -DESCRIPTION="Detect sequencing project contaminants by mapping reads to taxonomic groups" -HOMEPAGE="https://ccb.jhu.edu/software/kraken2/" -SRC_URI="https://github.com/DerrickWood/kraken2/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="MIT" -SLOT="2" -KEYWORDS="~amd64" - -# TODO: somehow avoid the file conflict with kraken-1 -DEPEND="" -RDEPEND="${DEPEND} - sci-biology/ncbi-tools++ - dev-lang/perl - net-misc/wget - !sci-biology/kraken:1 -" - -S="${WORKDIR}/${PN}2-${PV}" - -src_prepare(){ - default - sed -e 's/^CXX = /CXX ?= /' -e 's/^CXXFLAGS = /CXXFLAGS ?= /' -i src/Makefile || die - echo "exit 0" >> install_kraken2.sh || die -} - -src_compile(){ - ./install_kraken2.sh destdir || die -} - -src_install(){ - dodoc -r docs - perl_set_version - perl_domodule destdir/*.pm - dosym ../../"${VENDOR_LIB//${EPREFIX/}}/krakenlib.pm" /usr/bin/krakenlib.pm - insinto /usr/share/${PN}/util - doins destdir/*.pl - chmod -R a+rx "${ED}/usr/share/${PN}/util" - rm -f destdir/krakenlib.pm - dobin destdir/* -} - -pkg_postinst(){ - ewarn "Kraken may optionally need <=sci-biology/jellyfish-2 if you want to build your own dbs" - ewarn "Kraken needs high network bandwidth for its huge downloads, be sure to read" - ewarn "https://ccb.jhu.edu/software/kraken and prepare at least 160GB of disk space" - ewarn "Consider placing the db files in ramfs (needs root permissions) taking >75GB RAM" - ewarn "Results can be visualized with https://sourceforge.net/p/krona/home/krona" -} diff --git a/sci-biology/kraken/metadata.xml b/sci-biology/kraken/metadata.xml deleted file mode 100644 index 138cb7705..000000000 --- a/sci-biology/kraken/metadata.xml +++ /dev/null @@ -1,12 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-biology/last/Manifest b/sci-biology/last/Manifest deleted file mode 100644 index 1f6d0efe0..000000000 --- a/sci-biology/last/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST last-1179.zip 808701 BLAKE2B 9bbb0da004ccc0b20786c5f631dd48e266e5fecc1719eec040311d53785d4e95657d52ab5addf823709555a07d3617a98eb5e858d110660dea56afcfa84dfc1d SHA512 36aaa5be6a932e9a9c340d18f049d1e735e0ff6f41430c83c7b36bef39540a75a34dff91052c53ddc580e81d0d9a0cb24b5c50125341e0c6ecfd033ff4db84e1 diff --git a/sci-biology/last/last-1179.ebuild b/sci-biology/last/last-1179.ebuild deleted file mode 100644 index 6972a0312..000000000 --- a/sci-biology/last/last-1179.ebuild +++ /dev/null @@ -1,37 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7,8,9} ) - -inherit toolchain-funcs python-single-r1 - -DESCRIPTION="Genome-scale comparison of biological sequences" -HOMEPAGE="http://last.cbrc.jp/" -SRC_URI="http://last.cbrc.jp/${P}.zip" - -LICENSE="GPL-3" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -RDEPEND="${PYTHON_DEPS}" -DEPEND="app-arch/unzip" - -src_configure() { - tc-export CC CXX -} - -src_install() { - local DOCS=( doc/*.txt ChangeLog.txt README.txt ) - local HTML_DOCS=( doc/*html ) - einstalldocs - - dobin src/lastdb src/lastal src/last-split src/last-merge-batches \ - src/last-pair-probs src/lastdb8 src/lastal8 src/last-split8 - - cd scripts || die - dobin * -} diff --git a/sci-biology/last/metadata.xml b/sci-biology/last/metadata.xml deleted file mode 100644 index 8417d1580..000000000 --- a/sci-biology/last/metadata.xml +++ /dev/null @@ -1,8 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-biology/libBigWig/Manifest b/sci-biology/libBigWig/Manifest index 4a1880c5f..249395f6f 100644 --- a/sci-biology/libBigWig/Manifest +++ b/sci-biology/libBigWig/Manifest @@ -1 +1,2 @@ DIST libBigWig-0.4.4.tar.gz 272926 BLAKE2B ffde5fced9991b28cf1fdb8b296a88744d949ea6f044d3bc6f5bbcb3405bc8a08906d94a614d489758fbfc625361b910bbbdcf9ea721fa22dee0edf2f286fc08 SHA512 85e0b60e4ce541eb1328528d834f54ea827cc79b5890093688661dfc9bc72e417c8d293cfe5b93987973b4584b042f10a6edd77adca6ea6b1e57ed3741edba71 +DIST libBigWig-0.4.7.tar.gz 302341 BLAKE2B 667aff6153dc11a3491362e19673b64ff72a0779f5c722508d21f2af8ce4c5e9fb410c9685fc2ecfc3a1fade85454f40ada8d2969948eb1d3336b13ed3a816be SHA512 52f1b7c8e21e16238b3bb07baef6aa3611797b1b5ff44d912c874f8f4527c516a0676877fad21c103b8b25a733e84bef48530f28dc224a79d43f7764eae7ed40 diff --git a/sci-biology/libBigWig/libBigWig-0.4.7.ebuild b/sci-biology/libBigWig/libBigWig-0.4.7.ebuild new file mode 100644 index 000000000..7dc83ceed --- /dev/null +++ b/sci-biology/libBigWig/libBigWig-0.4.7.ebuild @@ -0,0 +1,31 @@ +# Copyright 1999-2020 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DESCRIPTION="C library for handling bigWig files (functionally replacing Jim Kent's lib)" +HOMEPAGE="https://github.com/dpryan79/libBigWig" + +if [[ ${PV} == 9999 ]] ; then + inherit git-r3 + EGIT_REPO_URI="https://github.com/dpryan79/libBigWig" +else + SRC_URI="https://github.com/dpryan79/libBigWig/archive/${PV}.tar.gz -> ${P}.tar.gz" + KEYWORDS="~amd64 ~x86" +fi + +LICENSE="MIT" +SLOT="0" + +DEPEND="net-misc/curl" +RDEPEND="${DEPEND}" + +src_prepare(){ + default + sed -e 's#/usr/local#$(DESTDIR)/usr#' -i Makefile || die + sed -e "s:/lib:/$(get_libdir):" -i Makefile || die +} + +src_install(){ + emake install DESTDIR="${ED}" +} diff --git a/sci-biology/libblasr/Manifest b/sci-biology/libblasr/Manifest deleted file mode 100644 index c575f4081..000000000 --- a/sci-biology/libblasr/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST libblasr-5.3.5.tar.gz 3950694 BLAKE2B 879910dbbfc60592528fab4de0e3bd975f8d12b7e68ca80e031577c9b18a6959a95c76186455fbdecbe3d8455320ba5b83db2c88318467d50a2470569860c514 SHA512 45997fce4fba12ff40c4624bc152990a683e4298d898b404f82e645493557a0565476ead2420fd9c28790e1985cdf3a88401c30181fdc57f84bbd61a707a8b5e diff --git a/sci-biology/libblasr/libblasr-5.3.5.ebuild b/sci-biology/libblasr/libblasr-5.3.5.ebuild deleted file mode 100644 index a12dc25ac..000000000 --- a/sci-biology/libblasr/libblasr-5.3.5.ebuild +++ /dev/null @@ -1,25 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -inherit meson - -DESCRIPTION="Library for blasr" -HOMEPAGE="http://www.smrtcommunity.com/SMRT-Analysis/Algorithms/BLASR" -SRC_URI="https://github.com/PacificBiosciences/blasr_libcpp/archive/${PV}.tar.gz -> ${P}.tar.gz" -S="${WORKDIR}/blasr_libcpp-${PV}" - -LICENSE="blasr" -SLOT="0" -KEYWORDS="~amd64" - -BDEPEND=" - dev-util/cmake - virtual/pkgconfig -" -DEPEND=" - sci-biology/pbbam - sci-libs/hdf5[cxx] -" -RDEPEND="${DEPEND}" diff --git a/sci-biology/libblasr/metadata.xml b/sci-biology/libblasr/metadata.xml deleted file mode 100644 index 8417d1580..000000000 --- a/sci-biology/libblasr/metadata.xml +++ /dev/null @@ -1,8 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-biology/longstitch/longstitch-1.0.1.ebuild b/sci-biology/longstitch/longstitch-1.0.1.ebuild index 6cd035d86..b14bdee87 100644 --- a/sci-biology/longstitch/longstitch-1.0.1.ebuild +++ b/sci-biology/longstitch/longstitch-1.0.1.ebuild @@ -1,15 +1,16 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 DESCRIPTION="Scaffold genome assemblies by Chromium/PacBio/Nanopore reads" HOMEPAGE="https://github.com/bcgsc/LongStitch" SRC_URI="https://github.com/bcgsc/LongStitch/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz" +S="${WORKDIR}/LongStitch-${PV}" LICENSE="GPL-3" SLOT="0" -KEYWORDS="" +KEYWORDS="~amd64" RESTRICT="test" @@ -20,8 +21,6 @@ RDEPEND=" sci-biology/samtools " -S="${WORKDIR}"/LongStitch-"${PV}" - src_install(){ dobin longstitch dodoc README.md LongStitch_overview.pdf diff --git a/sci-biology/longstitch/metadata.xml b/sci-biology/longstitch/metadata.xml index 138cb7705..b25087121 100644 --- a/sci-biology/longstitch/metadata.xml +++ b/sci-biology/longstitch/metadata.xml @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">bcgsc/LongStitch</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/lucy/lucy-1.20.ebuild b/sci-biology/lucy/lucy-1.20.ebuild index 4084ba298..a47e5fcf8 100644 --- a/sci-biology/lucy/lucy-1.20.ebuild +++ b/sci-biology/lucy/lucy-1.20.ebuild @@ -4,7 +4,7 @@ EAPI=7 DESCRIPTION="DNA sequence quality and vector trimming tool" -HOMEPAGE="http://lucy.sourceforge.net/" # no https +HOMEPAGE="https://lucy.sourceforge.net/" SRC_URI="https://sourceforge.net/projects/lucy/files/lucy/lucy%201.20/lucy${PV}.tar.gz" LICENSE="Artistic" diff --git a/sci-biology/mRNAmarkup/Manifest b/sci-biology/mRNAmarkup/Manifest deleted file mode 100644 index fb61347b3..000000000 --- a/sci-biology/mRNAmarkup/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST mRNAmarkup-5-21-2019.tar.gz 192535480 BLAKE2B 5aa385ddae79f2d18649ab70ac2939a478714abd84a59621d852888e9f7df4fd666baea8b8e905756a0f259471a35c6ca1fb5f7c2fa7a50769b4cf7c32dd431b SHA512 c05b685db7992e6278b56b34ad4e77c1f1c4bfb5b9f4880062fa07b5674272e5b950480bbfdd5cbfc037e6b87c10544d0fc67a8b55370037649203ce1c730d2a diff --git a/sci-biology/mRNAmarkup/mRNAmarkup-5.21.2019.ebuild b/sci-biology/mRNAmarkup/mRNAmarkup-5.21.2019.ebuild deleted file mode 100644 index fb37b69f9..000000000 --- a/sci-biology/mRNAmarkup/mRNAmarkup-5.21.2019.ebuild +++ /dev/null @@ -1,55 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -DESCRIPTION="Transcript annotation workflow" -HOMEPAGE="http://brendelgroup.org/bioinformatics2go/mRNAmarkup.php" -SRC_URI="http://www.brendelgroup.org/bioinformatics2go/Download/mRNAmarkup-${PV//./-}.tar.gz" # 184MB - -LICENSE="mRNAmarkup" -SLOT="0" -KEYWORDS="~amd64" - -DEPEND=" - sci-biology/ncbi-tools++ - sci-biology/estscan" -# sci-biology/MuSeqBox has fetch-restrict and probably only works with old BLAST plaintex output -# but, mRNAmarkup/INSTALL says: -# 'For convenience, a copy of the MuSeqBox code distribution is included in directory src/contributed -# -# has a slightly modified estscan copy in src/contributed -RDEPEND="${DEPEND}" - -S="${WORKDIR}/${PN}" - -src_prepare(){ - default - sed -e \ - "s#configfile=$installdir/mRNAmarkup.conf#configfile=/usr/share/mRNAmarkup/etc/mRNAmarkup.conf#" \ - -i bin/mRNAmarkup.orig || die - sed -e \ - "s#$installdir/bin/ESTScan.conf#/usr/share/mRNAmarkup/etc/ESTScan.conf#" \ - -i bin/mRNAmarkup.orig -} - -src_compile(){ - cd src - emake -} - -src_install(){ - mv bin/mRNAmarkup.orig bin/mRNAmarkup - sed -e 's#INSTALLDIR#/usr/share/mRNAmarkup/etc/#' -i bin/mRNAmarkup - dobin bin/mRNAmarkup bin/*.pl bin/dnatopro bin/genestat - # TODO: there are some more files in bin/ , sigh! - insinto /usr/share/mRNAmarkup/etc - mv mRNAmarkup.conf.orig mRNAmarkup.conf - doins mRNAmarkup.conf - doins bin/ESTScan.conf - dodoc 0README INSTALL -} - -pkg_postinst(){ - einfo "Please obtain a local copy of NCBI CDD dastabase" -} diff --git a/sci-biology/mRNAmarkup/metadata.xml b/sci-biology/mRNAmarkup/metadata.xml deleted file mode 100644 index 138cb7705..000000000 --- a/sci-biology/mRNAmarkup/metadata.xml +++ /dev/null @@ -1,12 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-biology/manatee-igs/Manifest b/sci-biology/manatee-igs/Manifest deleted file mode 100644 index 89599e152..000000000 --- a/sci-biology/manatee-igs/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST manatee-2.23.1_linux.tgz 19879146 BLAKE2B bd69d0d701c92ad4e4c8bbfdf8c9cb23184fa2778a924f71dd83e01901a8054296fb32adb58c5bb66d442b29c564c31c8690398479d214e020697726fc413a59 SHA512 50a76d36f69e3b8b80bcdf7fe28e1c9eb7c15bd8889bd8d130bc65f879ec99aa0caec6d0df495d7ab5804e6414599fc316073c9c55ecd1d370c5dd72aadd65ba diff --git a/sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild b/sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild deleted file mode 100644 index 8a21f8f36..000000000 --- a/sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild +++ /dev/null @@ -1,65 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -DESCRIPTION="IGS-modified version of the genome annotation tool using Chado database schema" -HOMEPAGE="http://manatee.sourceforge.net/igs" # no https -SRC_URI="https://downloads.sourceforge.net/project/manatee/igs_manatee/${PV}/manatee-${PV}_linux.tgz" - -LICENSE="Artistic-Manatee" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -DEPEND=" - >=dev-libs/expat-1.95.8 - >=media-libs/gd-2.0.34 - dev-perl/CGI - dev-perl/Bio-DB-Das-Chado - dev-perl/DBI - dev-perl/DBD-mysql - dev-perl/XML-Parser - dev-perl/XML-Twig - dev-perl/XML-Simple - dev-perl/XML-Writer - dev-perl/HTML-Template - dev-perl/Tree-DAG_Node - virtual/perl-File-Spec - virtual/perl-Data-Dumper - dev-perl/GD - dev-perl/GDTextUtil - dev-perl/GDGraph - virtual/perl-Storable - dev-perl/Log-Log4perl - dev-perl/Log-Cabin - dev-perl/Date-Manip - dev-perl/IO-Tee - dev-perl/MLDBM - dev-perl/JSON - dev-perl/JSON-Any - sci-biology/bioperl" -RDEPEND="${DEPEND} - >=virtual/mysql-5:* - >=www-servers/apache-2.2" - -S="${WORKDIR}/manatee-${PV}_linux" - -src_prepare(){ - default - find "${S}" -name \*.cgi | while read f; do sed -e 's|#!/usr/local/bin/perl|#!/usr/bin/perl|' -i $f; done - find "${S}" -name \*.pl | while read f; do sed -e 's|#!/usr/local/bin/perl|#!/usr/bin/perl|' -i $f; done - find "${S}" -name \*.pm | while read f; do sed -e 's|#!/usr/local/bin/perl|#!/usr/bin/perl|' -i $f; done -} - -src_install(){ - dodir /var/www/localhost/cgi-bin - cp -r src/cgi-bin/chado_prok_manatee "${D}"/var/www/localhost/cgi-bin - dodir /var/www/localhost/htdocs/manatee - cp -r src/htdocs/tdb "${D}"/var/www/localhost/htdocs/manatee - - einfo "Please read the "${S}"/databases/Makefile.PL and import the databases into your MySQL database" - - einfo "You have to fetch the 1.1 GB large file from https://sourceforge.net/projects/manatee/files/igs_manatee/"${PV}"/lookups-"${PV}"_linux.tgz" - einfo "You need to update it regularly." - einfo "Also fetch https://sourceforge.net/projects/manatee/files/igs_manatee/"${PV}"/blastdb-"${PV}".tgz (about 2MB in size)" -} diff --git a/sci-biology/manatee-igs/metadata.xml b/sci-biology/manatee-igs/metadata.xml deleted file mode 100644 index 8a3d26043..000000000 --- a/sci-biology/manatee-igs/metadata.xml +++ /dev/null @@ -1,15 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="sourceforge">manatee</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-biology/manatee-jcvi/Manifest b/sci-biology/manatee-jcvi/Manifest deleted file mode 100644 index 9efd473f9..000000000 --- a/sci-biology/manatee-jcvi/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST manatee-2.4.3.tgz 1840410 BLAKE2B e80b499e4a9a6fddc60851e1da126dc48356d675df36938f1ed1a920f19a5f76708fc4be295164ae69330d1978cebbf6e6b9c1f7c098e8049710a3e48eeee0d3 SHA512 0bfb9dff8bdaec1e602fdaa1ec6e2939cba1813ac639b95b9e2679e3473719ad74bb383ba54c56cf4dc0553eac002ea3955ae05a1bc87215c7553b9edb9f9fcf diff --git a/sci-biology/manatee-jcvi/manatee-jcvi-2.4.3.ebuild b/sci-biology/manatee-jcvi/manatee-jcvi-2.4.3.ebuild deleted file mode 100644 index 7bc28decf..000000000 --- a/sci-biology/manatee-jcvi/manatee-jcvi-2.4.3.ebuild +++ /dev/null @@ -1,54 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -DESCRIPTION="Genome annotation tool" -HOMEPAGE="http://manatee.sourceforge.net/jcvi/downloads.shtml" -SRC_URI="http://downloads.sourceforge.net/project/manatee/manatee/manatee-${PV}/manatee-2.4.3.tgz" - -LICENSE="Artistic-Manatee" -SLOT="0" -KEYWORDS="" - -DEPEND=">=dev-libs/expat-1.95.8 - >=media-libs/gd-2.0.34 - dev-perl/DBI - dev-perl/DBD-mysql - dev-perl/XML-Parser - dev-perl/XML-Twig - dev-perl/XML-Simple - dev-perl/XML-Writer - dev-perl/HTML-Template - dev-perl/Tree-DAG_Node - virtual/perl-File-Spec - virtual/perl-Data-Dumper - dev-perl/GD - virtual/perl-Storable - dev-perl/Log-Log4perl - dev-perl/Log-Cabin - dev-perl/IO-Tee - dev-perl/MLDBM - dev-perl/CGI - dev-perl/DBI - dev-perl/Apache-DBI - dev-perl/Date-Manip -" -# dev-perl/CGI-Carp -# dev-perl/CGI-Cookie -# dev-perl/GD-Text -# dev-perl/GD-Graph -# -RDEPEND="${DEPEND} - >=virtual/mysql-5:* - >=www-servers/apache-2.2" - -S="${WORKDIR}"/manatee-"${PV}" - -src_configure(){ - econf HTTPD=/usr/sbin/httpd HTTPD_SCRIPT_HOME=/var/www/cgi-bin HTTPD_DOC_HOME=/var/www/htdocs MYSQLD=/usr/sbin/mysqld -} - -src_compile(){ - default -} diff --git a/sci-biology/manatee-jcvi/metadata.xml b/sci-biology/manatee-jcvi/metadata.xml deleted file mode 100644 index 0f267b755..000000000 --- a/sci-biology/manatee-jcvi/metadata.xml +++ /dev/null @@ -1,15 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="sourceforge">downloads</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-biology/mappy/Manifest b/sci-biology/mappy/Manifest index 511c8e3d0..ff114e6ea 100644 --- a/sci-biology/mappy/Manifest +++ b/sci-biology/mappy/Manifest @@ -1 +1,2 @@ -DIST mappy-2.17.tar.gz 199280 BLAKE2B b79175016f26ed7f33bdff65cc5187c4c777849e5d89c44d0acb94d95189ccce7d89839cfc81c681d3bda6b29ae4ba1934205bd72472f7f228dbedc40dd78602 SHA512 399ceeb710f496c3d9bc409dcafb11122c5b93453dcfdf41c2f6d7d3a052d3600baff29ff08ed1322fcf10f1fc060434f9b0e79cb627c155d559f579b43dd267 +DIST mappy-2.24.tar.gz 140859 BLAKE2B af8ecf8f00c33951b2c7e81bec1e45fe39b7b41da1692fc8c4804b3ad5465320f453e2d53f771c09ce88fa681ad60c0c3706334ace8a682eee8b6f4ebccb02fc SHA512 5500b76ffb0f530aa8f1433c01f1805f5b95e329445ab103847e6ec6e0977a54e5c0dabe405869c7dd8d9103646db0b3cff0ef13b79d7021752ed266002a1dd4 +DIST mappy-2.26.tar.gz 135105 BLAKE2B 26c4c94eae3b719cfaadf2fe31a84faeaef4894b8b8c9ad6bbba46dbb17f609c62c61ecfd42e3be07a7eace38545d029ab03d1fee611868ac6839b3d3362698d SHA512 75949b705561455c317713bfb4bca2de24368881e6c0bb3bf2d11841db9f9e792c7eef0e46f00a7b27e38fe143db5b00be5f281fe058dca32130b745057dcb75 diff --git a/sci-biology/mappy/mappy-2.17.ebuild b/sci-biology/mappy/mappy-2.24.ebuild index 15399c913..0fa703188 100644 --- a/sci-biology/mappy/mappy-2.17.ebuild +++ b/sci-biology/mappy/mappy-2.24.ebuild @@ -1,15 +1,15 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 -PYTHON_COMPAT=( python3_{7,8} ) # compile failure with py3.9 +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..11} ) -inherit distutils-r1 +inherit distutils-r1 pypi DESCRIPTION="Minimap2 python binding" HOMEPAGE="https://github.com/haotianteng/chiron" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" LICENSE="MIT" SLOT="0" diff --git a/sci-biology/mappy/mappy-2.26.ebuild b/sci-biology/mappy/mappy-2.26.ebuild new file mode 100644 index 000000000..0fa703188 --- /dev/null +++ b/sci-biology/mappy/mappy-2.26.ebuild @@ -0,0 +1,16 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..11} ) + +inherit distutils-r1 pypi + +DESCRIPTION="Minimap2 python binding" +HOMEPAGE="https://github.com/haotianteng/chiron" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86" diff --git a/sci-biology/mappy/metadata.xml b/sci-biology/mappy/metadata.xml index 8417d1580..2b83a776c 100644 --- a/sci-biology/mappy/metadata.xml +++ b/sci-biology/mappy/metadata.xml @@ -5,4 +5,8 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">haotianteng/chiron</remote-id> + <remote-id type="pypi">mappy</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/minimap2/metadata.xml b/sci-biology/minimap2/metadata.xml index c9e82c96a..604410dd8 100644 --- a/sci-biology/minimap2/metadata.xml +++ b/sci-biology/minimap2/metadata.xml @@ -10,6 +10,6 @@ <name>Gentoo Biology Project</name> </maintainer> <upstream> - <remote-id type="github">minimap2</remote-id> + <remote-id type="github">lh3/minimap2</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/minimap2/minimap2-2.24.ebuild b/sci-biology/minimap2/minimap2-2.24.ebuild index f39de8ead..6934f2a74 100644 --- a/sci-biology/minimap2/minimap2-2.24.ebuild +++ b/sci-biology/minimap2/minimap2-2.24.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_10 ) DISTUTILS_OPTIONAL=1 inherit distutils-r1 diff --git a/sci-biology/mmseqs2/Manifest b/sci-biology/mmseqs2/Manifest new file mode 100644 index 000000000..dbfe85988 --- /dev/null +++ b/sci-biology/mmseqs2/Manifest @@ -0,0 +1 @@ +DIST mmseqs2-13.0.tar.gz 10199551 BLAKE2B 282d270c2b63a186d7534add93f6c23d625c5011392dc2cdff3cf11572ff23cb527726c19f5e9b092830216fa70a788faa46b1a4a2daafee05a513bff37a8a14 SHA512 90904392edd8a619577f79d75b44461b1bb647133850cc384caddb39bcfa3de0793392521edef0e86436ea0f76c9626298bd7975aba961ac7e846786eaf2e919 diff --git a/sci-biology/mmseqs2/files/mmseqs2-13.0-properly-handle-cpuflags.patch b/sci-biology/mmseqs2/files/mmseqs2-13.0-properly-handle-cpuflags.patch new file mode 100644 index 000000000..10884765c --- /dev/null +++ b/sci-biology/mmseqs2/files/mmseqs2-13.0-properly-handle-cpuflags.patch @@ -0,0 +1,40 @@ +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 1a677e3..df1d765 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -56,23 +56,29 @@ if (HAVE_AVX2) + set(MMSEQS_ARCH "${MMSEQS_ARCH} -mavx2 -mcx16 -Wa,-q") + endif () + set(X64 1) +-elseif (HAVE_SSE4_1) ++endif () ++if (HAVE_SSE4_1) + set(MMSEQS_ARCH "${MMSEQS_ARCH} -msse4.1 -mcx16") + set(X64 1) +-elseif (HAVE_SSE2) ++endif () ++if (HAVE_SSE2) + set(MMSEQS_ARCH "${MMSEQS_ARCH} -msse2") + set(DISABLE_IPS4O 1) + set(X64 1) +-elseif (HAVE_POWER9) ++endif () ++if (HAVE_POWER9) + set(MMSEQS_ARCH "${MMSEQS_ARCH} -mcpu=power9 -mvsx") + set(PPC64 1) +-elseif (HAVE_POWER8) ++endif () ++if (HAVE_POWER8) + set(MMSEQS_ARCH "${MMSEQS_ARCH} -mcpu=power8 -mvsx") + set(PPC64 1) +-elseif (HAVE_ARM8) ++endif () ++if (HAVE_ARM8) + set(MMSEQS_ARCH "${MMSEQS_ARCH} -march=armv8-a+simd") + set(ARM 1) +-elseif (HAVE_S390X) ++endif () ++if (HAVE_S390X) + set(MMSEQS_ARCH "${MMSEQS_ARCH} -mzarch -march=z14") + set(ZARCH 1) + endif () diff --git a/sci-biology/mmseqs2/metadata.xml b/sci-biology/mmseqs2/metadata.xml new file mode 100644 index 000000000..c957d777e --- /dev/null +++ b/sci-biology/mmseqs2/metadata.xml @@ -0,0 +1,22 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <upstream> + <remote-id type="github">soedinglab/mmseqs2</remote-id> + <doc>https://github.com/soedinglab/mmseqs2/wiki</doc> + </upstream> + <maintainer type="person"> + <email>joel@generisbio.com</email> + <name>Joel Berendzen</name> + </maintainer> + <longdescription> + MMseqs2 (Many-against-Many sequence searching) is a software suite toi + search and cluster huge protein and nucleotide sequence sets. + MMseqs2 is open source GPL-licensed software implemented in C++. + The software is designed to run on multiple cores and servers + and exhibits very good scalability. MMseqs2 can run 10000 times + faster than BLAST. At 100 times its speed it achieves almost the + same sensitivity. It can perform profile searches with the same + sensitivity as PSI-BLAST at over 400 times its speed. + </longdescription> +</pkgmetadata> diff --git a/sci-biology/mmseqs2/mmseqs2-13.0-r1.ebuild b/sci-biology/mmseqs2/mmseqs2-13.0-r1.ebuild new file mode 100644 index 000000000..6cbd139d8 --- /dev/null +++ b/sci-biology/mmseqs2/mmseqs2-13.0-r1.ebuild @@ -0,0 +1,55 @@ +# Copyright 2021-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit bash-completion-r1 cmake + +MY_PN="MMseqs2" + +# Must be manually updated with each release +COMMIT="45111b641859ed0ddd875b94d6fd1aef1a675b7e" + +DESCRIPTION="Fast and sensitive sequence search and clustering" +HOMEPAGE="https://github.com/soedinglab/MMseqs2" +SRC_URI="https://github.com/soedinglab/${MY_PN}/archive/${COMMIT}.tar.gz -> ${P}.tar.gz" +S="${WORKDIR}/${MY_PN}-${COMMIT}" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64" +IUSE="cpu_flags_x86_sse4_1 cpu_flags_x86_sse2 cpu_flags_x86_avx2" + +RDEPEND=" + app-arch/zstd[static-libs] + sys-libs/zlib + app-arch/bzip2 +" +DEPEND="${RDEPEND}" + +PATCHES=( + "${FILESDIR}/${P}-properly-handle-cpuflags.patch" +) + +src_configure() { + local mycmakeargs=( + # Need static libs: https://github.com/soedinglab/MMseqs2/issues/411 + -DBUILD_SHARED_LIBS=OFF + -DUSE_SYSTEM_ZSTD=ON + # Disable auto detection, build respecting cpu flags instead + -DNATIVE_ARCH=OFF + -DHAVE_AVX2="$(usex cpu_flags_x86_avx2)" + -DHAVE_SSE4_1="$(usex cpu_flags_x86_sse4_1)" + -DHAVE_SSE2="$(usex cpu_flags_x86_sse2)" + # We also have cpu flags for ppc/arm/s390x + -DVERSION_OVERRIDE=${PV} + ) + cmake_src_configure +} + +src_install(){ + cmake_src_install + # move the bashcomp to correct dir + newbashcomp "${ED}/usr/util/bash-completion.sh" "${PN}" + rm -r "${ED}/usr/util/" || die +} diff --git a/sci-biology/mouse-brain-atlases/Manifest b/sci-biology/mouse-brain-atlases/Manifest deleted file mode 100644 index 262bc49f7..000000000 --- a/sci-biology/mouse-brain-atlases/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -DIST mouse-brain-atlases-0.5.3.tar.xz 591935168 BLAKE2B ceabe728d65b9a73afc9ec18dde14146e26c8465a71b53fdb607ad05ff4626a748ac8cc3d56c2876a2dabf53015db9da0caa66dc48ce83fbaddffcd19c0becce SHA512 7d7ca79f99d03e4a9a97ccf6517fc6570770bee0cea80c2b31e7c4fb4500b8eb49ffb7df5579901c12dd982fd3efb6fc93490dcf53da715c167d47939ea44bdb -DIST mouse-brain-atlasesHD-0.5.3.tar.xz 915990788 BLAKE2B 3be900c9421849a32473a9f1fb1188f73b9fffd36f1e4edc7b6ead91b485bde3cfe211d03f73c4e09cfe194debdc92aad8639e72a64f66036d9a45f08a29cf47 SHA512 46c74d41d323d4cdd7cdf5e8c8ceec03eecf5e7b5c83bb95b7ad4814e55dc32ada7f781710dc40145ffd751d650d35eb5727c460920b831135ab706f5e136718 diff --git a/sci-biology/mouse-brain-atlases/mouse-brain-atlases-0.5.3.ebuild b/sci-biology/mouse-brain-atlases/mouse-brain-atlases-0.5.3.ebuild deleted file mode 100644 index 65963d55a..000000000 --- a/sci-biology/mouse-brain-atlases/mouse-brain-atlases-0.5.3.ebuild +++ /dev/null @@ -1,44 +0,0 @@ -# Copyright 1999-2018 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit check-reqs - -DESCRIPTION="A collection of mouse brain atlases in NIfTI format" -HOMEPAGE="https://github.com/IBT-FMI/mouse-brain-atlases" -SRC_URI=" - http://chymera.eu/distfiles/${P}.tar.xz - hires? ( http://chymera.eu/distfiles/${PN}HD-${PV}.tar.xz ) - " - -LICENSE="fairuse" -SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="hires" - -RDEPEND="" -DEPEND="" - -pkg_pretend() { - if use hires; then - CHECKREQS_DISK_BUILD="4G" - CHECKREQS_DISK_USR="4G" - CHECKREQS_DISK_VAR="8G" - else - CHECKREQS_DISK_BUILD="500M" - fi - check-reqs_pkg_pretend -} - -# We disable this phase to not check requirements twice. -pkg_setup() { :; } - -src_install() { - insinto "/usr/share/${PN}" - doins * - if use hires; then - cd "../${PN}HD-${PV}" - doins * - fi -} diff --git a/sci-biology/mouse-brain-templates/metadata.xml b/sci-biology/mouse-brain-templates/metadata.xml index 16fcf156a..97fbbcbf2 100644 --- a/sci-biology/mouse-brain-templates/metadata.xml +++ b/sci-biology/mouse-brain-templates/metadata.xml @@ -12,4 +12,7 @@ <use> <flag name="hires">Also install high-resolution atlases.</flag> </use> + <upstream> + <remote-id type="github">IBT-FMI/mouse-brain-templates_generator</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/mouse-brain-templates/mouse-brain-templates-0.5.3.ebuild b/sci-biology/mouse-brain-templates/mouse-brain-templates-0.5.3.ebuild index 1ba2221aa..60d06f934 100644 --- a/sci-biology/mouse-brain-templates/mouse-brain-templates-0.5.3.ebuild +++ b/sci-biology/mouse-brain-templates/mouse-brain-templates-0.5.3.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=7 @@ -6,10 +6,10 @@ EAPI=7 inherit check-reqs DESCRIPTION="A collection of mouse brain templates in NIfTI format" -HOMEPAGE="https://github.com/IBT-FMI/mouse-brain-atlases" +HOMEPAGE="https://github.com/IBT-FMI/mouse-brain-templates_generator" SRC_URI=" - http://chymera.eu/distfiles/${P}.tar.xz - hires? ( http://chymera.eu/distfiles/${PN}HD-${PV}.tar.xz ) + https://resources.chymera.eu/distfiles/${P}.tar.xz + hires? ( https://resources.chymera.eu/distfiles/${PN}HD-${PV}.tar.xz ) " LICENSE="fairuse" diff --git a/sci-biology/mreps/metadata.xml b/sci-biology/mreps/metadata.xml index 8417d1580..a60e8c1b5 100644 --- a/sci-biology/mreps/metadata.xml +++ b/sci-biology/mreps/metadata.xml @@ -5,4 +5,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">gregorykucherov/mreps</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/mrsfast/Manifest b/sci-biology/mrsfast/Manifest deleted file mode 100644 index b6da5c3dd..000000000 --- a/sci-biology/mrsfast/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST mrsfast-3.4.2.tar.gz 47451 BLAKE2B e8dc3d06ec53d036ef2b556fc536b5430c6bc392846341e86afcd3131f38cc2ac2a642e8f4cf97e2bb56039604b18e839f0bc3803665a713cdb13374eee0fb46 SHA512 3ca0e166a165b338a3949fea1f80c6e3f228e36663af3cd6de57eb22ac05fa0d8a4c5fa8c2ca5ee5ce8cfe17d7df05362f26a9ae77f9d117ea256461a3c3e9a0 diff --git a/sci-biology/mrsfast/metadata.xml b/sci-biology/mrsfast/metadata.xml deleted file mode 100644 index 309390097..000000000 --- a/sci-biology/mrsfast/metadata.xml +++ /dev/null @@ -1,11 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="sourceforge">mrsfast</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-biology/mrsfast/mrsfast-3.4.2.ebuild b/sci-biology/mrsfast/mrsfast-3.4.2.ebuild deleted file mode 100644 index 91f7d771c..000000000 --- a/sci-biology/mrsfast/mrsfast-3.4.2.ebuild +++ /dev/null @@ -1,28 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit toolchain-funcs - -DESCRIPTION="Micro Read Fast Alignment Search Tool" -HOMEPAGE="https://sfu-compbio.github.io/mrsfast/" -SRC_URI="https://github.com/sfu-compbio/mrsfast/archive/v${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="" - -src_prepare() { - default - sed \ - -e "s:gcc:$(tc-getCC) ${LDFLAGS}:g" \ - -e '/^CFLAGS/d' \ - -e '/^LDFLAGS/d' \ - -i Makefile || die - tc-export CC -} - -src_install() { - dobin ${PN} -} diff --git a/sci-biology/multiqc/Manifest b/sci-biology/multiqc/Manifest new file mode 100644 index 000000000..3585038a3 --- /dev/null +++ b/sci-biology/multiqc/Manifest @@ -0,0 +1 @@ +DIST multiqc-1.19.tar.gz 1159781 BLAKE2B 32d592dba5675f8cb673c8fced9f8ed32977ecd2baf1407aff4ef16b88d8bdad6a9541748717b90d5ab755f6354166e2de62cb1abd282d0e5ce9d1c89529d249 SHA512 75ef5a1b6c6433d68b878e2a1d51b6f420b8c77831cb1279a0b87aff5d6dee7a65bcca5d1f4deb04d4957feef0f27a1155198e244bd165404b08a23bfc8a9354 diff --git a/sci-biology/salmon/metadata.xml b/sci-biology/multiqc/metadata.xml index 1907254d6..09bd2b6e6 100644 --- a/sci-biology/salmon/metadata.xml +++ b/sci-biology/multiqc/metadata.xml @@ -1,15 +1,12 @@ -<?xml version="1.0" encoding="UTF-8"?> +<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> <maintainer type="person"> <email>mschu.dev@gmail.com</email> <name>Michael Schubert</name> </maintainer> <upstream> - <remote-id type="github">COMBINE-lab/salmon</remote-id> + <remote-id type="github">ewels/MultiQC</remote-id> + <remote-id type="pypi">multiqc</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/multiqc/multiqc-1.19.ebuild b/sci-biology/multiqc/multiqc-1.19.ebuild new file mode 100644 index 000000000..187f06c22 --- /dev/null +++ b/sci-biology/multiqc/multiqc-1.19.ebuild @@ -0,0 +1,40 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..11} ) + +inherit pypi distutils-r1 + +DESCRIPTION="Aggregate bioinformatics results across many samples into a single report" +HOMEPAGE="https://multiqc.info/" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64 ~amd64-linux" + +RDEPEND="dev-python/matplotlib[${PYTHON_USEDEP}] + dev-python/networkx[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/click[${PYTHON_USEDEP}] + dev-python/coloredlogs[${PYTHON_USEDEP}] + dev-python/future[${PYTHON_USEDEP}] + dev-python/jinja[${PYTHON_USEDEP}] + dev-python/lzstring[${PYTHON_USEDEP}] + dev-python/markdown[${PYTHON_USEDEP}] + dev-python/packaging[${PYTHON_USEDEP}] + dev-python/pyyaml[${PYTHON_USEDEP}] + dev-python/requests[${PYTHON_USEDEP}] + dev-python/rich[${PYTHON_USEDEP}] + dev-python/rich-click[${PYTHON_USEDEP}] + dev-python/simplejson[${PYTHON_USEDEP}] + dev-python/spectra[${PYTHON_USEDEP}] + dev-python/importlib-metadata[$PYTHON_USEDEP] + dev-python/humanize[$PYTHON_USEDEP] + dev-python/pyaml-env[$PYTHON_USEDEP]" + +# pypi tarball does not include tests +RESTRICT="test" +#distutils_enable_tests pytest diff --git a/sci-biology/ncbi-blast+/Manifest b/sci-biology/ncbi-blast+/Manifest deleted file mode 100644 index afe8a43ef..000000000 --- a/sci-biology/ncbi-blast+/Manifest +++ /dev/null @@ -1,5 +0,0 @@ -DIST ncbi-blast-2.11.0+-src.tar.gz 58493096 BLAKE2B cfd6e7c66b379bee7065d306d2e426b798ec13fea5ed736c05c48b45c2fd7389c5050cc920b67d5e0f58102a4ef1108decbde791012fab28fe7402f9c8747808 SHA512 617994a0e3a4675a5f7048f165ac405bbd6a715ece9aba115d7c26b6be446b889b817dd496a2e15673545e5b594684c83fc4edb22cb5ecca2fd6d342c3bd642e -DIST ncbi-blast-2.2.30+-src.tar.gz 18985378 BLAKE2B 59e749964ee5c6e30ac0286fc928fa8806abfd01aa70d937751642929de4d4e8ebc2109061f5dc82baf7e517a8718e1e11b9372c84f8be3b4140f55708ab264b SHA512 501727486aaa384ee5c40368332243ec2e19f22ab88f50c9396b4d33738bde4dbb5d3a1025ae599c1b5f4b4dd3d065ba4d0eb30305f42bfc781c95bbc4140a17 -DIST ncbi-blast-2.2.31+-src.tar.gz 18971327 BLAKE2B 4f6b124ddf6c892a0be36cbdcb00fe20a15b6f7a49af3f022e31a757ebd48d95c52219ecb2d56fa7787f936dbc08853affe07250ddf5461aff2f7fa5a9742be7 SHA512 2681a4394cc250d1ee545cd85dc962d73b1dbbdd987790a029bf51a58e74cbb08b5c8cf4a02b9b7c95916e3fb0d1613e2ed8631bb7ad683156759421081bb4ca -DIST ncbi-blast-2.6.0+-src.tar.gz 20025526 BLAKE2B d97d1245e3f2030025e99323d67d889e6cecaa719fe525dbe1574a916e5f8b7b620880d44efe51851d64b9d1cdd0538f13161bfea8e233dcca6a223548d5090d SHA512 ea6444892a0b10459193d33d243b5960ad206b702e01e94a554a5ebda0291ff45e1ce43479713c23a96eba676b40bb8c57a7ef9dd2118729feef6b2cd98560c6 -DIST ncbi-blast-2.8.1+-src.tar.gz 24973554 BLAKE2B d13dee5cdd0218cb409898ac999fe5613e534375958c4b814a4c52d9954152a8da491d4866d6090c11bbb94916542be4809744a7f474c189a3b2f3dc9bc8e207 SHA512 3f408c5f76704183578828df3272bab7d59dd6052364e73e1831cd005b87d87dcc086bb1799b316b09e639e4af0edea6404b93a4b3e3c159d27cef34fff93d6f diff --git a/sci-biology/ncbi-blast+/files/disable-testsuite-compilation.txt b/sci-biology/ncbi-blast+/files/disable-testsuite-compilation.txt deleted file mode 100644 index aeaf75e45..000000000 --- a/sci-biology/ncbi-blast+/files/disable-testsuite-compilation.txt +++ /dev/null @@ -1,3 +0,0 @@ -.* --.*/test --.*/unit_test diff --git a/sci-biology/ncbi-blast+/files/ncbi-blast+-2.2.30__fix_lib_deps.patch b/sci-biology/ncbi-blast+/files/ncbi-blast+-2.2.30__fix_lib_deps.patch deleted file mode 100644 index 13dffeee7..000000000 --- a/sci-biology/ncbi-blast+/files/ncbi-blast+-2.2.30__fix_lib_deps.patch +++ /dev/null @@ -1,668 +0,0 @@ -Subject: ensure that all libraries link against all direct dependencies
-
- * src/**/Makefile.*.lib: set DLL_(D)LIB correctly. Break the dependency
- loop between libxblast and libxalgoblastdbindex by having the former
- provide only the C++ BLAST API, leaving the C core only in libblast.
- * src/build-system/library_relations.txt: Change xblast's
- relationship to blast from includes to needs, accordingly.
- * src/algo/blast/dbindex*/*/Makefile.*.app: Link against libxconnect
- rather than libconnect for consistency with libblast, which uses the
- former to keep the aforementioned cycle-breaking from causing
- inconsistency elsewhere.
-
-Debian-Bug: 633567.
-Author: Aaron M. Ucko <ucko@debian.org>
-Last-Update: 2014-12-02
---- a/c++/src/algo/blast/core/Makefile.blast.lib
-+++ b/c++/src/algo/blast/core/Makefile.blast.lib
-@@ -21,6 +21,7 @@ LIB = blast
- CFLAGS = $(FAST_CFLAGS)
- LDFLAGS = $(FAST_LDFLAGS)
-
-+DLL_LIB = composition_adjustment xconnect tables
-
- WATCHERS = madden camacho
-
---- a/c++/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib
-+++ b/c++/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib
-@@ -11,6 +11,8 @@ SRC = sequence_istream_fasta \
- CXXFLAGS = -DDO_INLINE $(FAST_CXXFLAGS)
- LDFLAGS = $(FAST_LDFLAGS)
-
-+DLL_LIB = blast seqdb xobjread xobjutil xobjmgr seqset seq xser xutil xncbi
-+
- ASN_DEP = seqset
-
- WATCHERS = morgulis
---- a/c++/src/algo/blast/format/Makefile.xblastformat.lib
-+++ b/c++/src/algo/blast/format/Makefile.xblastformat.lib
-@@ -7,7 +7,8 @@ SRC = blastfmtutil blastxml_format blast
-
- CPPFLAGS = -DNCBI_MODULE=BLASTFORMAT $(ORIG_CPPFLAGS)
-
--DLL_LIB = align_format blastxml blastxml2 xhtml xcgi
-+DLL_LIB = xblast align_format xalnmgr xobjmgr xnetblast scoremat blastxml \
-+ seq general xser tables xncbi blastxml2
-
- WATCHERS = jianye zaretska madden camacho fongah2
-
---- a/c++/src/algo/winmask/Makefile.xalgowinmask.lib
-+++ b/c++/src/algo/winmask/Makefile.xalgowinmask.lib
-@@ -21,7 +21,7 @@ SRC = seq_masker seq_masker_score_mean s
- CXXFLAGS = $(FAST_CXXFLAGS)
- LDFLAGS = $(FAST_LDFLAGS)
-
--
-+DLL_LIB = seqmasks_io xobjread xobjutil xobjmgr seq xncbi
-
- USES_LIBRARIES = \
- seqmasks_io
---- a/c++/src/cgi/Makefile.cgi.lib
-+++ b/c++/src/cgi/Makefile.cgi.lib
-@@ -9,6 +9,8 @@ SRC = ncbicgi cgiapp cgictx ncbicgir ncb
- user_agent
- LIB = xcgi
-
-+DLL_LIB = xutil xncbi
-+
- CPPFLAGS = $(ORIG_CPPFLAGS) $(FASTCGI_INCLUDE)
-
- WATCHERS = vakatov
---- a/c++/src/html/Makefile.html.lib
-+++ b/c++/src/html/Makefile.html.lib
-@@ -7,6 +7,8 @@ SRC = node html htmlhelper page pager se
- commentdiag indentstream html_exception writer_htmlenc
- LIB = xhtml
-
-+DLL_LIB = xncbi
-+
- WATCHERS = ivanov
-
-
---- a/c++/src/objects/blast/Makefile.xnetblastcli.lib
-+++ b/c++/src/objects/blast/Makefile.xnetblastcli.lib
-@@ -3,6 +3,7 @@ ASN_DEP = xnetblast
- LIB = xnetblastcli
- SRC = blastclient blastclient_
-
-+DLL_LIB = xnetblast xser xconnect xutil xncbi
-
- USES_LIBRARIES = \
- xconnect xnetblast
---- a/c++/src/objtools/align_format/Makefile.align_format.lib
-+++ b/c++/src/objtools/align_format/Makefile.align_format.lib
-@@ -13,6 +13,10 @@ SRC = format_flags align_format_util sho
-
- CPPFLAGS = -DNCBI_MODULE=BLASTFORMAT $(ORIG_CPPFLAGS)
-
-+DLL_LIB = xalnmgr ncbi_xloader_genbank seqdb blast_services xobjread xobjutil \
-+ xobjmgr xnetblast blastdb gene_info seqset seq general xser \
-+ xcgi xhtml tables xncbi
-+
- ### EXAMPLES OF OTHER SETTINGS THAT MIGHT BE OF INTEREST
- # CFLAGS = $(FAST_CFLAGS)
- # CXXFLAGS = $(FAST_CXXFLAGS)
---- a/c++/src/objtools/alnmgr/Makefile.alnmgr.lib
-+++ b/c++/src/objtools/alnmgr/Makefile.alnmgr.lib
-@@ -12,7 +12,7 @@ SRC = aln_builders aln_converters aln_ge
-
- WATCHERS = todorov dicuccio grichenk
-
--
-+DLL_LIB = xobjmgr seqset seq xser tables xncbi
-
- USES_LIBRARIES = \
- tables xobjutil
---- a/c++/src/objtools/readers/Makefile.xobjread.lib
-+++ b/c++/src/objtools/readers/Makefile.xobjread.lib
-@@ -21,7 +21,7 @@ SRC = read_util format_guess_ex \
- message_listener line_error
-
-
--DLL_LIB = creaders
-+DLL_LIB = submit seqset seq pub general xser creaders sequtil xutil xncbi
-
-
-
---- a/c++/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib
-+++ b/c++/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib
-@@ -12,7 +12,7 @@ mask_writer_seqloc \
- mask_writer_blastdb_maskinfo
-
- ASN_DEP = seqset
--DLL_LIB = seqdb blastdb
-+DLL_LIB = seqdb xobjread xobjutil xobjmgr blastdb seqset seq xser xncbi
-
- WATCHERS = morgulis camacho
-
---- a/c++/src/objtools/simple/Makefile.xobjsimple.lib
-+++ b/c++/src/objtools/simple/Makefile.xobjsimple.lib
-@@ -7,6 +7,8 @@ WATCHERS = jcherry
-
- ASN_DEP = seqset
-
-+DLL_LIB = ncbi_xloader_genbank xobjmgr seq xncbi
-+
- LIB = xobjsimple
- SRC = simple_om
-
---- a/c++/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib
-+++ b/c++/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib
-@@ -24,6 +24,8 @@ seqdbobj
-
- LIB = seqdb
-
-+DLL_LIB = blastdb xobjmgr seq general xser sequtil xncbi
-+
- CFLAGS = $(FAST_CFLAGS)
- CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_CPPFLAGS)
- CXXFLAGS = $(FAST_CXXFLAGS)
---- a/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib
-+++ b/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib
-@@ -7,6 +7,8 @@ CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_
-
- ASN_DEP = blastdb seqset
-
-+DLL_LIB = seqdb xobjmgr seqset seq xncbi
-+
- WATCHERS = camacho
-
-
---- a/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib
-+++ b/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib
-@@ -5,6 +5,8 @@ SRC = bdbloader_rmt remote_blastdb_adapt
-
- CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_CPPFLAGS)
-
-+DLL_LIB = ncbi_xloader_blastdb blast_services xobjmgr seq xncbi
-+
- ASN_DEP = blastdb xnetblast
-
- WATCHERS = camacho
---- a/c++/src/algo/blast/api/Makefile.xblast.lib
-+++ b/c++/src/algo/blast/api/Makefile.xblast.lib
-@@ -74,14 +74,15 @@ cdd_pssm_input \
- deltablast_options \
- deltablast
-
--SRC = $(SRC_C:%=.core_%) $(SRC_CXX)
-+SRC = $(SRC_CXX) # $(SRC_C:%=.core_%)
-
- LIB = xblast
-
- DLL_LIB = xalgoblastdbindex composition_adjustment xalgowinmask \
- xalgodustmask seqmasks_io seqdb $(OBJREAD_LIBS) xobjutil \
- blastdb xnetblastcli xnetblast scoremat xconnect tables \
-- $(SOBJMGR_LIBS)
-+ $(SOBJMGR_LIBS) blast seqdb seqset seq general \
-+ xser xconnect sequtil tables xutil xncbi
-
- CFLAGS = $(FAST_CFLAGS)
- CPPFLAGS = -DNCBI_MODULE=BLAST $(ORIG_CPPFLAGS)
---- a/c++/src/algo/blast/blastinput/Makefile.blastinput.lib
-+++ b/c++/src/algo/blast/blastinput/Makefile.blastinput.lib
-@@ -24,7 +24,9 @@ SRC = $(SRC_CXX)
-
- LIB = blastinput
-
--DLL_LIB = xblast align_format ncbi_xloader_blastdb_rmt ncbi_xloader_blastdb seqdb $(OBJREAD_LIBS) $(OBJMGR_LIBS) xutil
-+ DLL_LIB = xblast align_format ncbi_xloader_blastdb_rmt ncbi_xloader_blastdb seqdb xobjread \
-+ $(OBJREAD_LIBS) $(OBJMGR_LIBS) xutil ncbi_xloader_genbank ncbi_xreader_id2 ncbi_xreader \
-+ scoremat seqset seq xser xutil xncbi
-
- # should be redundant, given the above :-/
- ASN_DEP = seqset xnetblast
---- a/c++/src/algo/dustmask/Makefile.xalgodustmask.lib
-+++ b/c++/src/algo/dustmask/Makefile.xalgodustmask.lib
-@@ -8,6 +8,8 @@ LIB = xalgodustmask
-
- SRC = symdust
-
-+DLL_LIB = xobjmgr seq xncbi
-+
- CXXFLAGS = $(FAST_CXXFLAGS)
- LDFLAGS = $(FAST_LDFLAGS)
-
---- a/c++/src/connect/Makefile.xconnect.lib
-+++ b/c++/src/connect/Makefile.xconnect.lib
-@@ -14,6 +14,8 @@ UNIX_SRC = $(LOCAL_LBSM)
- LIB = xconnect
- PROJ_TAG = core
-
-+DLL_LIB = xncbi
-+
- LIBS = $(NETWORK_LIBS) $(ORIG_LIBS)
-
- WATCHERS = lavr
---- a/c++/src/connect/ext/Makefile.xconnext.lib
-+++ b/c++/src/connect/ext/Makefile.xconnext.lib
-@@ -6,6 +6,8 @@ SRC = $(SRC_C) ncbi_dblb_svcmapper
-
- LIB = xconnext
-
-+DLL_LIB = xconnect xncbi
-+
- WATCHERS = lavr
-
-
---- a/c++/src/objects/blast/Makefile.blast.lib
-+++ b/c++/src/objects/blast/Makefile.blast.lib
-@@ -1,6 +1,8 @@
- LIB = xnetblast
- SRC = blast__ blast___ names
-
-+DLL_LIB = scoremat seqset seq xser xncbi
-+
- WATCHERS = camacho
-
-
---- a/c++/src/objects/blastxml/Makefile.blastxml.lib
-+++ b/c++/src/objects/blastxml/Makefile.blastxml.lib
-@@ -1,6 +1,8 @@
- LIB = blastxml
- SRC = blastxml__ blastxml___
-
-+DLL_LIB = xser xncbi
-+
-
- USES_LIBRARIES = \
- xser
---- a/c++/src/objects/scoremat/Makefile.scoremat.lib
-+++ b/c++/src/objects/scoremat/Makefile.scoremat.lib
-@@ -1,6 +1,8 @@
- LIB = scoremat
- SRC = scoremat__ scoremat___
-
-+DLL_LIB = seqset seq general xser xncbi
-+
-
- USES_LIBRARIES = \
- seqset
---- a/c++/src/objects/seqedit/Makefile.seqedit.lib
-+++ b/c++/src/objects/seqedit/Makefile.seqedit.lib
-@@ -1,6 +1,7 @@
- LIB = seqedit
- SRC = seqedit__ seqedit___
--
-+
-+DLL_LIB = seqset seq general xser xncbi
-
-
- USES_LIBRARIES = \
---- a/c++/src/objects/submit/Makefile.submit.lib
-+++ b/c++/src/objects/submit/Makefile.submit.lib
-@@ -1,6 +1,8 @@
- LIB = submit
- SRC = submit__ submit___
-
-+DLL_LIB = seqset seq biblio general xser xncbi
-+
-
- USES_LIBRARIES = \
- seqset
---- a/c++/src/objmgr/util/Makefile.util.lib
-+++ b/c++/src/objmgr/util/Makefile.util.lib
-@@ -8,6 +8,8 @@ ASN_DEP = submit
- SRC = weight sequence feature seqtitle create_defline obj_sniff seq_loc_util seq_align_util seq_trimmer bioseqgaps_ci
- LIB = xobjutil
-
-+DLL_LIB = xobjmgr seqset seq pub biblio general xser sequtil xutil xncbi
-+
- WATCHERS = ucko vasilche kornbluh
-
-
---- a/c++/src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib
-+++ b/c++/src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib
-@@ -11,6 +11,7 @@ SRC = seq_writer blastdb_dataextract bla
-
- CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_CPPFLAGS)
-
-+DLL_LIB = seqdb xobjutil xobjmgr seq xser sequtil xutil xncbi
-
- ### EXAMPLES OF OTHER SETTINGS THAT MIGHT BE OF INTEREST
- # CFLAGS = $(FAST_CFLAGS)
---- a/c++/src/objtools/blast/services/Makefile.blast_services.lib
-+++ b/c++/src/objtools/blast/services/Makefile.blast_services.lib
-@@ -8,6 +8,8 @@ SRC = blast_services
-
- LIB = blast_services
-
-+DLL_LIB = xnetblastcli xnetblast xser xconnect xutil xncbi
-+
- CFLAGS = $(FAST_CFLAGS)
- CPPFLAGS = -DNCBI_MODULE=NETBLAST $(ORIG_CPPFLAGS)
- CXXFLAGS = $(FAST_CXXFLAGS)
---- a/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib
-+++ b/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib
-@@ -12,6 +12,9 @@ LIB_OR_DLL = both
- # Dependencies for shared library
- DLL_LIB = ncbi_xreader$(DLL)
-
-+DLL_DLIB = ncbi_xreader_cache ncbi_xreader_id1 ncbi_xreader_id2 \
-+ id2 id1 ncbi_xreader xobjmgr seq xutil xncbi
-+
- WATCHERS = vasilche
-
-
---- a/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib
-+++ b/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib
-@@ -15,6 +15,9 @@ LIB_OR_DLL = both
- DLL_LIB =
- DLL_DLIB = $(GENBANK_READER_LDEP)
-
-+DLL_DLIB = xobjmgr id2 seqsplit id1 seqset seq general \
-+ xser xconnect xcompress xutil xncbi
-+
- WATCHERS = vasilche
-
-
---- a/c++/src/objtools/data_loaders/genbank/cache/Makefile.ncbi_xreader_cache.lib
-+++ b/c++/src/objtools/data_loaders/genbank/cache/Makefile.ncbi_xreader_cache.lib
-@@ -12,6 +12,8 @@ LIB_OR_DLL = both
- # Dependencies for shared library
- DLL_LIB = ncbi_xreader$(DLL)
-
-+DLL_DLIB = ncbi_xreader xobjmgr seq xser xncbi
-+
- CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE)
-
- WATCHERS = vasilche
---- a/c++/src/objtools/data_loaders/genbank/id1/Makefile.ncbi_xreader_id1.lib
-+++ b/c++/src/objtools/data_loaders/genbank/id1/Makefile.ncbi_xreader_id1.lib
-@@ -12,6 +12,8 @@ LIB_OR_DLL = both
- # Dependencies for shared library
- DLL_LIB = xconnect ncbi_xreader$(DLL)
-
-+DLL_DLIB = ncbi_xreader xobjmgr id1 seq general xser xconnect xutil xncbi
-+
- CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE)
-
- WATCHERS = vasilche
---- a/c++/src/objtools/data_loaders/genbank/id2/Makefile.ncbi_xreader_id2.lib
-+++ b/c++/src/objtools/data_loaders/genbank/id2/Makefile.ncbi_xreader_id2.lib
-@@ -12,7 +12,10 @@ LIB_OR_DLL = both
- CPPFLAGS = $(ORIG_CPPFLAGS) $(Z_INCLUDE)
-
- # Dependencies for shared library (disabled due to problems on Darwin)
--# DLL_LIB = xconnect ncbi_xreader$(DLL)
-+DLL_LIB = xconnect ncbi_xreader$(DLL)
-+
-+DLL_DLIB = ncbi_xreader xobjmgr id2 seqsplit seq xser xconnect xncbi
-+
-
- WATCHERS = vasilche
-
---- a/c++/src/util/compress/api/Makefile.compress.lib
-+++ b/c++/src/util/compress/api/Makefile.compress.lib
-@@ -7,7 +7,7 @@ LIB = xcompress
-
- CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE)
-
--DLL_LIB = $(BZ2_LIB) $(Z_LIB) $(LZO_LIB)
-+DLL_LIB = $(BZ2_LIB) $(Z_LIB) $(LZO_LIB) xutil xncbi
- LIBS = $(BZ2_LIBS) $(Z_LIBS) $(LZO_LIBS) $(ORIG_LIBS)
-
- WATCHERS = ivanov
---- a/c++/src/util/sequtil/Makefile.sequtil.lib
-+++ b/c++/src/util/sequtil/Makefile.sequtil.lib
-@@ -3,6 +3,8 @@
- LIB = sequtil
- SRC = sequtil sequtil_convert sequtil_convert_imp sequtil_manip sequtil_tables sequtil_shared
-
-+DLL_LIB = xncbi
-+
- WATCHERS = shomrat
-
-
---- a/c++/src/corelib/Makefile.test_boost.lib
-+++ b/c++/src/corelib/Makefile.test_boost.lib
-@@ -3,6 +3,8 @@
- SRC = test_boost teamcity_messages
- LIB = test_boost
-
-+DLL_LIB = xncbi
-+
- CPPFLAGS = $(ORIG_CPPFLAGS) $(BOOST_INCLUDE)
-
- REQUIRES = Boost.Test.Included
---- a/c++/src/corelib/Makefile.test_mt.lib
-+++ b/c++/src/corelib/Makefile.test_mt.lib
-@@ -3,6 +3,8 @@
- SRC = test_mt
- LIB = test_mt
-
-+DLL_LIB = xncbi
-+
- # REQUIRES = MT
-
- USE_PCH = no
---- a/c++/src/objects/biblio/Makefile.biblio.lib
-+++ b/c++/src/objects/biblio/Makefile.biblio.lib
-@@ -1,6 +1,8 @@
- LIB = biblio
- SRC = biblio__ biblio___ citation_base
-
-+DLL_LIB = general xser xncbi
-+
-
- USES_LIBRARIES = \
- general
---- a/c++/src/objects/blastdb/Makefile.blastdb.lib
-+++ b/c++/src/objects/blastdb/Makefile.blastdb.lib
-@@ -1,5 +1,7 @@
- # $Id: Makefile.blastdb.lib 427424 2014-02-20 13:38:50Z gouriano $
-
-+
-+DLL_LIB = seq xser xncbi
- LIB = blastdb
- SRC = blastdb__ blastdb___
-
---- a/c++/src/objects/general/Makefile.general.lib
-+++ b/c++/src/objects/general/Makefile.general.lib
-@@ -1,6 +1,8 @@
- LIB = general
- SRC = general__ general___ uoconv
-
-+DLL_LIB = xser xncbi
-+
-
- USES_LIBRARIES = \
- xser
---- a/c++/src/objects/genomecoll/Makefile.genome_collection.lib
-+++ b/c++/src/objects/genomecoll/Makefile.genome_collection.lib
-@@ -3,6 +3,8 @@
- LIB = genome_collection
- SRC = genome_collection__ genome_collection___
-
-+DLL_LIB = seq general xser xncbi
-+
- WATCHERS = dicuccio
-
-
---- a/c++/src/objects/id1/Makefile.id1.lib
-+++ b/c++/src/objects/id1/Makefile.id1.lib
-@@ -3,6 +3,8 @@ ASN_DEP = seq
- LIB = id1
- SRC = id1__ id1___
-
-+DLL_LIB = seqset seq xser xncbi
-+
- WATCHERS = vasilche
-
-
---- a/c++/src/objects/id2/Makefile.id2.lib
-+++ b/c++/src/objects/id2/Makefile.id2.lib
-@@ -1,6 +1,8 @@
- LIB = id2
- SRC = id2__ id2___
-
-+DLL_LIB = seqsplit seq xser xncbi
-+
- WATCHERS = vasilche
-
-
---- a/c++/src/objects/medline/Makefile.medline.lib
-+++ b/c++/src/objects/medline/Makefile.medline.lib
-@@ -1,6 +1,8 @@
- LIB = medline
- SRC = medline__ medline___
-
-+DLL_LIB = biblio general xser xncbi
-+
-
- USES_LIBRARIES = \
- biblio
---- a/c++/src/objects/pub/Makefile.pub.lib
-+++ b/c++/src/objects/pub/Makefile.pub.lib
-@@ -1,6 +1,8 @@
- LIB = pub
- SRC = pub__ pub___
-
-+DLL_LIB = medline biblio xser xncbi
-+
-
- USES_LIBRARIES = \
- medline
---- a/c++/src/objects/seq/Makefile.seq.lib
-+++ b/c++/src/objects/seq/Makefile.seq.lib
-@@ -12,6 +12,8 @@ SRC = $(ASN:%=%__) $(ASN:%=%___) seqport
- seq_loc_mapper_base seq_align_mapper_base seqlocinfo sofa_map \
- seq_loc_from_string seq_loc_reverse_complementer
-
-+DLL_LIB = seqcode pub biblio general xser sequtil xutil xncbi
-+
- WATCHERS = vasilche grichenk
-
-
---- a/c++/src/objects/seqcode/Makefile.seqcode.lib
-+++ b/c++/src/objects/seqcode/Makefile.seqcode.lib
-@@ -1,6 +1,8 @@
- LIB = seqcode
- SRC = seqcode__ seqcode___
-
-+DLL_LIB = xser xncbi
-+
-
- USES_LIBRARIES = \
- xser
---- a/c++/src/objects/seqset/Makefile.seqset.lib
-+++ b/c++/src/objects/seqset/Makefile.seqset.lib
-@@ -1,6 +1,8 @@
- LIB = seqset
- SRC = seqset__ seqset___ gb_release_file
-
-+DLL_LIB = seq general xser xncbi
-+
-
- USES_LIBRARIES = \
- $(SEQ_LIBS) pub
---- a/c++/src/objects/seqsplit/Makefile.seqsplit.lib
-+++ b/c++/src/objects/seqsplit/Makefile.seqsplit.lib
-@@ -1,6 +1,8 @@
- LIB = seqsplit
- SRC = seqsplit__ seqsplit___
-
-+DLL_LIB = seqset seq xser xncbi
-+
- WATCHERS = vasilche
-
-
---- a/c++/src/serial/Makefile.serial.lib
-+++ b/c++/src/serial/Makefile.serial.lib
-@@ -18,6 +18,8 @@ SRC = \
-
- LIB = xser
-
-+DLL_LIB = xutil xncbi
-+
- WATCHERS = gouriano
-
-
---- a/c++/src/util/Makefile.util.lib
-+++ b/c++/src/util/Makefile.util.lib
-@@ -12,6 +12,7 @@ SRC = random_gen utf8 checksum bytesrc s
- LIB = xutil
- PROJ_TAG = core
-
-+DLL_LIB = xncbi
- LIBS = $(ORIG_LIBS)
-
- WATCHERS = vakatov kornbluh
---- a/c++/src/util/xregexp/Makefile.xregexp.lib
-+++ b/c++/src/util/xregexp/Makefile.xregexp.lib
-@@ -6,7 +6,7 @@ LIB = xregexp
-
- CPPFLAGS = $(ORIG_CPPFLAGS) $(PCRE_INCLUDE)
-
--DLL_LIB = $(PCRE_LIB)
-+DLL_LIB = $(PCRE_LIB) xncbi
- LIBS = $(PCRE_LIBS)
-
- WATCHERS = ivanov
---- a/c++/src/algo/segmask/Makefile.xalgosegmask.lib
-+++ b/c++/src/algo/segmask/Makefile.xalgosegmask.lib
-@@ -8,6 +8,8 @@ LIB = xalgosegmask
-
- SRC = segmask
-
-+DLL_LIB = blast xobjmgr xncbi
-+
- CXXFLAGS = $(FAST_CXXFLAGS)
- LDFLAGS = $(FAST_LDFLAGS)
-
---- a/c++/src/objmgr/split/Makefile.id2_split.lib
-+++ b/c++/src/objmgr/split/Makefile.id2_split.lib
-@@ -17,7 +17,7 @@ LIB = id2_split
-
- CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE)
-
--DLL_LIB = $(SOBJMGR_LIBS)
-+DLL_LIB = xobjmgr seqsplit seqset seq general xser xcompress xncbi
-
- WATCHERS = vasilche
-
---- a/c++/src/objtools/blast/seqdb_writer/Makefile.writedb.lib
-+++ b/c++/src/objtools/blast/seqdb_writer/Makefile.writedb.lib
-@@ -8,6 +8,9 @@ SRC = writedb writedb_impl writedb_volum
-
- LIB = writedb
-
-+DLL_LIB = seqdb xobjread xobjmgr blastdb seqset seq general \
-+ xser sequtil xutil xncbi
-+
- CFLAGS = $(FAST_CFLAGS)
- CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_CPPFLAGS)
- CXXFLAGS = $(FAST_CXXFLAGS)
---- a/c++/src/algo/blast/Makefile.blast_macros.mk
-+++ b/c++/src/algo/blast/Makefile.blast_macros.mk
-@@ -18,7 +18,7 @@ BLAST_INPUT_LIBS = blastinput \
- BLAST_SRA_LIBS=blast_sra $(SRAXF_LIBS) vxf $(SRA_LIBS)
-
- # BLAST_FORMATTER_LIBS and BLAST_INPUT_LIBS need $BLAST_LIBS
--BLAST_LIBS = xblast xalgoblastdbindex composition_adjustment \
-+BLAST_LIBS = xblast xalgoblastdbindex blast composition_adjustment \
- xalgodustmask xalgowinmask seqmasks_io seqdb blast_services xobjutil \
- $(OBJREAD_LIBS) xnetblastcli xnetblast blastdb scoremat tables xalnmgr
- # BLAST additionally needs xconnect $(SOBJMGR_LIBS) or $(OBJMGR_LIBS)
---- a/c++/src/algo/blast/dbindex/makeindex/Makefile.makeindex.app
-+++ b/c++/src/algo/blast/dbindex/makeindex/Makefile.makeindex.app
-@@ -2,7 +2,7 @@ APP = makembindex
- SRC = main mkindex_app
-
- LIB_ = xalgoblastdbindex blast composition_adjustment seqdb blastdb \
-- $(OBJREAD_LIBS) xobjutil tables connect $(SOBJMGR_LIBS)
-+ $(OBJREAD_LIBS) xobjutil tables xconnect $(SOBJMGR_LIBS)
- LIB = $(LIB_:%=%$(STATIC))
-
- CXXFLAGS = $(FAST_CXXFLAGS)
---- a/c++/src/build-system/library_relations.txt
-+++ b/c++/src/build-system/library_relations.txt
-@@ -1189,7 +1189,7 @@ xasmcompare needs $(SEQ_LIBS)
- xasmcompare needs pub
- xasn needs xhtml
- xasn needs3party $(NCBI_C_ncbi)
--xblast includes blast
-+xblast needs blast
- xblast needs xalgoblastdbindex
- xblast needs xalgodustmask
- xblast needs xalgowinmask
diff --git a/sci-biology/ncbi-blast+/metadata.xml b/sci-biology/ncbi-blast+/metadata.xml deleted file mode 100644 index 93556eaa7..000000000 --- a/sci-biology/ncbi-blast+/metadata.xml +++ /dev/null @@ -1,23 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <use> - <flag name="boost">Undocumented USE</flag> - <flag name="cppunit">Undocumented USE</flag> - <flag name="freetype">Undocumented USE</flag> - <flag name="mesa">Undocumented USE</flag> - <flag name="muparser">Undocumented USE</flag> - <flag name="sablotron">Undocumented USE</flag> - <flag name="xerces">Undocumented USE</flag> - <flag name="xalan">Undocumented USE</flag> - <flag name="xslt">Undocumented USE</flag> - </use> -</pkgmetadata> diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.11.0.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.11.0.ebuild deleted file mode 100644 index 623759901..000000000 --- a/sci-biology/ncbi-blast+/ncbi-blast+-2.11.0.ebuild +++ /dev/null @@ -1,361 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7,8,9} ) - -inherit python-single-r1 toolchain-funcs - -MY_P="ncbi-blast-${PV}+-src" -# workdir/ncbi-blast-2.2.30+-src -# ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.30/ncbi-blast-2.2.30+-src.tar.gz -# ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.3.0+-src.tar.gz - -DESCRIPTION="A subset of NCBI C++ Toolkit containing just the NCBI BLAST+" -HOMEPAGE="https://ncbi.github.io/cxx-toolkit/" -SRC_URI=" - ftp://ftp.ncbi.nih.gov/blast/executables/blast+/${PV}/${MY_P}.tar.gz" -# http://dev.gentoo.org/~jlec/distfiles/${PN}-${PV#0.}-asneeded.patch.xz" - -# should also install ftp://ftp.ncbi.nlm.nih.gov/blast/db/taxdb.tar.gz -# see http://www.biostars.org/p/76551/ and http://blastedbio.blogspot.cz/2012/05/blast-tabular-missing-descriptions.html -LICENSE="public-domain" -SLOT="0" -IUSE=" - debug static-libs static threads pch - test wxwidgets odbc - berkdb boost bzip2 cppunit curl expat fltk freetype gif - glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python - sablotron sqlite tiff xerces xalan xml xpm xslt X" -KEYWORDS="~amd64 ~x86" -RESTRICT="!test? ( test )" - -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -# sys-libs/db should be compiled with USE=cxx -DEPEND=" - <sys-devel/gcc-10:= - !sci-biology/ncbi-tools++ - !sci-biology/sra_sdk - berkdb? ( sys-libs/db:=[cxx(-)] ) - boost? ( dev-libs/boost ) - curl? ( net-misc/curl ) - sqlite? ( dev-db/sqlite:3 ) - mysql? ( virtual/mysql ) - fltk? ( x11-libs/fltk ) - opengl? ( virtual/opengl media-libs/glew:0= ) - mesa? ( media-libs/mesa[osmesa] ) - glut? ( media-libs/freeglut ) - freetype? ( media-libs/freetype ) - gnutls? ( net-libs/gnutls ) - python? ( ${PYTHON_DEPS} ) - cppunit? ( dev-util/cppunit ) - icu? ( dev-libs/icu ) - expat? ( dev-libs/expat ) - sablotron? ( app-text/sablotron ) - xml? ( dev-libs/libxml2 ) - xslt? ( dev-libs/libxslt ) - xerces? ( dev-libs/xerces-c ) - xalan? ( dev-libs/xalan-c ) - muparser? ( dev-cpp/muParser ) - hdf5? ( sci-libs/hdf5[cxx] ) - gif? ( media-libs/giflib ) - jpeg? ( virtual/jpeg:0= ) - png? ( media-libs/libpng:0= ) - tiff? ( media-libs/tiff:0= ) - xpm? ( x11-libs/libXpm ) - dev-libs/lzo - app-arch/bzip2 - dev-libs/libpcre - dev-db/lmdb" -# USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC OEChem sge -# Intentionally omitted USE flags: -# ftds? ( dev-db/freetds ) # support for outside FreeTDS installations is currently broken. -# The default (heavily patched) embedded copy should work, or you can -# leave it off altogether -- the only public apps that make use of it are -# samples and tests, since NCBI's database servers are of course firewalled. - -# seems muParser is required, also glew is required. configure exits otherwise if these are explicitly passed to it (due to USE flag enabled) - -RDEPEND="${DEPEND}" - -S="${WORKDIR}/${MY_P}/c++" -# ncbi-blast-2.2.30+-src/c++ - -src_prepare() { -# filter-ldflags -Wl,--as-needed -# append-ldflags -Wl,--no-undefined -# sed -i -e 's/-print-file-name=libstdc++.a//' \ -# -e '/sed/ s/\([gO]\[0-9\]\)\*/\1\\+/' \ -# src/build-system/configure || die -# epatch \ -# "${FILESDIR}"/${PN}-${PV#0.}-fix-order-of-libs.patch \ -# "${FILESDIR}"/curl-types.patch \ -# "${FILESDIR}"/malloc_initialize_upstream_fix.patch \ -# "${FILESDIR}"/respect_CXXFLAGS_configure.ac.patch \ -# "${FILESDIR}"/respect_CXXFLAGS_configure.patch \ -# "${FILESDIR}"/report_project_settings_configure.ac.patch \ -# "${FILESDIR}"/report_project_settings_configure.patch \ -# "${FILESDIR}"/make_install.patch - -# "${FILESDIR}"/${PN}-${PV#0.}-disable_test_compress.patch - -# "${FILESDIR}"/${PN}-${PV#0.}-gcc46.patch \ -# "${FILESDIR}"/${PN}-${PV#0.}-gcc47.patch \ -# "${WORKDIR}"/${PN}-${PV#0.}-asneeded.patch \ -# "${FILESDIR}"/${PN}-${PV#0.}-libpng15.patch \ -# "${FILESDIR}"/${PN}-${PV#0.}-glibc-214.patch - -# use prefix && append-ldflags -Wl,-rpath,"${EPREFIX}/usr/$(get_libdir)/${PN}" - -# The conf-opts.patch and as-needed.patch need to be adjusted for 12.0.0 line numbers -## local PATCHES=( -## "${FILESDIR}"/${P}-conf-opts.patch -## "${FILESDIR}"/${P}-fix-svn-URL-upstream.patch -## "${FILESDIR}"/${P}-linkage-tuneups.patch -## "${FILESDIR}"/${P}-more-patches.patch -## "${FILESDIR}"/${P}-linkage-tuneups-addons.patch -## "${FILESDIR}"/${P}-configure.patch -## "${FILESDIR}"/${P}-drop-STATIC-from-LIB.patch -## "${FILESDIR}"/${P}-fix-install.patch -## ) - # "${FILESDIR}"/${P}-support-autoconf-2.60.patch -## epatch ${PATCHES[@]} - - # use a Debian patch from http://anonscm.debian.org/viewvc/debian-med/trunk/packages/ncbi-blast%2B/trunk/debian/patches/fix_lib_deps?revision=18535&view=markup - # the patches for 2.2.30+ do not apply to 2.2.31, mostly DLL_LIB is gone but somewhere - # it is still present, plus in a few places was something else patched - # staying without any patches for now and lets see is it works on Gentoo - # epatch "${FILESDIR}"/fix_lib_deps.patch - # make sure this one is the last one and contains the actual patches applied unless we can have autoconf-2.59 or 2.60 - # https://bugs.gentoo.org/show_bug.cgi?id=514706 - - tc-export CXX CC - -## cd src/build-system || die -# eautoreconf - - # Temporarily disabling eautoconf because we patch configure via ${P}-support-autoconf-2.60.patch - # eautoconf # keep it disabled until we can ensure 2.59 is installed - # beware 12.0.0. and previous required autoconf-2.59, a patch for 12.0.0 brings autoconf-2.60 support - default -} - -# possibly place modified contents of ${W}/src/build-system/config.site.ncbi and {W}/src/build-system/config.site.ex into ${W}/src/build-system/config.site -src_configure() { - local myconf=() - #--without-optimization turn off optimization flags in non-debug mode - #--with-profiling build profiled versions of libs and apps - #--with-tcheck(=DIR) build for Intel Thread Checker (in DIR) - #--with-plugin-auto-load always enable the plugin manager by default - #--with-bundles build bundles in addition to dylibs on Mac OS X - #--with-bin-release build executables suitable for public release - # no dll and such - #--with-64 compile to 64-bit code - #--with-universal build universal binaries on Mac OS X - #--with-universal=CPUs build universal binaries targeting the given CPUs - #--without-exe do not build executables - #--with-relative-runpath=P specify an executable-relative DLL search path - #--with-hard-runpath hard-code runtime path, ignoring LD_LIBRARY_PATH - #--with-limited-linker don't attempt to build especially large projects - #--with-extra-action= script to call after the configuration is complete - #--with-autodep automatic generation of dependencies (GNU make) - #--with-fake-root=DIR appear to have been built under DIR - #--with-build-root-sfx=X add a user-specified suffix to the build dir name - #--without-execopy do not copy built executables to the BIN area - #--with-lib-rebuilds ensure that apps use up-to-date libraries - #--with-lib-rebuilds=ask ask whether to update each app's libraries - #--without-deactivation keep old copies of libraries that no longer build - #--without-makefile-auto-update do not auto-update generated makefiles - #--with-projects=FILE build projects listed in FILE by default - #--without-flat-makefile do not generate an all-encompassing flat makefile - #--with-configure-dialog allow interactive flat makefile project selection - #--with-saved-settings=F load configuration settings from the file F - #--with-check-tools=... use the specified tools for testing - #--with-ncbi-public ensure compatibility for all in-house platforms - #--with-sybase-local=DIR use local SYBASE install (DIR is optional) - #--with-sybase-new use newer SYBASE install (12.5 rather than 12.0) - #--without-sp do not use SP libraries - #--without-orbacus do not use ORBacus CORBA libraries - #--with-orbacus=DIR use ORBacus installation in DIR - #--with-jni(=JDK-DIR) build Java bindings (against the JDK in JDK-DIR) - #--with-sablot=DIR use Sablotron installation in DIR - #--without-sablot, do not use Sablotron - #--with-oechem=DIR use OpenEye OEChem installation in DIR - #--without-oechem do not use OEChem - #--with-sge=DIR use Sun Grid Engine installation in DIR - #--without-sge do not use Sun Grid Engine - #--with-magic=DIR use libmagic installation in DIR - #--without-magic do not use libmagic - #--without-local-lbsm turn off support for IPC with locally running LBSMD - #--without-ncbi-crypt use a dummy stubbed-out version of ncbi_crypt - #--without-connext do not build non-public CONNECT library extensions - #--without-serial do not build the serialization library and tools - #--without-objects do not generate/build serializeable objects from ASNs - #--without-dbapi do not build database connectivity libraries - #--without-app do not build standalone applications like ID1_FETCH - #--without-gui do not build most graphical projects - #--without-algo do not build CPU-intensive algorithms - #--without-internal do not build internal projects - #--with-gbench ensure that Genome Workbench can be built - #--without-gbench do not build Genome Workbench - myconf+=( - --with-dll - --with-lfs - --with-build-root="${S}"_build - --without-suffix - --without-hostspec - --without-version - --with-bincopy - --without-strip - --without-ccache - --without-distcc -# --with-ncbi-c - --without-ctools -# --with-sss -# --with-sssutils -# --with-sssdb -# --with-included-sss - --with-z="${EPREFIX}/usr" - --with-bz2="${EPREFIX}/usr" - --without-sybase - --with-autodep -# --with-3psw=std:netopt favor standard (system) builds of the above pkgs - $(use_with debug) - $(use_with debug max-debug) - $(use_with debug symbols) - $(use_with static-libs static) - $(use_with static static-exe) - $(use_with threads mt) - $(use_with prefix runpath "${EPREFIX}/usr/$(get_libdir)/${PN}") - $(use_with test check) - $(use_with pch) - $(use_with lzo lzo "${EPREFIX}/usr") - $(use_with pcre pcre "${EPREFIX}/usr") - $(use_with gnutls gnutls "${EPREFIX}/usr") - $(use_with mysql mysql "${EPREFIX}/usr") - $(use_with muparser muparser "${EPREFIX}/usr") - $(usex fltk --with-fltk="${EPREFIX}/usr" "") - $(use_with opengl opengl "${EPREFIX}/usr") - $(use_with mesa mesa "${EPREFIX}/usr") - $(use_with opengl glut "${EPREFIX}/usr") - $(use_with opengl glew "${EPREFIX}/usr") - # - # GLEW 2.0 dropped support for this, see https://bugs.gentoo.org/show_bug.cgi?id=611302 - # $(use_with opengl glew-mx) - $(use_with wxwidgets wxwidgets "${EPREFIX}/usr") - $(use_with wxwidgets wxwidgets-ucs) - $(use_with freetype freetype "${EPREFIX}/usr") -# $(use_with berkdb bdb "${EPREFIX}/usr") # not in ncbi-blast+ - $(usex odbc --with-odbc="${EPREFIX}/usr" "") - $(use_with python python "${EPREFIX}/usr") - $(use_with boost boost "${EPREFIX}/usr") - $(use_with sqlite sqlite3 "${EPREFIX}/usr") - $(use_with icu icu "${EPREFIX}/usr") - $(use_with expat expat "${EPREFIX}/usr") - $(use_with xml libxml "${EPREFIX}/usr") - $(use_with xml libxslt "${EPREFIX}/usr") - $(use_with xerces xerces "${EPREFIX}/usr") - $(use_with hdf5 hdf5 "${EPREFIX}/usr") - $(use_with xalan xalan "${EPREFIX}/usr") -# $(use_with gif gif "${EPREFIX}/usr") # prevent compilation failure in "ncbi-tools++-12.0.0/src/util/image/image_io_gif.cpp:351: error: 'QuantizeBuffer' was not declared in this scope" - --without-gif - $(use_with jpeg jpeg "${EPREFIX}/usr") - $(use_with tiff tiff "${EPREFIX}/usr") - $(use_with png png "${EPREFIX}/usr") - $(use_with xpm xpm "${EPREFIX}/usr") - $(use_with curl curl "${EPREFIX}/usr") -# $(use_with X x "${EPREFIX}/usr") -# $(use_with X x) # there is no --with-x option - # prevent downloading VDB sources from https://github.com/ncbi/ncbi-vdb.git during configure execution - --without-vdb - ) - - # http://www.ncbi.nlm.nih.gov/books/NBK7167/ - use test || myconf+=( --with-projects="${FILESDIR}"/disable-testsuite-compilation.txt ) - - # TODO - # copy optimization -O options from CXXFLAGS to DEF_FAST_FLAGS and pass that also to configure - # otherwise your -O2 will be dropped in some subdirectories and replaced by e.g. -O9 - - einfo "bash ./src/build-system/configure --srcdir="${S}" --prefix="${EPREFIX}/usr" --libdir=/usr/lib64 ${myconf[@]}" - -# ECONF_SOURCE="src/build-system" \ -# econf \ - bash \ - ./src/build-system/configure \ - --srcdir="${S}" \ - --prefix="${EPREFIX}/usr" \ - --libdir=/usr/lib64 \ - --with-flat-makefile \ - ${myconf[@]} || die "Maybe try new src/build-system/cmake/cmake-configure instead?" -#--without-debug \ -# --with-bin-release \ -# --with-bincopy \ -# --without-static \ -# --with-dll \ -# --with-mt \ -# --with-openmp \ -# --with-lfs \ -# --prefix="${ED}"/usr \ -# --libdir="${ED}"/usr/$(get_libdir)/"${PN}" \ -# ${myconf} LDFLAGS="-Wl,--no-as-needed" \ -# || die -# econf ${myconf[@]} -} - -src_compile() { - ## all_r would ignore the --with-projects contents and build more - ## emake all_r -C GCC*-Release*/build || die - ## all_p with compile only selected/required components - ##cd "${S}"_build &&\ - ##emake all_p -C GCC*-Release*/build || die "gcc-4.5.3 crashes at src/objects/valerr/ValidError.cpp:226:1: internal compiler error: Segmentation fault, right?" - #emake all_p -C "${S}"_build/build - - # - # Re: /usr/lib64/ncbi-tools++/libdbapi_driver.so: undefined reference to `ncbi::NcbiGetlineEOL(std::istream&, std::string&)' - # - # The next release should automatically address such underlinking, albeit - # only in --with-flat-makefile configurations. For now (12.0.0), you'll need to - # add or extend more DLL_LIB settings, to which end you may find the - # resources at http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/ - # helpful. For instance, - # - # http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/dbapi_driver.html - # - # indicates that src/dbapi/driver/Makefile.dbapi_driver.lib should set - # - # DLL_LIB = xncbi - # - # (You can find the path to that makefile by examining - # .../status/.dbapi_driver.dep or .../build/Makefile.flat.) - # - # To take full advantage of --with-flat-makefile, you'll need the following (instead of 'emake all_p -C "${S}"_build/build') and call configure --with-flat-makefile: - emake -C "${S}"_build/build -f Makefile.flat -} - -src_install() { - rm -rvf "${S}"_build/lib/ncbi || die - emake install prefix="${ED}/usr" libdir="${ED}/usr/$(get_libdir)/${PN}" - -# dobin "${S}"_build/bin/* -# dolib.so "${S}"_build/lib/*so* -# dolib.a "${S}"_build/lib/*.a -# doheader "${S}"_build/inc/* - - # File collisions with sci-biology/ncbi-tools - mv "${ED}"/usr/bin/asn2asn "${ED}"/usr/bin/asn2asn+ - mv "${ED}"/usr/bin/rpsblast "${ED}"/usr/bin/rpsblast+ - mv -f "${ED}"/usr/bin/test_regexp "${ED}"/usr/bin/test_regexp+ # drop the eventually mistakenly compiled binaries - mv "${ED}"/usr/bin/vecscreen "${ED}"/usr/bin/vecscreen+ - mv "${ED}"/usr/bin/seedtop "${ED}"/usr/bin/seedtop+ - - echo "LDPATH=${EPREFIX}/usr/$(get_libdir)/${PN}" > ${S}/99${PN} - doenvd "${S}/99${PN}" -} - -pkg_postinst() { - einfo 'Please run "source /etc/profile" before using this package in the current shell.' - einfo 'Documentation is at http://www.ncbi.nlm.nih.gov/books/NBK7167/' -} diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild deleted file mode 100644 index d4ae93742..000000000 --- a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild +++ /dev/null @@ -1,351 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit toolchain-funcs - -MY_P="ncbi-blast-${PV}+-src" -# workdir/ncbi-blast-2.2.30+-src -# ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.30/ncbi-blast-2.2.30+-src.tar.gz - -DESCRIPTION="A subset of NCBI C++ Toolkit containing just the NCBI BLAST+" -HOMEPAGE="https://ncbi.github.io/cxx-toolkit/" -SRC_URI=" - ftp://ftp.ncbi.nih.gov/blast/executables/blast+/${PV}/${MY_P}.tar.gz" -# http://dev.gentoo.org/~jlec/distfiles/${PN}-${PV#0.}-asneeded.patch.xz" - -# should also install ftp://ftp.ncbi.nlm.nih.gov/blast/db/taxdb.tar.gz -# see http://www.biostars.org/p/76551/ and http://blastedbio.blogspot.cz/2012/05/blast-tabular-missing-descriptions.html -LICENSE="public-domain" -SLOT="0" -IUSE=" - debug static-libs static threads pch - test wxwidgets odbc - berkdb boost bzip2 cppunit curl expat fltk freetype gif - glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png - sablotron sqlite tiff xerces xalan xml xpm xslt X" -KEYWORDS="~amd64 ~x86" -RESTRICT="!test? ( test )" - -# sys-libs/db should be compiled with USE=cxx -DEPEND=" - <sys-devel/gcc-10:= - !sci-biology/ncbi-tools++ - !sci-biology/sra_sdk - berkdb? ( sys-libs/db:=[cxx(-)] ) - boost? ( dev-libs/boost ) - curl? ( net-misc/curl ) - sqlite? ( dev-db/sqlite:3 ) - mysql? ( virtual/mysql ) - fltk? ( x11-libs/fltk ) - opengl? ( virtual/opengl media-libs/glew:0= ) - mesa? ( media-libs/mesa[osmesa] ) - glut? ( media-libs/freeglut ) - freetype? ( media-libs/freetype ) - gnutls? ( net-libs/gnutls ) - cppunit? ( dev-util/cppunit ) - icu? ( dev-libs/icu ) - expat? ( dev-libs/expat ) - sablotron? ( app-text/sablotron ) - xml? ( dev-libs/libxml2 ) - xslt? ( dev-libs/libxslt ) - xerces? ( dev-libs/xerces-c ) - xalan? ( dev-libs/xalan-c ) - muparser? ( dev-cpp/muParser ) - hdf5? ( sci-libs/hdf5[cxx] ) - gif? ( media-libs/giflib ) - jpeg? ( virtual/jpeg:0= ) - png? ( media-libs/libpng:0= ) - tiff? ( media-libs/tiff:0= ) - xpm? ( x11-libs/libXpm ) - dev-libs/lzo - app-arch/bzip2 - dev-libs/libpcre" -# USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC OEChem sge -# Intentionally omitted USE flags: -# ftds? ( dev-db/freetds ) # support for outside FreeTDS installations is currently broken. -# The default (heavily patched) embedded copy should work, or you can -# leave it off altogether -- the only public apps that make use of it are -# samples and tests, since NCBI's database servers are of course firewalled. - -# seems muParser is required, also glew is required. configure exits otherwise if these are explicitly passed to it (due to USE flag enabled) - -RDEPEND="${DEPEND}" - -S="${WORKDIR}/${MY_P}/c++" -# ncbi-blast-2.2.30+-src/c++ - -PATCHES=( - "${FILESDIR}"/"${P}"__fix_lib_deps.patch -) - -src_prepare() { -# filter-ldflags -Wl,--as-needed -# append-ldflags -Wl,--no-undefined -# sed -i -e 's/-print-file-name=libstdc++.a//' \ -# -e '/sed/ s/\([gO]\[0-9\]\)\*/\1\\+/' \ -# src/build-system/configure || die -# epatch \ -# "${FILESDIR}"/${PN}-${PV#0.}-fix-order-of-libs.patch \ -# "${FILESDIR}"/curl-types.patch \ -# "${FILESDIR}"/malloc_initialize_upstream_fix.patch \ -# "${FILESDIR}"/respect_CXXFLAGS_configure.ac.patch \ -# "${FILESDIR}"/respect_CXXFLAGS_configure.patch \ -# "${FILESDIR}"/report_project_settings_configure.ac.patch \ -# "${FILESDIR}"/report_project_settings_configure.patch \ -# "${FILESDIR}"/make_install.patch - -# "${FILESDIR}"/${PN}-${PV#0.}-disable_test_compress.patch - -# "${FILESDIR}"/${PN}-${PV#0.}-gcc46.patch \ -# "${FILESDIR}"/${PN}-${PV#0.}-gcc47.patch \ -# "${WORKDIR}"/${PN}-${PV#0.}-asneeded.patch \ -# "${FILESDIR}"/${PN}-${PV#0.}-libpng15.patch \ -# "${FILESDIR}"/${PN}-${PV#0.}-glibc-214.patch - -# use prefix && append-ldflags -Wl,-rpath,"${EPREFIX}/usr/$(get_libdir)/${PN}" - -# The conf-opts.patch and as-needed.patch need to be adjusted for 12.0.0 line numbers -## local PATCHES=( -## "${FILESDIR}"/${P}-conf-opts.patch -## "${FILESDIR}"/${P}-fix-svn-URL-upstream.patch -## "${FILESDIR}"/${P}-linkage-tuneups.patch -## "${FILESDIR}"/${P}-more-patches.patch -## "${FILESDIR}"/${P}-linkage-tuneups-addons.patch -## "${FILESDIR}"/${P}-configure.patch -## "${FILESDIR}"/${P}-drop-STATIC-from-LIB.patch -## "${FILESDIR}"/${P}-fix-install.patch -## ) - # "${FILESDIR}"/${P}-support-autoconf-2.60.patch -## epatch ${PATCHES[@]} - - # use a Debian patch from http://anonscm.debian.org/viewvc/debian-med/trunk/packages/ncbi-blast%2B/trunk/debian/patches/fix_lib_deps?revision=18535&view=markup - # make sure this one is the last one and contains the actual patches applied unless we can have autoconf-2.59 or 2.60 - # https://bugs.gentoo.org/show_bug.cgi?id=514706 - - tc-export CXX CC - -## cd src/build-system || die -# eautoreconf - - # Temporarily disabling eautoconf because we patch configure via ${P}-support-autoconf-2.60.patch - # eautoconf # keep it disabled until we can ensure 2.59 is installed - # beware 12.0.0. and previous required autoconf-2.59, a patch for 12.0.0 brings autoconf-2.60 support - default -} - -# possibly place modified contents of ${W}/src/build-system/config.site.ncbi and {W}/src/build-system/config.site.ex into ${W}/src/build-system/config.site -src_configure() { - local myconf=() - #--without-optimization turn off optimization flags in non-debug mode - #--with-profiling build profiled versions of libs and apps - #--with-tcheck(=DIR) build for Intel Thread Checker (in DIR) - #--with-plugin-auto-load always enable the plugin manager by default - #--with-bundles build bundles in addition to dylibs on Mac OS X - #--with-bin-release build executables suitable for public release - # no dll and such - #--with-64 compile to 64-bit code - #--with-universal build universal binaries on Mac OS X - #--with-universal=CPUs build universal binaries targeting the given CPUs - #--without-exe do not build executables - #--with-relative-runpath=P specify an executable-relative DLL search path - #--with-hard-runpath hard-code runtime path, ignoring LD_LIBRARY_PATH - #--with-limited-linker don't attempt to build especially large projects - #--with-extra-action= script to call after the configuration is complete - #--with-autodep automatic generation of dependencies (GNU make) - #--with-fake-root=DIR appear to have been built under DIR - #--with-build-root-sfx=X add a user-specified suffix to the build dir name - #--without-execopy do not copy built executables to the BIN area - #--with-lib-rebuilds ensure that apps use up-to-date libraries - #--with-lib-rebuilds=ask ask whether to update each app's libraries - #--without-deactivation keep old copies of libraries that no longer build - #--without-makefile-auto-update do not auto-update generated makefiles - #--with-projects=FILE build projects listed in FILE by default - #--without-flat-makefile do not generate an all-encompassing flat makefile - #--with-configure-dialog allow interactive flat makefile project selection - #--with-saved-settings=F load configuration settings from the file F - #--with-check-tools=... use the specified tools for testing - #--with-ncbi-public ensure compatibility for all in-house platforms - #--with-sybase-local=DIR use local SYBASE install (DIR is optional) - #--with-sybase-new use newer SYBASE install (12.5 rather than 12.0) - #--without-sp do not use SP libraries - #--without-orbacus do not use ORBacus CORBA libraries - #--with-orbacus=DIR use ORBacus installation in DIR - #--with-jni(=JDK-DIR) build Java bindings (against the JDK in JDK-DIR) - #--with-sablot=DIR use Sablotron installation in DIR - #--without-sablot, do not use Sablotron - #--with-oechem=DIR use OpenEye OEChem installation in DIR - #--without-oechem do not use OEChem - #--with-sge=DIR use Sun Grid Engine installation in DIR - #--without-sge do not use Sun Grid Engine - #--with-magic=DIR use libmagic installation in DIR - #--without-magic do not use libmagic - #--without-local-lbsm turn off support for IPC with locally running LBSMD - #--without-ncbi-crypt use a dummy stubbed-out version of ncbi_crypt - #--without-connext do not build non-public CONNECT library extensions - #--without-serial do not build the serialization library and tools - #--without-objects do not generate/build serializeable objects from ASNs - #--without-dbapi do not build database connectivity libraries - #--without-app do not build standalone applications like ID1_FETCH - #--without-gui do not build most graphical projects - #--without-algo do not build CPU-intensive algorithms - #--without-internal do not build internal projects - #--with-gbench ensure that Genome Workbench can be built - #--without-gbench do not build Genome Workbench - myconf+=( - --with-dll - --with-lfs - --with-build-root="${S}"_build - --without-suffix - --without-hostspec - --without-version - --with-bincopy - --without-strip - --without-ccache - --without-distcc -# --with-ncbi-c - --without-ctools -# --with-sss -# --with-sssutils -# --with-sssdb -# --with-included-sss - --with-z="${EPREFIX}/usr" - --with-bz2="${EPREFIX}/usr" - --without-sybase - --with-autodep -# --with-3psw=std:netopt favor standard (system) builds of the above pkgs - $(use_with debug) - $(use_with debug max-debug) - $(use_with debug symbols) - $(use_with static-libs static) - $(use_with static static-exe) - $(use_with threads mt) - $(use_with prefix runpath "${EPREFIX}/usr/$(get_libdir)/${PN}") - $(use_with test check) - $(use_with pch) - $(use_with lzo lzo "${EPREFIX}/usr") - $(use_with pcre pcre "${EPREFIX}/usr") - $(use_with gnutls gnutls "${EPREFIX}/usr") - $(use_with mysql mysql "${EPREFIX}/usr") - $(use_with muparser muparser "${EPREFIX}/usr") - $(usex fltk --with-fltk="${EPREFIX}/usr" "") - $(use_with opengl opengl "${EPREFIX}/usr") - $(use_with mesa mesa "${EPREFIX}/usr") - $(use_with opengl glut "${EPREFIX}/usr") - $(use_with opengl glew "${EPREFIX}/usr") - $(use_with opengl glew-mx) - $(use_with wxwidgets wxwidgets "${EPREFIX}/usr") - $(use_with wxwidgets wxwidgets-ucs) - $(use_with freetype freetype "${EPREFIX}/usr") -# $(use_with berkdb bdb "${EPREFIX}/usr") # not in ncbi-blast+ - $(usex odbc --with-odbc="${EPREFIX}/usr" "") - # is python2 - --without-python - $(use_with boost boost "${EPREFIX}/usr") - $(use_with sqlite sqlite3 "${EPREFIX}/usr") - $(use_with icu icu "${EPREFIX}/usr") - $(use_with expat expat "${EPREFIX}/usr") - $(use_with xml libxml "${EPREFIX}/usr") - $(use_with xml libxslt "${EPREFIX}/usr") - $(use_with xerces xerces "${EPREFIX}/usr") - $(use_with hdf5 hdf5 "${EPREFIX}/usr") - $(use_with xalan xalan "${EPREFIX}/usr") -# $(use_with gif gif "${EPREFIX}/usr") # prevent compilation failure in "ncbi-tools++-12.0.0/src/util/image/image_io_gif.cpp:351: error: 'QuantizeBuffer' was not declared in this scope" - --without-gif - $(use_with jpeg jpeg "${EPREFIX}/usr") - $(use_with tiff tiff "${EPREFIX}/usr") - $(use_with png png "${EPREFIX}/usr") - $(use_with xpm xpm "${EPREFIX}/usr") - $(use_with curl curl "${EPREFIX}/usr") -# $(use_with X x "${EPREFIX}/usr") -# $(use_with X x) # there is no --with-x option - ) - - # http://www.ncbi.nlm.nih.gov/books/NBK7167/ - use test || myconf+=( --with-projects="${FILESDIR}"/disable-testsuite-compilation.txt ) - - # TODO - # copy optimization -O options from CXXFLAGS to DEF_FAST_FLAGS and pass that also to configure - # otherwise your -O2 will be dropped in some subdirectories and replaced by e.g. -O9 - - einfo "bash ./src/build-system/configure --srcdir="${S}" --prefix="${EPREFIX}/usr" --libdir=/usr/lib64 ${myconf[@]}" - -# ECONF_SOURCE="src/build-system" \ -# econf \ - bash \ - ./src/build-system/configure \ - --srcdir="${S}" \ - --prefix="${EPREFIX}/usr" \ - --libdir=/usr/lib64 \ - --with-flat-makefile \ - ${myconf[@]} || die "gcc 7 or newer were not used by upstream hence unsupported" -#--without-debug \ -# --with-bin-release \ -# --with-bincopy \ -# --without-static \ -# --with-dll \ -# --with-mt \ -# --with-openmp \ -# --with-lfs \ -# --prefix="${ED}"/usr \ -# --libdir="${ED}"/usr/$(get_libdir)/"${PN}" \ -# ${myconf} LDFLAGS="-Wl,--no-as-needed" \ -# || die -# econf ${myconf[@]} -} - -src_compile() { - ## all_r would ignore the --with-projects contents and build more - ## emake all_r -C GCC*-Release*/build || die - ## all_p with compile only selected/required components - ##cd "${S}"_build &&\ - ##emake all_p -C GCC*-Release*/build || die "gcc-4.5.3 crashes at src/objects/valerr/ValidError.cpp:226:1: internal compiler error: Segmentation fault, right?" - #emake all_p -C "${S}"_build/build - - # - # Re: /usr/lib64/ncbi-tools++/libdbapi_driver.so: undefined reference to `ncbi::NcbiGetlineEOL(std::istream&, std::string&)' - # - # The next release should automatically address such underlinking, albeit - # only in --with-flat-makefile configurations. For now (12.0.0), you'll need to - # add or extend more DLL_LIB settings, to which end you may find the - # resources at http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/ - # helpful. For instance, - # - # http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/dbapi_driver.html - # - # indicates that src/dbapi/driver/Makefile.dbapi_driver.lib should set - # - # DLL_LIB = xncbi - # - # (You can find the path to that makefile by examining - # .../status/.dbapi_driver.dep or .../build/Makefile.flat.) - # - # To take full advantage of --with-flat-makefile, you'll need the following (instead of 'emake all_p -C "${S}"_build/build') and call configure --with-flat-makefile: - emake -C "${S}"_build/build -f Makefile.flat -} - -src_install() { - rm -rvf "${S}"_build/lib/ncbi || die - emake install prefix="${ED}/usr" libdir="${ED}/usr/$(get_libdir)/${PN}" - -# dobin "${S}"_build/bin/* -# dolib.so "${S}"_build/lib/*so* -# dolib.a "${S}"_build/lib/*.a -# doheader "${S}"_build/inc/* - - # File collisions with sci-biology/ncbi-tools - mv "${ED}"/usr/bin/asn2asn "${ED}"/usr/bin/asn2asn+ - mv "${ED}"/usr/bin/rpsblast "${ED}"/usr/bin/rpsblast+ - mv -f "${ED}"/usr/bin/test_regexp "${ED}"/usr/bin/test_regexp+ # drop the eventually mistakenly compiled binaries - mv "${ED}"/usr/bin/vecscreen "${ED}"/usr/bin/vecscreen+ - mv "${ED}"/usr/bin/seedtop "${ED}"/usr/bin/seedtop+ - - echo "LDPATH=${EPREFIX}/usr/$(get_libdir)/${PN}" > ${S}/99${PN} - doenvd "${S}/99${PN}" -} - -pkg_postinst() { - einfo 'Please run "source /etc/profile" before using this package in the current shell.' - einfo 'Documentation is at http://www.ncbi.nlm.nih.gov/books/NBK7167/' -} diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild deleted file mode 100644 index f0269f0b5..000000000 --- a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild +++ /dev/null @@ -1,351 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit toolchain-funcs - -MY_P="ncbi-blast-${PV}+-src" -# workdir/ncbi-blast-2.2.30+-src -# ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.30/ncbi-blast-2.2.30+-src.tar.gz - -DESCRIPTION="A subset of NCBI C++ Toolkit containing just the NCBI BLAST+" -HOMEPAGE="https://ncbi.github.io/cxx-toolkit/t" -SRC_URI=" - ftp://ftp.ncbi.nih.gov/blast/executables/blast+/${PV}/${MY_P}.tar.gz" -# http://dev.gentoo.org/~jlec/distfiles/${PN}-${PV#0.}-asneeded.patch.xz" - -# should also install ftp://ftp.ncbi.nlm.nih.gov/blast/db/taxdb.tar.gz -# see http://www.biostars.org/p/76551/ and http://blastedbio.blogspot.cz/2012/05/blast-tabular-missing-descriptions.html -LICENSE="public-domain" -SLOT="0" -IUSE=" - debug static-libs static threads pch - test wxwidgets odbc - berkdb boost bzip2 cppunit curl expat fltk freetype gif - glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png - sablotron sqlite tiff xerces xalan xml xpm xslt X" -KEYWORDS="~amd64 ~x86" -RESTRICT="!test? ( test )" - -# sys-libs/db should be compiled with USE=cxx -DEPEND=" - <sys-devel/gcc-10:= - !sci-biology/ncbi-tools++ - !sci-biology/sra_sdk - berkdb? ( sys-libs/db:=[cxx(-)] ) - boost? ( dev-libs/boost ) - curl? ( net-misc/curl ) - sqlite? ( dev-db/sqlite:3 ) - mysql? ( virtual/mysql ) - fltk? ( x11-libs/fltk ) - opengl? ( virtual/opengl media-libs/glew:0= ) - mesa? ( media-libs/mesa[osmesa] ) - glut? ( media-libs/freeglut ) - freetype? ( media-libs/freetype ) - gnutls? ( net-libs/gnutls ) - cppunit? ( dev-util/cppunit ) - icu? ( dev-libs/icu ) - expat? ( dev-libs/expat ) - sablotron? ( app-text/sablotron ) - xml? ( dev-libs/libxml2 ) - xslt? ( dev-libs/libxslt ) - xerces? ( dev-libs/xerces-c ) - xalan? ( dev-libs/xalan-c ) - muparser? ( dev-cpp/muParser ) - hdf5? ( sci-libs/hdf5[cxx] ) - gif? ( media-libs/giflib ) - jpeg? ( virtual/jpeg:0= ) - png? ( media-libs/libpng:0= ) - tiff? ( media-libs/tiff:0= ) - xpm? ( x11-libs/libXpm ) - dev-libs/lzo - app-arch/bzip2 - dev-libs/libpcre" -# USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC OEChem sge -# Intentionally omitted USE flags: -# ftds? ( dev-db/freetds ) # support for outside FreeTDS installations is currently broken. -# The default (heavily patched) embedded copy should work, or you can -# leave it off altogether -- the only public apps that make use of it are -# samples and tests, since NCBI's database servers are of course firewalled. - -# seems muParser is required, also glew is required. configure exits otherwise if these are explicitly passed to it (due to USE flag enabled) - -RDEPEND="${DEPEND}" - -S="${WORKDIR}/${MY_P}/c++" -# ncbi-blast-2.2.30+-src/c++ - -src_prepare() { -# filter-ldflags -Wl,--as-needed -# append-ldflags -Wl,--no-undefined -# sed -i -e 's/-print-file-name=libstdc++.a//' \ -# -e '/sed/ s/\([gO]\[0-9\]\)\*/\1\\+/' \ -# src/build-system/configure || die -# epatch \ -# "${FILESDIR}"/${PN}-${PV#0.}-fix-order-of-libs.patch \ -# "${FILESDIR}"/curl-types.patch \ -# "${FILESDIR}"/malloc_initialize_upstream_fix.patch \ -# "${FILESDIR}"/respect_CXXFLAGS_configure.ac.patch \ -# "${FILESDIR}"/respect_CXXFLAGS_configure.patch \ -# "${FILESDIR}"/report_project_settings_configure.ac.patch \ -# "${FILESDIR}"/report_project_settings_configure.patch \ -# "${FILESDIR}"/make_install.patch - -# "${FILESDIR}"/${PN}-${PV#0.}-disable_test_compress.patch - -# "${FILESDIR}"/${PN}-${PV#0.}-gcc46.patch \ -# "${FILESDIR}"/${PN}-${PV#0.}-gcc47.patch \ -# "${WORKDIR}"/${PN}-${PV#0.}-asneeded.patch \ -# "${FILESDIR}"/${PN}-${PV#0.}-libpng15.patch \ -# "${FILESDIR}"/${PN}-${PV#0.}-glibc-214.patch - -# use prefix && append-ldflags -Wl,-rpath,"${EPREFIX}/usr/$(get_libdir)/${PN}" - -# The conf-opts.patch and as-needed.patch need to be adjusted for 12.0.0 line numbers -## local PATCHES=( -## "${FILESDIR}"/${P}-conf-opts.patch -## "${FILESDIR}"/${P}-fix-svn-URL-upstream.patch -## "${FILESDIR}"/${P}-linkage-tuneups.patch -## "${FILESDIR}"/${P}-more-patches.patch -## "${FILESDIR}"/${P}-linkage-tuneups-addons.patch -## "${FILESDIR}"/${P}-configure.patch -## "${FILESDIR}"/${P}-drop-STATIC-from-LIB.patch -## "${FILESDIR}"/${P}-fix-install.patch -## ) - # "${FILESDIR}"/${P}-support-autoconf-2.60.patch -## epatch ${PATCHES[@]} - - # use a Debian patch from http://anonscm.debian.org/viewvc/debian-med/trunk/packages/ncbi-blast%2B/trunk/debian/patches/fix_lib_deps?revision=18535&view=markup - # the patches for 2.2.30+ do not apply to 2.2.31, mostly DLL_LIB is gone but somewhere - # it is still present, plus in a few places was something else patched - # staying without any patches for now and lets see is it works on Gentoo - # epatch "${FILESDIR}"/fix_lib_deps.patch - # make sure this one is the last one and contains the actual patches applied unless we can have autoconf-2.59 or 2.60 - # https://bugs.gentoo.org/show_bug.cgi?id=514706 - - tc-export CXX CC - -## cd src/build-system || die -# eautoreconf - - # Temporarily disabling eautoconf because we patch configure via ${P}-support-autoconf-2.60.patch - # eautoconf # keep it disabled until we can ensure 2.59 is installed - # beware 12.0.0. and previous required autoconf-2.59, a patch for 12.0.0 brings autoconf-2.60 support - default -} - -# possibly place modified contents of ${W}/src/build-system/config.site.ncbi and {W}/src/build-system/config.site.ex into ${W}/src/build-system/config.site -src_configure() { - local myconf=() - #--without-optimization turn off optimization flags in non-debug mode - #--with-profiling build profiled versions of libs and apps - #--with-tcheck(=DIR) build for Intel Thread Checker (in DIR) - #--with-plugin-auto-load always enable the plugin manager by default - #--with-bundles build bundles in addition to dylibs on Mac OS X - #--with-bin-release build executables suitable for public release - # no dll and such - #--with-64 compile to 64-bit code - #--with-universal build universal binaries on Mac OS X - #--with-universal=CPUs build universal binaries targeting the given CPUs - #--without-exe do not build executables - #--with-relative-runpath=P specify an executable-relative DLL search path - #--with-hard-runpath hard-code runtime path, ignoring LD_LIBRARY_PATH - #--with-limited-linker don't attempt to build especially large projects - #--with-extra-action= script to call after the configuration is complete - #--with-autodep automatic generation of dependencies (GNU make) - #--with-fake-root=DIR appear to have been built under DIR - #--with-build-root-sfx=X add a user-specified suffix to the build dir name - #--without-execopy do not copy built executables to the BIN area - #--with-lib-rebuilds ensure that apps use up-to-date libraries - #--with-lib-rebuilds=ask ask whether to update each app's libraries - #--without-deactivation keep old copies of libraries that no longer build - #--without-makefile-auto-update do not auto-update generated makefiles - #--with-projects=FILE build projects listed in FILE by default - #--without-flat-makefile do not generate an all-encompassing flat makefile - #--with-configure-dialog allow interactive flat makefile project selection - #--with-saved-settings=F load configuration settings from the file F - #--with-check-tools=... use the specified tools for testing - #--with-ncbi-public ensure compatibility for all in-house platforms - #--with-sybase-local=DIR use local SYBASE install (DIR is optional) - #--with-sybase-new use newer SYBASE install (12.5 rather than 12.0) - #--without-sp do not use SP libraries - #--without-orbacus do not use ORBacus CORBA libraries - #--with-orbacus=DIR use ORBacus installation in DIR - #--with-jni(=JDK-DIR) build Java bindings (against the JDK in JDK-DIR) - #--with-sablot=DIR use Sablotron installation in DIR - #--without-sablot, do not use Sablotron - #--with-oechem=DIR use OpenEye OEChem installation in DIR - #--without-oechem do not use OEChem - #--with-sge=DIR use Sun Grid Engine installation in DIR - #--without-sge do not use Sun Grid Engine - #--with-magic=DIR use libmagic installation in DIR - #--without-magic do not use libmagic - #--without-local-lbsm turn off support for IPC with locally running LBSMD - #--without-ncbi-crypt use a dummy stubbed-out version of ncbi_crypt - #--without-connext do not build non-public CONNECT library extensions - #--without-serial do not build the serialization library and tools - #--without-objects do not generate/build serializeable objects from ASNs - #--without-dbapi do not build database connectivity libraries - #--without-app do not build standalone applications like ID1_FETCH - #--without-gui do not build most graphical projects - #--without-algo do not build CPU-intensive algorithms - #--without-internal do not build internal projects - #--with-gbench ensure that Genome Workbench can be built - #--without-gbench do not build Genome Workbench - myconf+=( - --with-dll - --with-lfs - --with-build-root="${S}"_build - --without-suffix - --without-hostspec - --without-version - --with-bincopy - --without-strip - --without-ccache - --without-distcc -# --with-ncbi-c - --without-ctools -# --with-sss -# --with-sssutils -# --with-sssdb -# --with-included-sss - --with-z="${EPREFIX}/usr" - --with-bz2="${EPREFIX}/usr" - --without-sybase - --with-autodep -# --with-3psw=std:netopt favor standard (system) builds of the above pkgs - $(use_with debug) - $(use_with debug max-debug) - $(use_with debug symbols) - $(use_with static-libs static) - $(use_with static static-exe) - $(use_with threads mt) - $(use_with prefix runpath "${EPREFIX}/usr/$(get_libdir)/${PN}") - $(use_with test check) - $(use_with pch) - $(use_with lzo lzo "${EPREFIX}/usr") - $(use_with pcre pcre "${EPREFIX}/usr") - $(use_with gnutls gnutls "${EPREFIX}/usr") - $(use_with mysql mysql "${EPREFIX}/usr") - $(use_with muparser muparser "${EPREFIX}/usr") - $(usex fltk --with-fltk="${EPREFIX}/usr" "") - $(use_with opengl opengl "${EPREFIX}/usr") - $(use_with mesa mesa "${EPREFIX}/usr") - $(use_with opengl glut "${EPREFIX}/usr") - $(use_with opengl glew "${EPREFIX}/usr") - $(use_with opengl glew-mx) - $(use_with wxwidgets wxwidgets "${EPREFIX}/usr") - $(use_with wxwidgets wxwidgets-ucs) - $(use_with freetype freetype "${EPREFIX}/usr") -# $(use_with berkdb bdb "${EPREFIX}/usr") # not in ncbi-blast+ - $(usex odbc --with-odbc="${EPREFIX}/usr" "") - # is python2 - --without-python - $(use_with boost boost "${EPREFIX}/usr") - $(use_with sqlite sqlite3 "${EPREFIX}/usr") - $(use_with icu icu "${EPREFIX}/usr") - $(use_with expat expat "${EPREFIX}/usr") - $(use_with xml libxml "${EPREFIX}/usr") - $(use_with xml libxslt "${EPREFIX}/usr") - $(use_with xerces xerces "${EPREFIX}/usr") - $(use_with hdf5 hdf5 "${EPREFIX}/usr") - $(use_with xalan xalan "${EPREFIX}/usr") -# $(use_with gif gif "${EPREFIX}/usr") # prevent compilation failure in "ncbi-tools++-12.0.0/src/util/image/image_io_gif.cpp:351: error: 'QuantizeBuffer' was not declared in this scope" - --without-gif - $(use_with jpeg jpeg "${EPREFIX}/usr") - $(use_with tiff tiff "${EPREFIX}/usr") - $(use_with png png "${EPREFIX}/usr") - $(use_with xpm xpm "${EPREFIX}/usr") - $(use_with curl curl "${EPREFIX}/usr") -# $(use_with X x "${EPREFIX}/usr") -# $(use_with X x) # there is no --with-x option - ) - - # http://www.ncbi.nlm.nih.gov/books/NBK7167/ - use test || myconf+=( --with-projects="${FILESDIR}"/disable-testsuite-compilation.txt ) - - # TODO - # copy optimization -O options from CXXFLAGS to DEF_FAST_FLAGS and pass that also to configure - # otherwise your -O2 will be dropped in some subdirectories and replaced by e.g. -O9 - - einfo "bash ./src/build-system/configure --srcdir="${S}" --prefix="${EPREFIX}/usr" --libdir=/usr/lib64 ${myconf[@]}" - -# ECONF_SOURCE="src/build-system" \ -# econf \ - bash \ - ./src/build-system/configure \ - --srcdir="${S}" \ - --prefix="${EPREFIX}/usr" \ - --libdir=/usr/lib64 \ - --with-flat-makefile \ - ${myconf[@]} || die "gcc 7 or newer were not used by upstream hence unsupported" -#--without-debug \ -# --with-bin-release \ -# --with-bincopy \ -# --without-static \ -# --with-dll \ -# --with-mt \ -# --with-openmp \ -# --with-lfs \ -# --prefix="${ED}"/usr \ -# --libdir="${ED}"/usr/$(get_libdir)/"${PN}" \ -# ${myconf} LDFLAGS="-Wl,--no-as-needed" \ -# || die -# econf ${myconf[@]} -} - -src_compile() { - ## all_r would ignore the --with-projects contents and build more - ## emake all_r -C GCC*-Release*/build || die - ## all_p with compile only selected/required components - ##cd "${S}"_build &&\ - ##emake all_p -C GCC*-Release*/build || die "gcc-4.5.3 crashes at src/objects/valerr/ValidError.cpp:226:1: internal compiler error: Segmentation fault, right?" - #emake all_p -C "${S}"_build/build - - # - # Re: /usr/lib64/ncbi-tools++/libdbapi_driver.so: undefined reference to `ncbi::NcbiGetlineEOL(std::istream&, std::string&)' - # - # The next release should automatically address such underlinking, albeit - # only in --with-flat-makefile configurations. For now (12.0.0), you'll need to - # add or extend more DLL_LIB settings, to which end you may find the - # resources at http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/ - # helpful. For instance, - # - # http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/dbapi_driver.html - # - # indicates that src/dbapi/driver/Makefile.dbapi_driver.lib should set - # - # DLL_LIB = xncbi - # - # (You can find the path to that makefile by examining - # .../status/.dbapi_driver.dep or .../build/Makefile.flat.) - # - # To take full advantage of --with-flat-makefile, you'll need the following (instead of 'emake all_p -C "${S}"_build/build') and call configure --with-flat-makefile: - emake -C "${S}"_build/build -f Makefile.flat -} - -src_install() { - rm -rvf "${S}"_build/lib/ncbi || die - emake install prefix="${ED}/usr" libdir="${ED}/usr/$(get_libdir)/${PN}" - -# dobin "${S}"_build/bin/* -# dolib.so "${S}"_build/lib/*so* -# dolib.a "${S}"_build/lib/*.a -# doheader "${S}"_build/inc/* - - # File collisions with sci-biology/ncbi-tools - mv "${ED}"/usr/bin/asn2asn "${ED}"/usr/bin/asn2asn+ - mv "${ED}"/usr/bin/rpsblast "${ED}"/usr/bin/rpsblast+ - mv -f "${ED}"/usr/bin/test_regexp "${ED}"/usr/bin/test_regexp+ # drop the eventually mistakenly compiled binaries - mv "${ED}"/usr/bin/vecscreen "${ED}"/usr/bin/vecscreen+ - mv "${ED}"/usr/bin/seedtop "${ED}"/usr/bin/seedtop+ - - echo "LDPATH=${EPREFIX}/usr/$(get_libdir)/${PN}" > ${S}/99${PN} - doenvd "${S}/99${PN}" -} - -pkg_postinst() { - einfo 'Please run "source /etc/profile" before using this package in the current shell.' - einfo 'Documentation is at http://www.ncbi.nlm.nih.gov/books/NBK7167/' -} diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild deleted file mode 100644 index b232894b4..000000000 --- a/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild +++ /dev/null @@ -1,356 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit toolchain-funcs - -MY_P="ncbi-blast-${PV}+-src" -# workdir/ncbi-blast-2.2.30+-src -# ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.30/ncbi-blast-2.2.30+-src.tar.gz -# ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.3.0+-src.tar.gz - -DESCRIPTION="A subset of NCBI C++ Toolkit containing just the NCBI BLAST+" -HOMEPAGE="https://ncbi.github.io/cxx-toolkit/" -SRC_URI=" - ftp://ftp.ncbi.nih.gov/blast/executables/blast+/${PV}/${MY_P}.tar.gz" -# http://dev.gentoo.org/~jlec/distfiles/${PN}-${PV#0.}-asneeded.patch.xz" - -# should also install ftp://ftp.ncbi.nlm.nih.gov/blast/db/taxdb.tar.gz -# see http://www.biostars.org/p/76551/ and http://blastedbio.blogspot.cz/2012/05/blast-tabular-missing-descriptions.html -LICENSE="public-domain" -SLOT="0" -IUSE=" - debug static-libs static threads pch - test wxwidgets odbc - berkdb boost bzip2 cppunit curl expat fltk freetype gif - glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png - sablotron sqlite tiff xerces xalan xml xpm xslt X" -KEYWORDS="~amd64 ~x86" -RESTRICT="!test? ( test )" - -# sys-libs/db should be compiled with USE=cxx -DEPEND=" - <sys-devel/gcc-10:= - !sci-biology/ncbi-tools++ - !sci-biology/sra_sdk - berkdb? ( sys-libs/db:=[cxx(-)] ) - boost? ( dev-libs/boost ) - curl? ( net-misc/curl ) - sqlite? ( dev-db/sqlite:3 ) - mysql? ( virtual/mysql ) - fltk? ( x11-libs/fltk ) - opengl? ( virtual/opengl media-libs/glew:0= ) - mesa? ( media-libs/mesa[osmesa] ) - glut? ( media-libs/freeglut ) - freetype? ( media-libs/freetype ) - gnutls? ( net-libs/gnutls ) - cppunit? ( dev-util/cppunit ) - icu? ( dev-libs/icu ) - expat? ( dev-libs/expat ) - sablotron? ( app-text/sablotron ) - xml? ( dev-libs/libxml2 ) - xslt? ( dev-libs/libxslt ) - xerces? ( dev-libs/xerces-c ) - xalan? ( dev-libs/xalan-c ) - muparser? ( dev-cpp/muParser ) - hdf5? ( sci-libs/hdf5[cxx] ) - gif? ( media-libs/giflib ) - jpeg? ( virtual/jpeg:0= ) - png? ( media-libs/libpng:0= ) - tiff? ( media-libs/tiff:0= ) - xpm? ( x11-libs/libXpm ) - dev-libs/lzo - app-arch/bzip2 - dev-libs/libpcre" -# USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC OEChem sge -# Intentionally omitted USE flags: -# ftds? ( dev-db/freetds ) # support for outside FreeTDS installations is currently broken. -# The default (heavily patched) embedded copy should work, or you can -# leave it off altogether -- the only public apps that make use of it are -# samples and tests, since NCBI's database servers are of course firewalled. - -# seems muParser is required, also glew is required. configure exits otherwise if these are explicitly passed to it (due to USE flag enabled) - -RDEPEND="${DEPEND}" - -S="${WORKDIR}/${MY_P}/c++" -# ncbi-blast-2.2.30+-src/c++ - -src_prepare() { -# filter-ldflags -Wl,--as-needed -# append-ldflags -Wl,--no-undefined -# sed -i -e 's/-print-file-name=libstdc++.a//' \ -# -e '/sed/ s/\([gO]\[0-9\]\)\*/\1\\+/' \ -# src/build-system/configure || die -# epatch \ -# "${FILESDIR}"/${PN}-${PV#0.}-fix-order-of-libs.patch \ -# "${FILESDIR}"/curl-types.patch \ -# "${FILESDIR}"/malloc_initialize_upstream_fix.patch \ -# "${FILESDIR}"/respect_CXXFLAGS_configure.ac.patch \ -# "${FILESDIR}"/respect_CXXFLAGS_configure.patch \ -# "${FILESDIR}"/report_project_settings_configure.ac.patch \ -# "${FILESDIR}"/report_project_settings_configure.patch \ -# "${FILESDIR}"/make_install.patch - -# "${FILESDIR}"/${PN}-${PV#0.}-disable_test_compress.patch - -# "${FILESDIR}"/${PN}-${PV#0.}-gcc46.patch \ -# "${FILESDIR}"/${PN}-${PV#0.}-gcc47.patch \ -# "${WORKDIR}"/${PN}-${PV#0.}-asneeded.patch \ -# "${FILESDIR}"/${PN}-${PV#0.}-libpng15.patch \ -# "${FILESDIR}"/${PN}-${PV#0.}-glibc-214.patch - -# use prefix && append-ldflags -Wl,-rpath,"${EPREFIX}/usr/$(get_libdir)/${PN}" - -# The conf-opts.patch and as-needed.patch need to be adjusted for 12.0.0 line numbers -## local PATCHES=( -## "${FILESDIR}"/${P}-conf-opts.patch -## "${FILESDIR}"/${P}-fix-svn-URL-upstream.patch -## "${FILESDIR}"/${P}-linkage-tuneups.patch -## "${FILESDIR}"/${P}-more-patches.patch -## "${FILESDIR}"/${P}-linkage-tuneups-addons.patch -## "${FILESDIR}"/${P}-configure.patch -## "${FILESDIR}"/${P}-drop-STATIC-from-LIB.patch -## "${FILESDIR}"/${P}-fix-install.patch -## ) - # "${FILESDIR}"/${P}-support-autoconf-2.60.patch -## epatch ${PATCHES[@]} - - # use a Debian patch from http://anonscm.debian.org/viewvc/debian-med/trunk/packages/ncbi-blast%2B/trunk/debian/patches/fix_lib_deps?revision=18535&view=markup - # the patches for 2.2.30+ do not apply to 2.2.31, mostly DLL_LIB is gone but somewhere - # it is still present, plus in a few places was something else patched - # staying without any patches for now and lets see is it works on Gentoo - # epatch "${FILESDIR}"/fix_lib_deps.patch - # make sure this one is the last one and contains the actual patches applied unless we can have autoconf-2.59 or 2.60 - # https://bugs.gentoo.org/show_bug.cgi?id=514706 - - tc-export CXX CC - -## cd src/build-system || die -# eautoreconf - - # Temporarily disabling eautoconf because we patch configure via ${P}-support-autoconf-2.60.patch - # eautoconf # keep it disabled until we can ensure 2.59 is installed - # beware 12.0.0. and previous required autoconf-2.59, a patch for 12.0.0 brings autoconf-2.60 support - default -} - -# possibly place modified contents of ${W}/src/build-system/config.site.ncbi and {W}/src/build-system/config.site.ex into ${W}/src/build-system/config.site -src_configure() { - local myconf=() - #--without-optimization turn off optimization flags in non-debug mode - #--with-profiling build profiled versions of libs and apps - #--with-tcheck(=DIR) build for Intel Thread Checker (in DIR) - #--with-plugin-auto-load always enable the plugin manager by default - #--with-bundles build bundles in addition to dylibs on Mac OS X - #--with-bin-release build executables suitable for public release - # no dll and such - #--with-64 compile to 64-bit code - #--with-universal build universal binaries on Mac OS X - #--with-universal=CPUs build universal binaries targeting the given CPUs - #--without-exe do not build executables - #--with-relative-runpath=P specify an executable-relative DLL search path - #--with-hard-runpath hard-code runtime path, ignoring LD_LIBRARY_PATH - #--with-limited-linker don't attempt to build especially large projects - #--with-extra-action= script to call after the configuration is complete - #--with-autodep automatic generation of dependencies (GNU make) - #--with-fake-root=DIR appear to have been built under DIR - #--with-build-root-sfx=X add a user-specified suffix to the build dir name - #--without-execopy do not copy built executables to the BIN area - #--with-lib-rebuilds ensure that apps use up-to-date libraries - #--with-lib-rebuilds=ask ask whether to update each app's libraries - #--without-deactivation keep old copies of libraries that no longer build - #--without-makefile-auto-update do not auto-update generated makefiles - #--with-projects=FILE build projects listed in FILE by default - #--without-flat-makefile do not generate an all-encompassing flat makefile - #--with-configure-dialog allow interactive flat makefile project selection - #--with-saved-settings=F load configuration settings from the file F - #--with-check-tools=... use the specified tools for testing - #--with-ncbi-public ensure compatibility for all in-house platforms - #--with-sybase-local=DIR use local SYBASE install (DIR is optional) - #--with-sybase-new use newer SYBASE install (12.5 rather than 12.0) - #--without-sp do not use SP libraries - #--without-orbacus do not use ORBacus CORBA libraries - #--with-orbacus=DIR use ORBacus installation in DIR - #--with-jni(=JDK-DIR) build Java bindings (against the JDK in JDK-DIR) - #--with-sablot=DIR use Sablotron installation in DIR - #--without-sablot, do not use Sablotron - #--with-oechem=DIR use OpenEye OEChem installation in DIR - #--without-oechem do not use OEChem - #--with-sge=DIR use Sun Grid Engine installation in DIR - #--without-sge do not use Sun Grid Engine - #--with-magic=DIR use libmagic installation in DIR - #--without-magic do not use libmagic - #--without-local-lbsm turn off support for IPC with locally running LBSMD - #--without-ncbi-crypt use a dummy stubbed-out version of ncbi_crypt - #--without-connext do not build non-public CONNECT library extensions - #--without-serial do not build the serialization library and tools - #--without-objects do not generate/build serializeable objects from ASNs - #--without-dbapi do not build database connectivity libraries - #--without-app do not build standalone applications like ID1_FETCH - #--without-gui do not build most graphical projects - #--without-algo do not build CPU-intensive algorithms - #--without-internal do not build internal projects - #--with-gbench ensure that Genome Workbench can be built - #--without-gbench do not build Genome Workbench - myconf+=( - --with-dll - --with-lfs - --with-build-root="${S}"_build - --without-suffix - --without-hostspec - --without-version - --with-bincopy - --without-strip - --without-ccache - --without-distcc -# --with-ncbi-c - --without-ctools -# --with-sss -# --with-sssutils -# --with-sssdb -# --with-included-sss - --with-z="${EPREFIX}/usr" - --with-bz2="${EPREFIX}/usr" - --without-sybase - --with-autodep -# --with-3psw=std:netopt favor standard (system) builds of the above pkgs - $(use_with debug) - $(use_with debug max-debug) - $(use_with debug symbols) - $(use_with static-libs static) - $(use_with static static-exe) - $(use_with threads mt) - $(use_with prefix runpath "${EPREFIX}/usr/$(get_libdir)/${PN}") - $(use_with test check) - $(use_with pch) - $(use_with lzo lzo "${EPREFIX}/usr") - $(use_with pcre pcre "${EPREFIX}/usr") - $(use_with gnutls gnutls "${EPREFIX}/usr") - $(use_with mysql mysql "${EPREFIX}/usr") - $(use_with muparser muparser "${EPREFIX}/usr") - $(usex fltk --with-fltk="${EPREFIX}/usr" "") - $(use_with opengl opengl "${EPREFIX}/usr") - $(use_with mesa mesa "${EPREFIX}/usr") - $(use_with opengl glut "${EPREFIX}/usr") - $(use_with opengl glew "${EPREFIX}/usr") - # - # GLEW 2.0 dropped support for this, see https://bugs.gentoo.org/show_bug.cgi?id=611302 - # $(use_with opengl glew-mx) - $(use_with wxwidgets wxwidgets "${EPREFIX}/usr") - $(use_with wxwidgets wxwidgets-ucs) - $(use_with freetype freetype "${EPREFIX}/usr") -# $(use_with berkdb bdb "${EPREFIX}/usr") # not in ncbi-blast+ - $(usex odbc --with-odbc="${EPREFIX}/usr" "") - # is python2 - --without-python - $(use_with boost boost "${EPREFIX}/usr") - $(use_with sqlite sqlite3 "${EPREFIX}/usr") - $(use_with icu icu "${EPREFIX}/usr") - $(use_with expat expat "${EPREFIX}/usr") - $(use_with xml libxml "${EPREFIX}/usr") - $(use_with xml libxslt "${EPREFIX}/usr") - $(use_with xerces xerces "${EPREFIX}/usr") - $(use_with hdf5 hdf5 "${EPREFIX}/usr") - $(use_with xalan xalan "${EPREFIX}/usr") -# $(use_with gif gif "${EPREFIX}/usr") # prevent compilation failure in "ncbi-tools++-12.0.0/src/util/image/image_io_gif.cpp:351: error: 'QuantizeBuffer' was not declared in this scope" - --without-gif - $(use_with jpeg jpeg "${EPREFIX}/usr") - $(use_with tiff tiff "${EPREFIX}/usr") - $(use_with png png "${EPREFIX}/usr") - $(use_with xpm xpm "${EPREFIX}/usr") - $(use_with curl curl "${EPREFIX}/usr") -# $(use_with X x "${EPREFIX}/usr") -# $(use_with X x) # there is no --with-x option - # prevent downloading VDB sources from https://github.com/ncbi/ncbi-vdb.git during configure execution - --without-vdb - ) - - # http://www.ncbi.nlm.nih.gov/books/NBK7167/ - use test || myconf+=( --with-projects="${FILESDIR}"/disable-testsuite-compilation.txt ) - - # TODO - # copy optimization -O options from CXXFLAGS to DEF_FAST_FLAGS and pass that also to configure - # otherwise your -O2 will be dropped in some subdirectories and replaced by e.g. -O9 - - einfo "bash ./src/build-system/configure --srcdir="${S}" --prefix="${EPREFIX}/usr" --libdir=/usr/lib64 ${myconf[@]}" - -# ECONF_SOURCE="src/build-system" \ -# econf \ - bash \ - ./src/build-system/configure \ - --srcdir="${S}" \ - --prefix="${EPREFIX}/usr" \ - --libdir=/usr/lib64 \ - --with-flat-makefile \ - ${myconf[@]} || die -#--without-debug \ -# --with-bin-release \ -# --with-bincopy \ -# --without-static \ -# --with-dll \ -# --with-mt \ -# --with-openmp \ -# --with-lfs \ -# --prefix="${ED}"/usr \ -# --libdir="${ED}"/usr/$(get_libdir)/"${PN}" \ -# ${myconf} LDFLAGS="-Wl,--no-as-needed" \ -# || die -# econf ${myconf[@]} -} - -src_compile() { - ## all_r would ignore the --with-projects contents and build more - ## emake all_r -C GCC*-Release*/build || die - ## all_p with compile only selected/required components - ##cd "${S}"_build &&\ - ##emake all_p -C GCC*-Release*/build || die "gcc-4.5.3 crashes at src/objects/valerr/ValidError.cpp:226:1: internal compiler error: Segmentation fault, right?" - #emake all_p -C "${S}"_build/build - - # - # Re: /usr/lib64/ncbi-tools++/libdbapi_driver.so: undefined reference to `ncbi::NcbiGetlineEOL(std::istream&, std::string&)' - # - # The next release should automatically address such underlinking, albeit - # only in --with-flat-makefile configurations. For now (12.0.0), you'll need to - # add or extend more DLL_LIB settings, to which end you may find the - # resources at http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/ - # helpful. For instance, - # - # http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/dbapi_driver.html - # - # indicates that src/dbapi/driver/Makefile.dbapi_driver.lib should set - # - # DLL_LIB = xncbi - # - # (You can find the path to that makefile by examining - # .../status/.dbapi_driver.dep or .../build/Makefile.flat.) - # - # To take full advantage of --with-flat-makefile, you'll need the following (instead of 'emake all_p -C "${S}"_build/build') and call configure --with-flat-makefile: - emake -C "${S}"_build/build -f Makefile.flat -} - -src_install() { - rm -rvf "${S}"_build/lib/ncbi || die - emake install prefix="${ED}/usr" libdir="${ED}/usr/$(get_libdir)/${PN}" - -# dobin "${S}"_build/bin/* -# dolib.so "${S}"_build/lib/*so* -# dolib.a "${S}"_build/lib/*.a -# doheader "${S}"_build/inc/* - - # File collisions with sci-biology/ncbi-tools - mv "${ED}"/usr/bin/asn2asn "${ED}"/usr/bin/asn2asn+ - mv "${ED}"/usr/bin/rpsblast "${ED}"/usr/bin/rpsblast+ - mv -f "${ED}"/usr/bin/test_regexp "${ED}"/usr/bin/test_regexp+ # drop the eventually mistakenly compiled binaries - mv "${ED}"/usr/bin/vecscreen "${ED}"/usr/bin/vecscreen+ - mv "${ED}"/usr/bin/seedtop "${ED}"/usr/bin/seedtop+ - - echo "LDPATH=${EPREFIX}/usr/$(get_libdir)/${PN}" > ${S}/99${PN} - doenvd "${S}/99${PN}" -} - -pkg_postinst() { - einfo 'Please run "source /etc/profile" before using this package in the current shell.' - einfo 'Documentation is at http://www.ncbi.nlm.nih.gov/books/NBK7167/' -} diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild deleted file mode 100644 index 623759901..000000000 --- a/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild +++ /dev/null @@ -1,361 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7,8,9} ) - -inherit python-single-r1 toolchain-funcs - -MY_P="ncbi-blast-${PV}+-src" -# workdir/ncbi-blast-2.2.30+-src -# ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.30/ncbi-blast-2.2.30+-src.tar.gz -# ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.3.0+-src.tar.gz - -DESCRIPTION="A subset of NCBI C++ Toolkit containing just the NCBI BLAST+" -HOMEPAGE="https://ncbi.github.io/cxx-toolkit/" -SRC_URI=" - ftp://ftp.ncbi.nih.gov/blast/executables/blast+/${PV}/${MY_P}.tar.gz" -# http://dev.gentoo.org/~jlec/distfiles/${PN}-${PV#0.}-asneeded.patch.xz" - -# should also install ftp://ftp.ncbi.nlm.nih.gov/blast/db/taxdb.tar.gz -# see http://www.biostars.org/p/76551/ and http://blastedbio.blogspot.cz/2012/05/blast-tabular-missing-descriptions.html -LICENSE="public-domain" -SLOT="0" -IUSE=" - debug static-libs static threads pch - test wxwidgets odbc - berkdb boost bzip2 cppunit curl expat fltk freetype gif - glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python - sablotron sqlite tiff xerces xalan xml xpm xslt X" -KEYWORDS="~amd64 ~x86" -RESTRICT="!test? ( test )" - -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -# sys-libs/db should be compiled with USE=cxx -DEPEND=" - <sys-devel/gcc-10:= - !sci-biology/ncbi-tools++ - !sci-biology/sra_sdk - berkdb? ( sys-libs/db:=[cxx(-)] ) - boost? ( dev-libs/boost ) - curl? ( net-misc/curl ) - sqlite? ( dev-db/sqlite:3 ) - mysql? ( virtual/mysql ) - fltk? ( x11-libs/fltk ) - opengl? ( virtual/opengl media-libs/glew:0= ) - mesa? ( media-libs/mesa[osmesa] ) - glut? ( media-libs/freeglut ) - freetype? ( media-libs/freetype ) - gnutls? ( net-libs/gnutls ) - python? ( ${PYTHON_DEPS} ) - cppunit? ( dev-util/cppunit ) - icu? ( dev-libs/icu ) - expat? ( dev-libs/expat ) - sablotron? ( app-text/sablotron ) - xml? ( dev-libs/libxml2 ) - xslt? ( dev-libs/libxslt ) - xerces? ( dev-libs/xerces-c ) - xalan? ( dev-libs/xalan-c ) - muparser? ( dev-cpp/muParser ) - hdf5? ( sci-libs/hdf5[cxx] ) - gif? ( media-libs/giflib ) - jpeg? ( virtual/jpeg:0= ) - png? ( media-libs/libpng:0= ) - tiff? ( media-libs/tiff:0= ) - xpm? ( x11-libs/libXpm ) - dev-libs/lzo - app-arch/bzip2 - dev-libs/libpcre - dev-db/lmdb" -# USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC OEChem sge -# Intentionally omitted USE flags: -# ftds? ( dev-db/freetds ) # support for outside FreeTDS installations is currently broken. -# The default (heavily patched) embedded copy should work, or you can -# leave it off altogether -- the only public apps that make use of it are -# samples and tests, since NCBI's database servers are of course firewalled. - -# seems muParser is required, also glew is required. configure exits otherwise if these are explicitly passed to it (due to USE flag enabled) - -RDEPEND="${DEPEND}" - -S="${WORKDIR}/${MY_P}/c++" -# ncbi-blast-2.2.30+-src/c++ - -src_prepare() { -# filter-ldflags -Wl,--as-needed -# append-ldflags -Wl,--no-undefined -# sed -i -e 's/-print-file-name=libstdc++.a//' \ -# -e '/sed/ s/\([gO]\[0-9\]\)\*/\1\\+/' \ -# src/build-system/configure || die -# epatch \ -# "${FILESDIR}"/${PN}-${PV#0.}-fix-order-of-libs.patch \ -# "${FILESDIR}"/curl-types.patch \ -# "${FILESDIR}"/malloc_initialize_upstream_fix.patch \ -# "${FILESDIR}"/respect_CXXFLAGS_configure.ac.patch \ -# "${FILESDIR}"/respect_CXXFLAGS_configure.patch \ -# "${FILESDIR}"/report_project_settings_configure.ac.patch \ -# "${FILESDIR}"/report_project_settings_configure.patch \ -# "${FILESDIR}"/make_install.patch - -# "${FILESDIR}"/${PN}-${PV#0.}-disable_test_compress.patch - -# "${FILESDIR}"/${PN}-${PV#0.}-gcc46.patch \ -# "${FILESDIR}"/${PN}-${PV#0.}-gcc47.patch \ -# "${WORKDIR}"/${PN}-${PV#0.}-asneeded.patch \ -# "${FILESDIR}"/${PN}-${PV#0.}-libpng15.patch \ -# "${FILESDIR}"/${PN}-${PV#0.}-glibc-214.patch - -# use prefix && append-ldflags -Wl,-rpath,"${EPREFIX}/usr/$(get_libdir)/${PN}" - -# The conf-opts.patch and as-needed.patch need to be adjusted for 12.0.0 line numbers -## local PATCHES=( -## "${FILESDIR}"/${P}-conf-opts.patch -## "${FILESDIR}"/${P}-fix-svn-URL-upstream.patch -## "${FILESDIR}"/${P}-linkage-tuneups.patch -## "${FILESDIR}"/${P}-more-patches.patch -## "${FILESDIR}"/${P}-linkage-tuneups-addons.patch -## "${FILESDIR}"/${P}-configure.patch -## "${FILESDIR}"/${P}-drop-STATIC-from-LIB.patch -## "${FILESDIR}"/${P}-fix-install.patch -## ) - # "${FILESDIR}"/${P}-support-autoconf-2.60.patch -## epatch ${PATCHES[@]} - - # use a Debian patch from http://anonscm.debian.org/viewvc/debian-med/trunk/packages/ncbi-blast%2B/trunk/debian/patches/fix_lib_deps?revision=18535&view=markup - # the patches for 2.2.30+ do not apply to 2.2.31, mostly DLL_LIB is gone but somewhere - # it is still present, plus in a few places was something else patched - # staying without any patches for now and lets see is it works on Gentoo - # epatch "${FILESDIR}"/fix_lib_deps.patch - # make sure this one is the last one and contains the actual patches applied unless we can have autoconf-2.59 or 2.60 - # https://bugs.gentoo.org/show_bug.cgi?id=514706 - - tc-export CXX CC - -## cd src/build-system || die -# eautoreconf - - # Temporarily disabling eautoconf because we patch configure via ${P}-support-autoconf-2.60.patch - # eautoconf # keep it disabled until we can ensure 2.59 is installed - # beware 12.0.0. and previous required autoconf-2.59, a patch for 12.0.0 brings autoconf-2.60 support - default -} - -# possibly place modified contents of ${W}/src/build-system/config.site.ncbi and {W}/src/build-system/config.site.ex into ${W}/src/build-system/config.site -src_configure() { - local myconf=() - #--without-optimization turn off optimization flags in non-debug mode - #--with-profiling build profiled versions of libs and apps - #--with-tcheck(=DIR) build for Intel Thread Checker (in DIR) - #--with-plugin-auto-load always enable the plugin manager by default - #--with-bundles build bundles in addition to dylibs on Mac OS X - #--with-bin-release build executables suitable for public release - # no dll and such - #--with-64 compile to 64-bit code - #--with-universal build universal binaries on Mac OS X - #--with-universal=CPUs build universal binaries targeting the given CPUs - #--without-exe do not build executables - #--with-relative-runpath=P specify an executable-relative DLL search path - #--with-hard-runpath hard-code runtime path, ignoring LD_LIBRARY_PATH - #--with-limited-linker don't attempt to build especially large projects - #--with-extra-action= script to call after the configuration is complete - #--with-autodep automatic generation of dependencies (GNU make) - #--with-fake-root=DIR appear to have been built under DIR - #--with-build-root-sfx=X add a user-specified suffix to the build dir name - #--without-execopy do not copy built executables to the BIN area - #--with-lib-rebuilds ensure that apps use up-to-date libraries - #--with-lib-rebuilds=ask ask whether to update each app's libraries - #--without-deactivation keep old copies of libraries that no longer build - #--without-makefile-auto-update do not auto-update generated makefiles - #--with-projects=FILE build projects listed in FILE by default - #--without-flat-makefile do not generate an all-encompassing flat makefile - #--with-configure-dialog allow interactive flat makefile project selection - #--with-saved-settings=F load configuration settings from the file F - #--with-check-tools=... use the specified tools for testing - #--with-ncbi-public ensure compatibility for all in-house platforms - #--with-sybase-local=DIR use local SYBASE install (DIR is optional) - #--with-sybase-new use newer SYBASE install (12.5 rather than 12.0) - #--without-sp do not use SP libraries - #--without-orbacus do not use ORBacus CORBA libraries - #--with-orbacus=DIR use ORBacus installation in DIR - #--with-jni(=JDK-DIR) build Java bindings (against the JDK in JDK-DIR) - #--with-sablot=DIR use Sablotron installation in DIR - #--without-sablot, do not use Sablotron - #--with-oechem=DIR use OpenEye OEChem installation in DIR - #--without-oechem do not use OEChem - #--with-sge=DIR use Sun Grid Engine installation in DIR - #--without-sge do not use Sun Grid Engine - #--with-magic=DIR use libmagic installation in DIR - #--without-magic do not use libmagic - #--without-local-lbsm turn off support for IPC with locally running LBSMD - #--without-ncbi-crypt use a dummy stubbed-out version of ncbi_crypt - #--without-connext do not build non-public CONNECT library extensions - #--without-serial do not build the serialization library and tools - #--without-objects do not generate/build serializeable objects from ASNs - #--without-dbapi do not build database connectivity libraries - #--without-app do not build standalone applications like ID1_FETCH - #--without-gui do not build most graphical projects - #--without-algo do not build CPU-intensive algorithms - #--without-internal do not build internal projects - #--with-gbench ensure that Genome Workbench can be built - #--without-gbench do not build Genome Workbench - myconf+=( - --with-dll - --with-lfs - --with-build-root="${S}"_build - --without-suffix - --without-hostspec - --without-version - --with-bincopy - --without-strip - --without-ccache - --without-distcc -# --with-ncbi-c - --without-ctools -# --with-sss -# --with-sssutils -# --with-sssdb -# --with-included-sss - --with-z="${EPREFIX}/usr" - --with-bz2="${EPREFIX}/usr" - --without-sybase - --with-autodep -# --with-3psw=std:netopt favor standard (system) builds of the above pkgs - $(use_with debug) - $(use_with debug max-debug) - $(use_with debug symbols) - $(use_with static-libs static) - $(use_with static static-exe) - $(use_with threads mt) - $(use_with prefix runpath "${EPREFIX}/usr/$(get_libdir)/${PN}") - $(use_with test check) - $(use_with pch) - $(use_with lzo lzo "${EPREFIX}/usr") - $(use_with pcre pcre "${EPREFIX}/usr") - $(use_with gnutls gnutls "${EPREFIX}/usr") - $(use_with mysql mysql "${EPREFIX}/usr") - $(use_with muparser muparser "${EPREFIX}/usr") - $(usex fltk --with-fltk="${EPREFIX}/usr" "") - $(use_with opengl opengl "${EPREFIX}/usr") - $(use_with mesa mesa "${EPREFIX}/usr") - $(use_with opengl glut "${EPREFIX}/usr") - $(use_with opengl glew "${EPREFIX}/usr") - # - # GLEW 2.0 dropped support for this, see https://bugs.gentoo.org/show_bug.cgi?id=611302 - # $(use_with opengl glew-mx) - $(use_with wxwidgets wxwidgets "${EPREFIX}/usr") - $(use_with wxwidgets wxwidgets-ucs) - $(use_with freetype freetype "${EPREFIX}/usr") -# $(use_with berkdb bdb "${EPREFIX}/usr") # not in ncbi-blast+ - $(usex odbc --with-odbc="${EPREFIX}/usr" "") - $(use_with python python "${EPREFIX}/usr") - $(use_with boost boost "${EPREFIX}/usr") - $(use_with sqlite sqlite3 "${EPREFIX}/usr") - $(use_with icu icu "${EPREFIX}/usr") - $(use_with expat expat "${EPREFIX}/usr") - $(use_with xml libxml "${EPREFIX}/usr") - $(use_with xml libxslt "${EPREFIX}/usr") - $(use_with xerces xerces "${EPREFIX}/usr") - $(use_with hdf5 hdf5 "${EPREFIX}/usr") - $(use_with xalan xalan "${EPREFIX}/usr") -# $(use_with gif gif "${EPREFIX}/usr") # prevent compilation failure in "ncbi-tools++-12.0.0/src/util/image/image_io_gif.cpp:351: error: 'QuantizeBuffer' was not declared in this scope" - --without-gif - $(use_with jpeg jpeg "${EPREFIX}/usr") - $(use_with tiff tiff "${EPREFIX}/usr") - $(use_with png png "${EPREFIX}/usr") - $(use_with xpm xpm "${EPREFIX}/usr") - $(use_with curl curl "${EPREFIX}/usr") -# $(use_with X x "${EPREFIX}/usr") -# $(use_with X x) # there is no --with-x option - # prevent downloading VDB sources from https://github.com/ncbi/ncbi-vdb.git during configure execution - --without-vdb - ) - - # http://www.ncbi.nlm.nih.gov/books/NBK7167/ - use test || myconf+=( --with-projects="${FILESDIR}"/disable-testsuite-compilation.txt ) - - # TODO - # copy optimization -O options from CXXFLAGS to DEF_FAST_FLAGS and pass that also to configure - # otherwise your -O2 will be dropped in some subdirectories and replaced by e.g. -O9 - - einfo "bash ./src/build-system/configure --srcdir="${S}" --prefix="${EPREFIX}/usr" --libdir=/usr/lib64 ${myconf[@]}" - -# ECONF_SOURCE="src/build-system" \ -# econf \ - bash \ - ./src/build-system/configure \ - --srcdir="${S}" \ - --prefix="${EPREFIX}/usr" \ - --libdir=/usr/lib64 \ - --with-flat-makefile \ - ${myconf[@]} || die "Maybe try new src/build-system/cmake/cmake-configure instead?" -#--without-debug \ -# --with-bin-release \ -# --with-bincopy \ -# --without-static \ -# --with-dll \ -# --with-mt \ -# --with-openmp \ -# --with-lfs \ -# --prefix="${ED}"/usr \ -# --libdir="${ED}"/usr/$(get_libdir)/"${PN}" \ -# ${myconf} LDFLAGS="-Wl,--no-as-needed" \ -# || die -# econf ${myconf[@]} -} - -src_compile() { - ## all_r would ignore the --with-projects contents and build more - ## emake all_r -C GCC*-Release*/build || die - ## all_p with compile only selected/required components - ##cd "${S}"_build &&\ - ##emake all_p -C GCC*-Release*/build || die "gcc-4.5.3 crashes at src/objects/valerr/ValidError.cpp:226:1: internal compiler error: Segmentation fault, right?" - #emake all_p -C "${S}"_build/build - - # - # Re: /usr/lib64/ncbi-tools++/libdbapi_driver.so: undefined reference to `ncbi::NcbiGetlineEOL(std::istream&, std::string&)' - # - # The next release should automatically address such underlinking, albeit - # only in --with-flat-makefile configurations. For now (12.0.0), you'll need to - # add or extend more DLL_LIB settings, to which end you may find the - # resources at http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/ - # helpful. For instance, - # - # http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/dbapi_driver.html - # - # indicates that src/dbapi/driver/Makefile.dbapi_driver.lib should set - # - # DLL_LIB = xncbi - # - # (You can find the path to that makefile by examining - # .../status/.dbapi_driver.dep or .../build/Makefile.flat.) - # - # To take full advantage of --with-flat-makefile, you'll need the following (instead of 'emake all_p -C "${S}"_build/build') and call configure --with-flat-makefile: - emake -C "${S}"_build/build -f Makefile.flat -} - -src_install() { - rm -rvf "${S}"_build/lib/ncbi || die - emake install prefix="${ED}/usr" libdir="${ED}/usr/$(get_libdir)/${PN}" - -# dobin "${S}"_build/bin/* -# dolib.so "${S}"_build/lib/*so* -# dolib.a "${S}"_build/lib/*.a -# doheader "${S}"_build/inc/* - - # File collisions with sci-biology/ncbi-tools - mv "${ED}"/usr/bin/asn2asn "${ED}"/usr/bin/asn2asn+ - mv "${ED}"/usr/bin/rpsblast "${ED}"/usr/bin/rpsblast+ - mv -f "${ED}"/usr/bin/test_regexp "${ED}"/usr/bin/test_regexp+ # drop the eventually mistakenly compiled binaries - mv "${ED}"/usr/bin/vecscreen "${ED}"/usr/bin/vecscreen+ - mv "${ED}"/usr/bin/seedtop "${ED}"/usr/bin/seedtop+ - - echo "LDPATH=${EPREFIX}/usr/$(get_libdir)/${PN}" > ${S}/99${PN} - doenvd "${S}/99${PN}" -} - -pkg_postinst() { - einfo 'Please run "source /etc/profile" before using this package in the current shell.' - einfo 'Documentation is at http://www.ncbi.nlm.nih.gov/books/NBK7167/' -} diff --git a/sci-biology/ncbi-genome-download/Manifest b/sci-biology/ncbi-genome-download/Manifest deleted file mode 100644 index 57adfb8ee..000000000 --- a/sci-biology/ncbi-genome-download/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST ncbi-genome-download-0.3.0.tar.gz 37355 BLAKE2B c8061f29c2130d26ee97e310ce702db304d30794735af26cb2d804db5acb38e32b05b30d7770c195fb627f3d005b33bff038208b49612380de52278823914dc2 SHA512 5bcd6e0d731bc4bb6792821dc6d233e2f7acac6ee6819ddd14014a881d475c43ad084ff000d78e12fc2528d179be0e3db076fbe15da4b83dc6815c37c188ab61 diff --git a/sci-biology/ncbi-genome-download/ncbi-genome-download-0.3.0.ebuild b/sci-biology/ncbi-genome-download/ncbi-genome-download-0.3.0.ebuild deleted file mode 100644 index 1afb771c5..000000000 --- a/sci-biology/ncbi-genome-download/ncbi-genome-download-0.3.0.ebuild +++ /dev/null @@ -1,24 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7,8,9} ) -DISTUTILS_USE_SETUPTOOLS=rdepend - -inherit distutils-r1 - -DESCRIPTION="Download genomes from the NCBI FTP servers" -HOMEPAGE="https://github.com/kblin/ncbi-genome-download" -SRC_URI="https://github.com/kblin/${PN}/archive/${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="Apache-2.0" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -BDEPEND="test? ( - dev-python/requests-mock[${PYTHON_USEDEP}] - dev-python/pytest-mock[${PYTHON_USEDEP}] -)" - -distutils_enable_tests pytest diff --git a/sci-biology/ncbi-tools++/Manifest b/sci-biology/ncbi-tools++/Manifest deleted file mode 100644 index 9dd3a53d8..000000000 --- a/sci-biology/ncbi-tools++/Manifest +++ /dev/null @@ -1,3 +0,0 @@ -DIST ncbi_cxx--12_0_0.tar.gz 37925914 BLAKE2B 45490961293d8b3ace24c21602f4039041003f9b45d9f1763957c97ba1e55d6d336c33b6116262b2e774cc26b9366cc3d61bead0c0c7fbd4c461cad2921d80d4 SHA512 1a79f2d95960efde6263289814102499460ec235dad36337dd398d668665e44015e06e40fd0e66a8fb16f526d326949adcaadcb667debeba5d8570b1a92e30ed -DIST ncbi_cxx--18_0_0.tar.gz 69807228 BLAKE2B 2221232e4ab38845708a9ec5601a94f1dd25c5dd6fff265bde3c3d64b9108eec00b8480a1888d2517881f25abe9127e547ba88528b95398480ecd09d133482a7 SHA512 70dd07597aafa3f48881640530bf2aeebcac6fa13843fada4c590ca101cb8fdfa1aabf240ed0177d371a1fc36c6d231d667125279096006cd1eba119ea9514f5 -DIST ncbi_cxx--22_0_0.tar.gz 56042079 BLAKE2B 8a358f9f09e2844c4007b99f4b1c5212e254f804237c26c2eb6620448755b88029d492ff124fff3fdb515189219400f3edaaa195eb4f0fa539ac7b122af4d7e1 SHA512 f6624b09aae1f27b30196b7036f3d962125f2c57e1369bef013b15c116828e2daf264e018a1c1e71fb57c55462d71c5df7580e429fcf9d736e02f89c71cbfbd0 diff --git a/sci-biology/ncbi-tools++/files/curl-types.patch b/sci-biology/ncbi-tools++/files/curl-types.patch deleted file mode 100644 index 3e6079057..000000000 --- a/sci-biology/ncbi-tools++/files/curl-types.patch +++ /dev/null @@ -1,24 +0,0 @@ -Index: libs/kns/url-fetcher-curl.c -=================================================================== ---- src/sra/sdk/libs/kns/url-fetcher-curl.c (revision 11878) -+++ src/sra/sdk/libs/kns/url-fetcher-curl.c (revision 11880) -@@ -38,7 +38,6 @@ - #include <string.h> - - #include <curl/curl.h> --#include <curl/types.h> - #include <curl/easy.h> - - /*-------------------------------------------------------------------------- -Index: tools/refseq-load/refseq-load.c -=================================================================== ---- src/sra/sdk/tools/refseq-load/refseq-load.c (revision 11878) -+++ src/sra/sdk/tools/refseq-load/refseq-load.c (revision 11880) -@@ -41,7 +41,6 @@ - #include <sysalloc.h> - - #include <curl/curl.h> --#include <curl/types.h> - #include <curl/easy.h> - - #include <stdlib.h> diff --git a/sci-biology/ncbi-tools++/files/disable-testsuite-compilation.txt b/sci-biology/ncbi-tools++/files/disable-testsuite-compilation.txt deleted file mode 100644 index fa27aa13b..000000000 --- a/sci-biology/ncbi-tools++/files/disable-testsuite-compilation.txt +++ /dev/null @@ -1,8 +0,0 @@ -.* --.*/test --.*/unit_test --.*/unit_tests --dbapi/driver/ftds.*/freetds/.*/unittests --sample --.*/demo --.*/samples diff --git a/sci-biology/ncbi-tools++/files/make_install.patch b/sci-biology/ncbi-tools++/files/make_install.patch deleted file mode 100644 index e98f1110d..000000000 --- a/sci-biology/ncbi-tools++/files/make_install.patch +++ /dev/null @@ -1,14 +0,0 @@ ---- src/build-system/Makefile.in.top.old 2013-01-07 23:07:29.970141951 +0100 -+++ src/build-system/Makefile.in.top 2013-01-07 23:08:37.940990190 +0100 -@@ -39,7 +39,10 @@ - -$(RMDIR) $(pincludedir) - $(INSTALL) -d $(bindir) $(libdir) $(pincludedir) - $(INSTALL) $(lbindir)/* $(bindir) -- $(INSTALL) -m 644 $(llibdir)/* $(libdir) -+ $(INSTALL) -m 644 $(llibdir)/*.* $(libdir) -+ if test -d $(llibdir)/ncbi; then \ -+ cp -pPR $(llibdir)/ncbi $(libdir)/; \ -+ fi - -rm -f $(libdir)/lib*-static.a - cd $(libdir) && \ - for x in *.a; do ln -s "$$x" "`basename \"$$x\" .a`-static.a"; done diff --git a/sci-biology/ncbi-tools++/files/malloc_initialize_upstream_fix.patch b/sci-biology/ncbi-tools++/files/malloc_initialize_upstream_fix.patch deleted file mode 100644 index 4900e529a..000000000 --- a/sci-biology/ncbi-tools++/files/malloc_initialize_upstream_fix.patch +++ /dev/null @@ -1,100 +0,0 @@ ---- trunk/c++/src/app/netcache/nc_memory.cpp 2011/12/16 17:42:54 52330 -+++ trunk/c++/src/app/netcache/nc_memory.cpp 2012/02/27 14:38:30 53136 -@@ -360,7 +360,7 @@ - m_ObjLock.Lock(); - ++m_SysFrees; - m_SystemMem -= alloced_size; -- m_LostMem -= alloced_size -= asked_size; -+ m_LostMem -= alloced_size - asked_size; - m_ObjLock.Unlock(); - } - -@@ -2539,7 +2539,7 @@ - bool - CNCMemManager::InitializeApp(void) - { -- try { -+ /*try { - CSQLITE_Global::SetCustomMallocFuncs(&s_NCMallocMethods); - } - catch (CSQLITE_Exception& ex) { -@@ -2547,13 +2547,15 @@ - return false; - } - -- return CNCMMCentral::RunLateInit(); -+ return CNCMMCentral::RunLateInit();*/ -+ g_InitNCThreadIndexes(); -+ return true; - } - - void - CNCMemManager::FinalizeApp(void) - { -- CNCMMCentral::PrepareToStop(); -+ //CNCMMCentral::PrepareToStop(); - } - - void -@@ -2571,28 +2573,29 @@ - void - CNCMemManager::PrintStats(CPrintTextProxy& proxy) - { -- CNCMMStats stats_sum; -+ /*CNCMMStats stats_sum; - CNCMMStats::CollectAllStats(&stats_sum); -- stats_sum.Print(proxy); -+ stats_sum.Print(proxy);*/ - } - - size_t - CNCMemManager::GetMemoryLimit(void) - { -- return CNCMMCentral::GetMemLimit(); -+ return 0;//CNCMMCentral::GetMemLimit(); - } - - size_t - CNCMemManager::GetMemoryUsed(void) - { -- CNCMMStats stat; -+ /*CNCMMStats stat; - CNCMMStats::CollectAllStats(&stat); -- return stat.GetSystemMem(); -+ return stat.GetSystemMem();*/ -+ return 0; - } - - END_NCBI_SCOPE - -- -+/* - void* - operator new (size_t size) - #ifndef NCBI_COMPILER_MSVC -@@ -2626,13 +2629,13 @@ - { - NCBI_NS_NCBI::CNCMMCentral::DeallocMemory(ptr); - } -- -+*/ - #ifdef __GLIBC__ - // glibc has special method of overriding C library allocation functions. - - #include <malloc.h> - -- -+/* - void* s_NCMallocHook(size_t size, const void* caller) - { - return NCBI_NS_NCBI::CNCMMCentral::AllocMemory(size); -@@ -2656,7 +2659,7 @@ - } - - void (*__malloc_initialize_hook) (void) = s_NCInitMallocHook; -- -+*/ - #elif !defined(NCBI_OS_MSWIN) - // Changing of C library allocation functions on Windows is very tricky (if - // possible at all) and NetCache will never run in production on Windows. So - diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-bdb6.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-bdb6.patch deleted file mode 100644 index 9589481d4..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-bdb6.patch +++ /dev/null @@ -1,114 +0,0 @@ -Index: include/db/bdb/bdb_file.hpp -=================================================================== ---- include/db/bdb/bdb_file.hpp (revision 470126) -+++ include/db/bdb/bdb_file.hpp (working copy) -@@ -660,6 +660,9 @@ - void x_ConstructKeyBuf(); - void x_ConstructDataBuf(); - -+ static int x_CompareShim(DB* db, const DBT* dbt1, const DBT* dbt2, -+ size_t* locp); -+ - private: - auto_ptr<CBDB_BufferManager> m_KeyBuf; - auto_ptr<CBDB_BufferManager> m_DataBuf; -Index: src/db/bdb/bdb_blob.cpp -=================================================================== ---- src/db/bdb/bdb_blob.cpp (revision 470126) -+++ src/db/bdb/bdb_blob.cpp (working copy) -@@ -583,12 +583,31 @@ - return m_DBT_Data->size; - } - -+#if DB_VERSION_MAJOR >= 6 -+extern "C" { -+ typedef int (*BDB_CompareFunction_V6)(DB*, const DBT*, const DBT*, -+ size_t*); -+ int BDB_Uint4Compare_V6(DB* db, const DBT* dbt1, const DBT* dbt2, size_t*) -+ { return BDB_Uint4Compare(db, dbt1, dbt2); } -+ int BDB_ByteSwap_Uint4Compare_V6(DB* db, const DBT* dbt1, const DBT* dbt2, -+ size_t*) -+ { return BDB_ByteSwap_Uint4Compare(db, dbt1, dbt2); } -+} -+#endif -+ - void CBDB_LobFile::SetCmp(DB*) - { -+#if DB_VERSION_MAJOR >= 6 -+ BDB_CompareFunction_V6 func = BDB_Uint4Compare_V6; -+ if (IsByteSwapped()) { -+ func = BDB_ByteSwap_Uint4Compare_V6; -+ } -+#else - BDB_CompareFunction func = BDB_Uint4Compare; - if (IsByteSwapped()) { - func = BDB_ByteSwap_Uint4Compare; - } -+#endif - - _ASSERT(func); - int ret = m_DB->set_bt_compare(m_DB, func); -Index: src/db/bdb/bdb_file.cpp -=================================================================== ---- src/db/bdb/bdb_file.cpp (revision 470126) -+++ src/db/bdb/bdb_file.cpp (working copy) -@@ -1535,12 +1535,27 @@ - } - - -+#if DB_VERSION_MAJOR >= 6 -+int CBDB_File::x_CompareShim(DB* db, const DBT* dbt1, const DBT* dbt2, size_t*) -+{ -+ const CBDB_BufferManager* key_buf -+ = static_cast<const CBDB_BufferManager*>(db->app_private); -+ _ASSERT(key_buf); -+ return (key_buf->GetCompareFunction())(db, dbt1, dbt2); -+} -+#endif -+ -+ - void CBDB_File::SetCmp(DB* db) - { - _ASSERT(m_DB_Type == eBtree); -+#if DB_VERSION_MAJOR >= 6 -+ int ret = db->set_bt_compare(db, x_CompareShim); -+#else - BDB_CompareFunction func = m_KeyBuf->GetCompareFunction(); - _ASSERT(func); - int ret = db->set_bt_compare(db, func); -+#endif - BDB_CHECK(ret, 0); - - if (m_PrefixCompress) { -@@ -2056,12 +2071,31 @@ - BindKey("id", &IdKey); - } - -+#if DB_VERSION_MAJOR >= 6 -+extern "C" { -+ typedef int (*BDB_CompareFunction_V6)(DB*, const DBT*, const DBT*, -+ size_t*); -+ int BDB_Int4Compare_V6(DB* db, const DBT* dbt1, const DBT* dbt2, size_t*) -+ { return BDB_Int4Compare(db, dbt1, dbt2); } -+ int BDB_ByteSwap_Int4Compare_V6(DB* db, const DBT* dbt1, const DBT* dbt2, -+ size_t*) -+ { return BDB_ByteSwap_Int4Compare(db, dbt1, dbt2); } -+} -+#endif -+ - void CBDB_IdFile::SetCmp(DB* /* db */) - { -+#if DB_VERSION_MAJOR >= 6 -+ BDB_CompareFunction_V6 func = BDB_Int4Compare_V6; -+ if (IsByteSwapped()) { -+ func = BDB_ByteSwap_Int4Compare_V6; -+ } -+#else - BDB_CompareFunction func = BDB_Int4Compare; - if (IsByteSwapped()) { - func = BDB_ByteSwap_Int4Compare; - } -+#endif - - _ASSERT(func); - int ret = m_DB->set_bt_compare(m_DB, func); diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-conf-opts.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-conf-opts.patch deleted file mode 100644 index 3ed3e7d5f..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-conf-opts.patch +++ /dev/null @@ -1,64 +0,0 @@ - src/build-system/configure.ac | 17 ++++++++++++++--- - 1 file changed, 14 insertions(+), 3 deletions(-) - -diff --git a/src/build-system/configure.ac b/src/build-system/configure.ac -index 03e34b4..336453d 100644 ---- a/src/build-system/configure.ac -+++ b/src/build-system/configure.ac -@@ -224,7 +224,7 @@ AC_ARG_WITH(ncbi-c, - AC_ARG_WITH(sss, - [ --without-sss do not use NCBI SSS libraries]) - AC_ARG_WITH(sssutils, -- [ --without-utils do not use NCBI SSS UTIL library]) -+ [ --without-sssutils do not use NCBI SSS UTIL library]) - AC_ARG_WITH(sssdb, - [ --without-sssdb do not use NCBI SSS DB library]) - AC_ARG_WITH(included-sss, -@@ -490,13 +490,13 @@ check ncbi-public strip pch caution ccache distcc \ - ncbi-c wxwidgets wxwidgets-ucs fastcgi sss sssdb sssutils included-sss \ - geo included-geo \ - z bz2 lzo pcre gcrypt gnutls openssl krb5 sybase sybase-local sybase-new \ --ftds mysql orbacus freetype ftgl opengl mesa glut glew glew-mx \ -+ftds mysql orbacus odbc freetype ftgl opengl mesa glut glew glew-mx \ - bdb python perl jni sqlite3 icu boost boost-tag \ - sp expat sablot libxml libxslt libexslt xerces xalan zorba \ - oechem sge muparser hdf5 \ - gif jpeg tiff png xpm magic curl mimetic 3psw \ - local-lbsm ncbi-crypt connext \ --serial objects dbapi app ctools gui algo internal gbench" -+serial objects dbapi app ctools gui algo internal gbench x" - - changequote(, )dnl - x_with_list=`echo "$x_with_list" | sed 's/\([^ ][^ ]*\)/--with-\1 --without-\1/g'` -@@ -522,6 +522,7 @@ for x_arg in "$@" ; do - case "$x_arg" in - --with-extra-action= | --exec-prefix= | --with-projects= | --srcdir= \ - | --cache-file= | --build= | --host= | --target= | --with-runpath= \ -+ | --mandir= | --infodir= | --datadir= | --sysconfdir= | --localstatedir= \ - | --with-relative-runpath= | --x-includes= | --x-libraries= ) - AC_MSG_ERROR([$x_arg: requires value; use --help to show usage]) - ;; -@@ -532,6 +533,7 @@ for x_arg in "$@" ; do - | --with-universal=* | --with-tcheck=* \ - | --cache-file=* | --build=* | --host=* | --prefix=* | --exec-prefix=* \ - | --libdir=* | --bindir=* | --includedir=* | --srcdir=* \ -+ | --mandir=* | --infodir=* | --datadir=* | --sysconfdir=* | --localstatedir=* \ - | [[A-Z]*=*] \ - | --with-z=* | --with-bz2=* | --with-lzo=* \ - | --with-pcre=* \ -@@ -647,6 +649,15 @@ if test -z "${DEF_FAST_FLAGS}${FAST_CXXFLAGS}"; then - *\ -O* | *\ -xO* ) skip_fast_flags=yes ;; - esac - fi -+if test -n "$with_projects"; then -+ case "$with_projects" in -+ /* ) abs_projects=$with_projects ;; -+ yes) abs_projects=$srcdir/projects ;; -+ * ) abs_projects=$srcdir/$with_projects ;; -+ esac -+ test -r "$abs_projects" || \ -+ AC_MSG_ERROR([unable to read requested projects file "$abs_projects".]) -+fi - - #### Always define this - AC_DEFINE(NCBI_CXX_TOOLKIT, 1, [This is the NCBI C++ Toolkit.]) diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-configure.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-configure.patch deleted file mode 100644 index d44993da2..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-configure.patch +++ /dev/null @@ -1,216 +0,0 @@ ---- ncbi_cxx--12_0_0/src/build-system/configure.ori 2014-06-25 23:47:05.000000000 +0200 -+++ ncbi_cxx--12_0_0/src/build-system/configure 2014-06-25 23:52:35.000000000 +0200 -@@ -927,7 +927,7 @@ - --without-distcc do not automatically use distcc if available - --without-ncbi-c do not use NCBI C Toolkit - --without-sss do not use NCBI SSS libraries -- --without-utils do not use NCBI SSS UTIL library -+ --without-sssutils do not use NCBI SSS UTIL library - --without-sssdb do not use NCBI SSS DB library - --with-included-sss use the in-tree copy of SSS - --with-z=DIR use zlib installation in DIR -@@ -2965,13 +2965,13 @@ - ncbi-c wxwidgets wxwidgets-ucs fastcgi sss sssdb sssutils included-sss \ - geo included-geo \ - z bz2 lzo pcre gcrypt gnutls openssl krb5 sybase sybase-local sybase-new \ --ftds mysql orbacus freetype ftgl opengl mesa glut glew glew-mx \ -+ftds mysql orbacus odbc freetype ftgl opengl mesa glut glew glew-mx \ - bdb python perl jni sqlite3 icu boost boost-tag \ - sp expat sablot libxml libxslt libexslt xerces xalan zorba \ - oechem sge muparser hdf5 \ - gif jpeg tiff png xpm magic curl mimetic 3psw \ - local-lbsm ncbi-crypt connext \ --serial objects dbapi app ctools gui algo internal gbench" -+serial objects dbapi app ctools gui algo internal gbench x" - - x_with_list=`echo "$x_with_list" | sed 's/\([^ ][^ ]*\)/--with-\1 --without-\1/g'` - -@@ -2995,6 +2995,7 @@ - case "$x_arg" in - --with-extra-action= | --exec-prefix= | --with-projects= | --srcdir= \ - | --cache-file= | --build= | --host= | --target= | --with-runpath= \ -+ | --mandir= | --infodir= | --datadir= | --sysconfdir= | --localstatedir= \ - | --with-relative-runpath= | --x-includes= | --x-libraries= ) - { { echo "$as_me:$LINENO: error: $x_arg: requires value; use --help to show usage" >&5 - echo "$as_me: error: $x_arg: requires value; use --help to show usage" >&2;} -@@ -3007,6 +3008,7 @@ - | --with-universal=* | --with-tcheck=* \ - | --cache-file=* | --build=* | --host=* | --prefix=* | --exec-prefix=* \ - | --libdir=* | --bindir=* | --includedir=* | --srcdir=* \ -+ | --mandir=* | --infodir=* | --datadir=* | --sysconfdir=* | --localstatedir=* \ - | [A-Z]*=* \ - | --with-z=* | --with-bz2=* | --with-lzo=* \ - | --with-pcre=* \ -@@ -3201,6 +3203,17 @@ - *\ -O* | *\ -xO* ) skip_fast_flags=yes ;; - esac - fi -+if test -n "$with_projects"; then -+ case "$with_projects" in -+ /* ) abs_projects=$with_projects ;; -+ yes) abs_projects=$srcdir/projects ;; -+ * ) abs_projects=$srcdir/$with_projects ;; -+ esac -+ test -r "$abs_projects" || \ -+ { { echo "$as_me:$LINENO: error: unable to read requested projects file \"$abs_projects\"." >&5 -+echo "$as_me: error: unable to read requested projects file \"$abs_projects\"." >&2;} -+ { (exit 1); exit 1; }; } -+fi - - #### Always define this - -@@ -17878,68 +17891,6 @@ - fi - - --echo "$as_me:$LINENO: checking for std::is_sorted<> in <algorithm>" >&5 --echo $ECHO_N "checking for std::is_sorted<> in <algorithm>... $ECHO_C" >&6 --if test "${ncbi_cv_func_is_sorted+set}" = set; then -- echo $ECHO_N "(cached) $ECHO_C" >&6 --else -- cat >conftest.$ac_ext <<_ACEOF --/* confdefs.h. */ --_ACEOF --cat confdefs.h >>conftest.$ac_ext --cat >>conftest.$ac_ext <<_ACEOF --/* end confdefs.h. */ --#include <algorithm> --int --main () --{ --int a[2]; return std::is_sorted(a, a+2) ? 0 : 1; -- ; -- return 0; --} --_ACEOF --rm -f conftest.$ac_objext --if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 -- (eval $ac_compile) 2>conftest.er1 -- ac_status=$? -- grep -v '^ *+' conftest.er1 >conftest.err -- rm -f conftest.er1 -- cat conftest.err >&5 -- echo "$as_me:$LINENO: \$? = $ac_status" >&5 -- (exit $ac_status); } && -- { ac_try='test -z "$ac_cxx_werror_flag" -- || test ! -s conftest.err' -- { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 -- (eval $ac_try) 2>&5 -- ac_status=$? -- echo "$as_me:$LINENO: \$? = $ac_status" >&5 -- (exit $ac_status); }; } && -- { ac_try='test -s conftest.$ac_objext' -- { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 -- (eval $ac_try) 2>&5 -- ac_status=$? -- echo "$as_me:$LINENO: \$? = $ac_status" >&5 -- (exit $ac_status); }; }; then -- ncbi_cv_func_is_sorted=yes --else -- echo "$as_me: failed program was:" >&5 --sed 's/^/| /' conftest.$ac_ext >&5 -- --ncbi_cv_func_is_sorted=no --fi --rm -f conftest.err conftest.$ac_objext conftest.$ac_ext --fi --echo "$as_me:$LINENO: result: $ncbi_cv_func_is_sorted" >&5 --echo "${ECHO_T}$ncbi_cv_func_is_sorted" >&6 --if test "$ncbi_cv_func_is_sorted" = yes; then -- --cat >>confdefs.h <<\_ACEOF --#define HAVE_IS_SORTED 1 --_ACEOF -- --fi -- -- - - echo "$as_me:$LINENO: checking for SysV semaphores" >&5 - echo $ECHO_N "checking for SysV semaphores... $ECHO_C" >&6 -@@ -18550,7 +18501,7 @@ - echo $ECHO_N "(cached) $ECHO_C" >&6 - else - ncbi_cv_c_restrict=no -- for restrict in restrict __restrict__ __restrict; do -+ for restrict in __restrict__ __restrict restrict; do - test "$ncbi_cv_c_restrict" = "no" || break - cat >conftest.$ac_ext <<_ACEOF - /* confdefs.h. */ -@@ -18620,7 +18571,7 @@ - echo $ECHO_N "(cached) $ECHO_C" >&6 - else - ncbi_cv_cxx_restrict=no -- for restrict in restrict __restrict__ __restrict; do -+ for restrict in __restrict__ __restrict restrict; do - test "$ncbi_cv_cxx_restrict" = "no" || break - cat >conftest.$ac_ext <<_ACEOF - /* confdefs.h. */ -@@ -19046,67 +18997,6 @@ - _ACEOF - - fi -- --echo "$as_me:$LINENO: checking whether $CXX supports C++0x nullptr" >&5 --echo $ECHO_N "checking whether $CXX supports C++0x nullptr... $ECHO_C" >&6 --if test "${ncbi_cv_cxx_nullptr+set}" = set; then -- echo $ECHO_N "(cached) $ECHO_C" >&6 --else -- cat >conftest.$ac_ext <<_ACEOF --/* confdefs.h. */ --_ACEOF --cat confdefs.h >>conftest.$ac_ext --cat >>conftest.$ac_ext <<_ACEOF --/* end confdefs.h. */ -- --int --main () --{ --void * p = nullptr; -- ; -- return 0; --} --_ACEOF --rm -f conftest.$ac_objext --if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 -- (eval $ac_compile) 2>conftest.er1 -- ac_status=$? -- grep -v '^ *+' conftest.er1 >conftest.err -- rm -f conftest.er1 -- cat conftest.err >&5 -- echo "$as_me:$LINENO: \$? = $ac_status" >&5 -- (exit $ac_status); } && -- { ac_try='test -z "$ac_cxx_werror_flag" -- || test ! -s conftest.err' -- { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 -- (eval $ac_try) 2>&5 -- ac_status=$? -- echo "$as_me:$LINENO: \$? = $ac_status" >&5 -- (exit $ac_status); }; } && -- { ac_try='test -s conftest.$ac_objext' -- { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 -- (eval $ac_try) 2>&5 -- ac_status=$? -- echo "$as_me:$LINENO: \$? = $ac_status" >&5 -- (exit $ac_status); }; }; then -- ncbi_cv_cxx_nullptr=yes --else -- echo "$as_me: failed program was:" >&5 --sed 's/^/| /' conftest.$ac_ext >&5 -- --ncbi_cv_cxx_nullptr=no --fi --rm -f conftest.err conftest.$ac_objext conftest.$ac_ext --fi --echo "$as_me:$LINENO: result: $ncbi_cv_cxx_nullptr" >&5 --echo "${ECHO_T}$ncbi_cv_cxx_nullptr" >&6 --if test "$ncbi_cv_cxx_nullptr" = yes; then -- --cat >>confdefs.h <<\_ACEOF --#define HAVE_NULLPTR 1 --_ACEOF -- --fi - - ### Check for the availability of other packages - ### -------------------------------------------- diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-drop-STATIC-from-LIB.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-drop-STATIC-from-LIB.patch deleted file mode 100644 index fad02c38e..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-drop-STATIC-from-LIB.patch +++ /dev/null @@ -1,44 +0,0 @@ ---- ncbi_cxx--12_0_0/src/app/speedtest/Makefile.speedtest.app.ori 2014-06-26 16:46:27.000000000 +0200 -+++ ncbi_cxx--12_0_0/src/app/speedtest/Makefile.speedtest.app 2014-06-26 16:47:26.000000000 +0200 -@@ -9,7 +9,7 @@ - APP = speedtest - SRC = speedtest - LIB = prosplign xalgoalignutil xalgoseq xcleanup taxon1 submit $(BLAST_LIBS) \ -- xqueryparse xregexp $(PCRE_LIB) $(OBJMGR_LIBS:%=%$(STATIC)) -+ xqueryparse xregexp $(PCRE_LIB) $(OBJMGR_LIBS) - - LIBS = $(CMPRS_LIBS) $(DL_LIBS) $(PCRE_LIBS) $(ORIG_LIBS) - ---- ncbi_cxx--12_0_0/src/app/compart/Makefile.compart.app.ori 2014-06-26 16:47:53.000000000 +0200 -+++ ncbi_cxx--12_0_0/src/app/compart/Makefile.compart.app 2014-06-26 16:48:07.000000000 +0200 -@@ -7,7 +7,7 @@ - - LIB = xalgoalignutil xalgoalignsplign xalgoalignnw xalgoseq \ - taxon1 xalnmgr xqueryparse xregexp $(PCRE_LIB) \ -- $(BLAST_LIBS:%=%$(STATIC)) $(OBJMGR_LIBS:%=%$(STATIC)) -+ $(BLAST_LIBS) $(OBJMGR_LIBS) - - LIBS = $(PCRE_LIBS) $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) - ---- ncbi_cxx--12_0_0/src/app/igblast/Makefile.igblastp.app.ori 2014-06-26 17:45:11.000000000 +0200 -+++ ncbi_cxx--12_0_0/src/app/igblast/Makefile.igblastp.app 2014-06-26 17:48:26.000000000 +0200 -@@ -3,7 +3,7 @@ - APP = igblastp - SRC = igblastp_app - LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS) --LIB = blast_app_util igblast $(LIB_:%=%$(STATIC)) -+LIB = blast_app_util igblast $(LIB_) - - # De-universalize Mac builds to work around a PPC toolchain limitation - CFLAGS = $(FAST_CFLAGS:ppc=i386) ---- ncbi_cxx--12_0_0/src/app/igblast/Makefile.igblastn.app.ori 2014-06-26 17:47:53.000000000 +0200 -+++ ncbi_cxx--12_0_0/src/app/igblast/Makefile.igblastn.app 2014-06-26 17:49:31.000000000 +0200 -@@ -3,7 +3,7 @@ - APP = igblastn - SRC = igblastn_app - LIB_ = $(BLAST_INPUT_LIBS) xalgoalignutil xqueryparse $(BLAST_LIBS) $(OBJMGR_LIBS) --LIB = blast_app_util igblast $(LIB_:%=%$(STATIC)) -+LIB = blast_app_util igblast $(LIB_) - - # De-universalize Mac builds to work around a PPC toolchain limitation - CFLAGS = $(FAST_CFLAGS:ppc=i386) diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-FreeTDS-upstream.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-FreeTDS-upstream.patch deleted file mode 100644 index fede70e51..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-FreeTDS-upstream.patch +++ /dev/null @@ -1,19 +0,0 @@ ---- src/app/agpconvert/Makefile.agpconvert.app.ori 2013-09-13 23:56:22.660032261 +0200 -+++ src/app/agpconvert/Makefile.agpconvert.app 2013-09-13 23:57:31.340032441 +0200 -@@ -6,13 +6,12 @@ - APP = agpconvert - SRC = agpconvert - --LIB = xalgoseq xobjedit $(OBJREAD_LIBS) taxon1 xalnmgr xobjutil submit \ -- ncbi_xdbapi_ftds $(FTDS_LIB) tables xregexp $(PCRE_LIB) $(OBJMGR_LIBS) --LIBS = $(FTDS_LIBS) $(CMPRS_LIBS) $(PCRE_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) -+LIB = $(OBJREAD_LIBS) taxon1 xregexp $(PCRE_LIB) $(OBJMGR_LIBS) -+LIBS = $(CMPRS_LIBS) $(PCRE_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) - - CXXFLAGS = $(FAST_CXXFLAGS) - LDFLAGS = $(FAST_LDFLAGS) - --REQUIRES = objects algo -+REQUIRES = objects - - WATCHERS = xiangcha diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-creaders-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-creaders-linking.patch deleted file mode 100644 index 46c2e83fb..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-creaders-linking.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- src/objtools/alnmgr/demo/Makefile.alnmrg.app.ori 2013-09-13 23:51:34.340031508 +0200 -+++ src/objtools/alnmgr/demo/Makefile.alnmrg.app 2013-09-13 23:51:36.660031514 +0200 -@@ -5,7 +5,7 @@ - SRC = alnmrg - - LIB = xalnmgr $(OBJREAD_LIBS) ncbi_xloader_blastdb seqdb xobjutil submit blastdb \ -- tables $(OBJMGR_LIBS) -+ tables creaders $(OBJMGR_LIBS) - - LIBS = $(CMPRS_LIBS) $(DL_LIBS) $(NETWORK_LIBS) $(ORIG_LIBS) - diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-install.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-install.patch deleted file mode 100644 index 97e845fdb..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-install.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- ncbi_cxx--12_0_0/src/build-system/Makefile.in.top.ori 2014-06-26 22:49:49.000000000 +0200 -+++ ncbi_cxx--12_0_0/src/build-system/Makefile.in.top 2014-06-26 22:50:57.000000000 +0200 -@@ -48,7 +48,7 @@ - for x in *.a; do ln -s "$$x" "`basename \"$$x\" .a`-static.a"; done - cd $(includedir0) && find * -name CVS -prune -o -print |\ - cpio -pd $(pincludedir) -- $(INSTALL) -m 644 $(incdir)/* $(pincludedir) -+ $(INSTALL) -m 644 $(incdir)/*.* $(pincludedir) - ## set up appropriate build and status directories somewhere under $(libdir)? - - install-gbench: diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-svn-URL-upstream.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-svn-URL-upstream.patch deleted file mode 100644 index 8bba91f1d..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-svn-URL-upstream.patch +++ /dev/null @@ -1,10 +0,0 @@ ---- scripts/common/new_project.sh (revision 408264) -+++ scripts/common/new_project.sh (working copy) -@@ -6,7 +6,7 @@ - svn_revision=`echo '$Revision$' | sed "s%\\$[R]evision: *\\([^$][^$]*\\) \\$.*%\\1%"` - def_builddir="$NCBI/c++/Debug/build" - --repository_url='https://svn.ncbi.nlm.nih.gov/repos/toolkit' -+repository_url='http://anonsvn.ncbi.nlm.nih.gov/repos/v1' - tmp_app_checkout_dir='tmp_app_sample' - stem='sample/app' diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-linkage-tuneups-addons.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-linkage-tuneups-addons.patch deleted file mode 100644 index 553e41d29..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-linkage-tuneups-addons.patch +++ /dev/null @@ -1,13 +0,0 @@ ---- ncbi_cxx--12_0_0/src/app/agpconvert/Makefile.agpconvert.app.ori (revision 439078) -+++ ncbi_cxx--12_0_0/src/app/agpconvert/Makefile.agpconvert.app (working copy) -@@ -7,8 +7,8 @@ - SRC = agpconvert - - LIB = xalgoseq xobjedit $(OBJREAD_LIBS) taxon1 xalnmgr xobjutil submit \ -- ncbi_xdbapi_ftds $(FTDS_LIB) tables xregexp $(PCRE_LIB) $(OBJMGR_LIBS) --LIBS = $(FTDS_LIBS) $(CMPRS_LIBS) $(PCRE_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) -+ tables xregexp $(PCRE_LIB) $(OBJMGR_LIBS) -+LIBS = $(CMPRS_LIBS) $(PCRE_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) - - CXXFLAGS = $(FAST_CXXFLAGS) - LDFLAGS = $(FAST_LDFLAGS) diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-linkage-tuneups.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-linkage-tuneups.patch deleted file mode 100644 index 86e96b865..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-linkage-tuneups.patch +++ /dev/null @@ -1,421 +0,0 @@ -Index: src/algo/blast/format/Makefile.xblastformat.lib -=================================================================== ---- src/algo/blast/format/Makefile.xblastformat.lib (revision 439078) -+++ src/algo/blast/format/Makefile.xblastformat.lib (working copy) -@@ -7,6 +7,6 @@ - - CPPFLAGS = -DNCBI_MODULE=BLASTFORMAT $(ORIG_CPPFLAGS) - --DLL_LIB = align_format blastxml xhtml xcgi -+DLL_LIB = align_format xblast xnetblast blastxml xhtml xcgi - - WATCHERS = jianye zaretska madden camacho fongah2 -Index: src/app/compart/Makefile.compart.app -=================================================================== ---- src/app/compart/Makefile.compart.app (revision 439078) -+++ src/app/compart/Makefile.compart.app (working copy) -@@ -5,11 +5,11 @@ - APP = compart - SRC = compart - --LIB = xalgoalignutil xalgoalignsplign xalgoalignnw xqueryparse xalnmgr \ -- $(BLAST_LIBS:%=%$(STATIC)) \ -- $(OBJMGR_LIBS:%=%$(STATIC)) -+LIB = xalgoalignutil xalgoalignsplign xalgoalignnw xalgoseq \ -+ taxon1 xalnmgr xqueryparse xregexp $(PCRE_LIB) \ -+ $(BLAST_LIBS:%=%$(STATIC)) $(OBJMGR_LIBS:%=%$(STATIC)) - --LIBS = $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) -+LIBS = $(PCRE_LIBS) $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) - - CXXFLAGS = $(FAST_CXXFLAGS) - LDFLAGS = $(FAST_LDFLAGS) -Index: src/app/compart/Makefile.compartp.app -=================================================================== ---- src/app/compart/Makefile.compartp.app (revision 439078) -+++ src/app/compart/Makefile.compartp.app (working copy) -@@ -5,7 +5,8 @@ - APP = compartp - SRC = compartp - --LIB = prosplign xalgoalignutil $(BLAST_LIBS) xqueryparse $(OBJMGR_LIBS) -+LIB = prosplign xalgoalignutil xalgoseq taxon1 $(BLAST_LIBS) \ -+ xqueryparse xregexp $(PCRE_LIB) $(OBJMGR_LIBS) - - LIBS = $(CMPRS_LIBS) $(PCRE_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) - -Index: src/app/grid/util/Makefile.ncfetch.app -=================================================================== ---- src/app/grid/util/Makefile.ncfetch.app (revision 439078) -+++ src/app/grid/util/Makefile.ncfetch.app (working copy) -@@ -5,7 +5,7 @@ - APP = ncfetch.cgi - SRC = ncfetch - --LIB = xcgi xconnserv xconnect xutil xncbi -+LIB = xcgi xconnserv xthrserv xconnect xutil xncbi - LIBS = $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) - - WATCHERS = kazimird -Index: src/app/hfilter/Makefile.hfilter.app -=================================================================== ---- src/app/hfilter/Makefile.hfilter.app (revision 439078) -+++ src/app/hfilter/Makefile.hfilter.app (working copy) -@@ -5,9 +5,10 @@ - APP = hfilter - SRC = hitfilter_app - --LIB = xalgoalignutil $(BLAST_LIBS) xqueryparse $(OBJMGR_LIBS) -+LIB = xalgoalignutil xalgoseq taxon1 $(BLAST_LIBS) xqueryparse \ -+ xregexp $(PCRE_LIB) $(OBJMGR_LIBS) - --LIBS = $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) -+LIBS = $(PCRE_LIBS) $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) - - CXXFLAGS = $(FAST_CXXFLAGS) - LDFLAGS = $(FAST_LDFLAGS) -Index: src/app/speedtest/Makefile.speedtest.app -=================================================================== ---- src/app/speedtest/Makefile.speedtest.app (revision 439078) -+++ src/app/speedtest/Makefile.speedtest.app (working copy) -@@ -8,7 +8,7 @@ - - APP = speedtest - SRC = speedtest --LIB = prosplign xalgoalignutil xcleanup submit $(BLAST_LIBS) \ -+LIB = prosplign xalgoalignutil xalgoseq xcleanup taxon1 submit $(BLAST_LIBS) \ - xqueryparse xregexp $(PCRE_LIB) $(OBJMGR_LIBS:%=%$(STATIC)) - - LIBS = $(CMPRS_LIBS) $(DL_LIBS) $(PCRE_LIBS) $(ORIG_LIBS) -Index: src/app/splign/Makefile.splign.app -=================================================================== ---- src/app/splign/Makefile.splign.app (revision 439078) -+++ src/app/splign/Makefile.splign.app (working copy) -@@ -12,7 +12,7 @@ - LIB = xalgoalignsplign xalgoalignutil xalgoalignnw \ - $(BLAST_DB_DATA_LOADER_LIBS) \ - ncbi_xloader_lds2 lds2 sqlitewrapp \ -- xqueryparse xalgoseq $(PCRE_LIB) \ -+ xqueryparse xalgoseq taxon1 xregexp $(PCRE_LIB) \ - $(BLAST_LIBS:%=%$(STATIC)) submit \ - $(OBJMGR_LIBS:%=%$(STATIC)) - -Index: src/connect/services/test/Makefile.test_nsstorage.app -=================================================================== ---- src/connect/services/test/Makefile.test_nsstorage.app (revision 439078) -+++ src/connect/services/test/Makefile.test_nsstorage.app (working copy) -@@ -2,7 +2,7 @@ - - APP = test_nsstorage - SRC = test_nsstorage --LIB = xconnserv xconnect xutil xncbi -+LIB = xconnserv xthrserv xconnect xutil xncbi - - LIBS = $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) - -Index: src/misc/hgvs/test/Makefile.hgvs2variation.app -=================================================================== ---- src/misc/hgvs/test/Makefile.hgvs2variation.app (revision 439078) -+++ src/misc/hgvs/test/Makefile.hgvs2variation.app (working copy) -@@ -6,7 +6,7 @@ - - CPPFLAGS = $(ORIG_CPPFLAGS) $(BOOST_INCLUDE) - --LIB_ = hgvs variation \ -+LIB_ = hgvs objcoords variation \ - entrez2cli entrez2 xregexp $(PCRE_LIB) xobjutil $(OBJMGR_LIBS) - LIB = $(LIB_:%=%$(STATIC)) - -Index: src/misc/hgvs/test/Makefile.test_hgvs_parser.app -=================================================================== ---- src/misc/hgvs/test/Makefile.test_hgvs_parser.app (revision 439078) -+++ src/misc/hgvs/test/Makefile.test_hgvs_parser.app (working copy) -@@ -5,7 +5,7 @@ - - CPPFLAGS = $(ORIG_CPPFLAGS) $(BOOST_INCLUDE) - --LIB_ = hgvs variation test_boost xregexp $(PCRE_LIB) xobjutil \ -+LIB_ = hgvs objcoords variation test_boost xregexp $(PCRE_LIB) xobjutil \ - entrez2cli entrez2 $(OBJMGR_LIBS) - - LIB = $(LIB_:%=%$(STATIC)) -Index: src/objects/biblio/Makefile.biblio.lib -=================================================================== ---- src/objects/biblio/Makefile.biblio.lib (revision 439078) -+++ src/objects/biblio/Makefile.biblio.lib (working copy) -@@ -1,2 +1,4 @@ - LIB = biblio - SRC = biblio__ biblio___ citation_base -+ -+DLL_LIB = general -Index: src/objects/blast/Makefile.blast.lib -=================================================================== ---- src/objects/blast/Makefile.blast.lib (revision 439078) -+++ src/objects/blast/Makefile.blast.lib (working copy) -@@ -1,4 +1,6 @@ - LIB = xnetblast - SRC = blast__ blast___ names - -+DLL_LIB = scoremat seqset -+ - WATCHERS = camacho -Index: src/objects/blast/Makefile.xnetblastcli.lib -=================================================================== ---- src/objects/blast/Makefile.xnetblastcli.lib (revision 439078) -+++ src/objects/blast/Makefile.xnetblastcli.lib (working copy) -@@ -2,3 +2,5 @@ - - LIB = xnetblastcli - SRC = blastclient blastclient_ -+ -+DLL_LIB = xnetblast xconnect -Index: src/objects/blastdb/Makefile.blastdb.lib -=================================================================== ---- src/objects/blastdb/Makefile.blastdb.lib (revision 439078) -+++ src/objects/blastdb/Makefile.blastdb.lib (working copy) -@@ -1,2 +1,4 @@ - LIB = blastdb - SRC = blastdb__ blastdb___ -+ -+DLL_LIB = seq -Index: src/objects/general/Makefile.general.lib -=================================================================== ---- src/objects/general/Makefile.general.lib (revision 439078) -+++ src/objects/general/Makefile.general.lib (working copy) -@@ -1,2 +1,4 @@ - LIB = general - SRC = general__ general___ uoconv -+ -+DLL_LIB = xser -Index: src/objects/medline/Makefile.medline.lib -=================================================================== ---- src/objects/medline/Makefile.medline.lib (revision 439078) -+++ src/objects/medline/Makefile.medline.lib (working copy) -@@ -1,2 +1,4 @@ - LIB = medline - SRC = medline__ medline___ -+ -+DLL_LIB = biblio general -Index: src/objects/pub/Makefile.pub.lib -=================================================================== ---- src/objects/pub/Makefile.pub.lib (revision 439078) -+++ src/objects/pub/Makefile.pub.lib (working copy) -@@ -1,2 +1,4 @@ - LIB = pub - SRC = pub__ pub___ -+ -+DLL_LIB = medline biblio -Index: src/objects/scoremat/Makefile.scoremat.lib -=================================================================== ---- src/objects/scoremat/Makefile.scoremat.lib (revision 439078) -+++ src/objects/scoremat/Makefile.scoremat.lib (working copy) -@@ -1,2 +1,4 @@ - LIB = scoremat - SRC = scoremat__ scoremat___ -+ -+DLL_LIB = seqset -Index: src/objects/seq/Makefile.seq.lib -=================================================================== ---- src/objects/seq/Makefile.seq.lib (revision 439078) -+++ src/objects/seq/Makefile.seq.lib (working copy) -@@ -13,3 +13,5 @@ - seq_loc_from_string seq_loc_reverse_complementer - - WATCHERS = vasilche grichenk -+ -+DLL_LIB = seqcode pub biblio general xser sequtil -Index: src/objects/seqset/Makefile.seqset.lib -=================================================================== ---- src/objects/seqset/Makefile.seqset.lib (revision 439078) -+++ src/objects/seqset/Makefile.seqset.lib (working copy) -@@ -1,2 +1,4 @@ - LIB = seqset - SRC = seqset__ seqset___ gb_release_file -+ -+DLL_LIB = xser -Index: src/objects/taxon1/Makefile.taxon1.lib -=================================================================== ---- src/objects/taxon1/Makefile.taxon1.lib (revision 439078) -+++ src/objects/taxon1/Makefile.taxon1.lib (working copy) -@@ -3,4 +3,6 @@ - LIB = taxon1 - SRC = taxon1__ taxon1___ taxon1 cache utils ctreecont - -+DLL_LIB = xconnect -+ - WATCHERS = domrach -Index: src/objmgr/util/Makefile.util.lib -=================================================================== ---- src/objmgr/util/Makefile.util.lib (revision 439078) -+++ src/objmgr/util/Makefile.util.lib (working copy) -@@ -8,5 +8,7 @@ - SRC = weight sequence feature seqtitle create_defline obj_sniff seq_loc_util seq_align_util - LIB = xobjutil - -+DLL_LIB = xobjmgr -+ - WATCHERS = ucko vasilche - -Index: src/objtools/blast/seqdb_reader/Makefile.seqdb.lib -=================================================================== ---- src/objtools/blast/seqdb_reader/Makefile.seqdb.lib (revision 439078) -+++ src/objtools/blast/seqdb_reader/Makefile.seqdb.lib (working copy) -@@ -29,4 +29,6 @@ - CXXFLAGS = $(FAST_CXXFLAGS) - LDFLAGS = $(FAST_LDFLAGS) - -+DLL_LIB = xobjmgr blastdb -+ - WATCHERS = maning camacho -Index: src/objtools/blast/services/Makefile.blast_services.lib -=================================================================== ---- src/objtools/blast/services/Makefile.blast_services.lib (revision 439078) -+++ src/objtools/blast/services/Makefile.blast_services.lib (working copy) -@@ -13,3 +13,4 @@ - CXXFLAGS = $(FAST_CXXFLAGS) - LDFLAGS = $(FAST_LDFLAGS) - -+DLL_LIB = xnetblastcli xconnect -Index: src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib -=================================================================== ---- src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib (revision 439078) -+++ src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib (working copy) -@@ -7,4 +7,6 @@ - - ASN_DEP = blastdb seqset - -+DLL_LIB = seqdb -+ - WATCHERS = camacho -Index: src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib -=================================================================== ---- src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib (revision 439078) -+++ src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib (working copy) -@@ -7,4 +7,6 @@ - - ASN_DEP = blastdb xnetblast - -+DLL_LIB = blast_services -+ - WATCHERS = camacho -Index: src/objtools/lds2/Makefile.lds2.lib -=================================================================== ---- src/objtools/lds2/Makefile.lds2.lib (revision 439078) -+++ src/objtools/lds2/Makefile.lds2.lib (working copy) -@@ -8,9 +8,9 @@ - SRC = lds2 lds2_db lds2_handlers - - # Dependencies for shared library --#DLL_LIB = sqlitewrapp -+DLL_LIB = sqlitewrapp $(COMPRESS_LIBS) - --LIBS = $(CMPRS_LIBS) $(ORIG_LIBS) -+LIBS = $(SQLITE3_LIBS) $(CMPRS_LIBS) $(ORIG_LIBS) - - CPPFLAGS = $(SQLITE3_INCLUDE) $(CMPRS_INCLUDE) $(ORIG_CPPFLAGS) - -Index: src/objtools/readers/Makefile.xobjread.lib -=================================================================== ---- src/objtools/readers/Makefile.xobjread.lib (revision 439078) -+++ src/objtools/readers/Makefile.xobjread.lib (working copy) -@@ -19,5 +19,6 @@ - best_feat_finder source_mod_parser fasta_exception - - --DLL_LIB = creaders -+DLL_LIB = seqset $(SEQ_LIBS) pub general creaders xutil - -+ -Index: src/sample/app/cgi/Makefile.cgi_session_sample.app -=================================================================== ---- src/sample/app/cgi/Makefile.cgi_session_sample.app (revision 439078) -+++ src/sample/app/cgi/Makefile.cgi_session_sample.app (working copy) -@@ -11,7 +11,7 @@ - # the lines reading "### BEGIN/END COPIED SETTINGS" in any way. - - ### BEGIN COPIED SETTINGS --LIB = xgridcgi xcgi xhtml xconnserv xconnect xutil xncbi -+LIB = xgridcgi xcgi xhtml xconnserv xthrserv xconnect xutil xncbi - - LIBS = $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) - -Index: src/sample/app/netcache/Makefile.netcache_cgi_sample.app -=================================================================== ---- src/sample/app/netcache/Makefile.netcache_cgi_sample.app (revision 439078) -+++ src/sample/app/netcache/Makefile.netcache_cgi_sample.app (working copy) -@@ -4,7 +4,7 @@ - SRC = netcache_cgi_sample - - ### BEGIN COPIED SETTINGS --LIB = xconnserv xconnect xcgi xhtml xutil xncbi -+LIB = xconnserv xthrserv xconnect xcgi xhtml xutil xncbi - - LIBS = $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) - ### END COPIED SETTINGS -Index: src/serial/Makefile.serial.lib -=================================================================== ---- src/serial/Makefile.serial.lib (revision 439078) -+++ src/serial/Makefile.serial.lib (working copy) -@@ -19,3 +19,5 @@ - LIB = xser - - WATCHERS = gouriano -+ -+DLL_LIB = xutil xncbi -Index: src/sra/data_loaders/bam/test/Makefile.test_bam_loader.app -=================================================================== ---- src/sra/data_loaders/bam/test/Makefile.test_bam_loader.app (revision 439078) -+++ src/sra/data_loaders/bam/test/Makefile.test_bam_loader.app (working copy) -@@ -7,7 +7,8 @@ - - CPPFLAGS = $(ORIG_CPPFLAGS) $(BOOST_INCLUDE) - --LIB = ncbi_xloader_bam bamread $(BAM_LIBS) xobjreadex xobjutil test_boost $(OBJMGR_LIBS) -+LIB = ncbi_xloader_bam bamread $(BAM_LIBS) \ -+ xobjreadex $(OBJREAD_LIBS) xobjutil test_boost $(OBJMGR_LIBS) - - LIBS = $(SRA_SDK_SYSLIBS) $(CMPRS_LIBS) $(NETWORK_LIBS) $(ORIG_LIBS) - -Index: src/sra/data_loaders/csra/test/Makefile.test_csra_loader.app -=================================================================== ---- src/sra/data_loaders/csra/test/Makefile.test_csra_loader.app (revision 439078) -+++ src/sra/data_loaders/csra/test/Makefile.test_csra_loader.app (working copy) -@@ -5,7 +5,8 @@ - - CPPFLAGS = $(ORIG_CPPFLAGS) $(BOOST_INCLUDE) - --LIB = ncbi_xloader_csra $(SRAREAD_LIBS) xobjreadex xobjutil test_boost $(OBJMGR_LIBS) -+LIB = ncbi_xloader_csra $(SRAREAD_LIBS) xobjreadex $(OBJREAD_LIBS) xobjutil \ -+ test_boost $(OBJMGR_LIBS) - - LIBS = $(SRA_SDK_SYSLIBS) $(CMPRS_LIBS) $(NETWORK_LIBS) $(ORIG_LIBS) - -Index: src/sra/readers/bam/test/Makefile.bam_test.app -=================================================================== ---- src/sra/readers/bam/test/Makefile.bam_test.app (revision 439078) -+++ src/sra/readers/bam/test/Makefile.bam_test.app (working copy) -@@ -9,7 +9,8 @@ - APP = bam_test - SRC = bam_test - --LIB = bamread xobjreadex xobjutil xobjsimple $(OBJMGR_LIBS) $(BAM_LIBS) -+LIB = bamread $(BAM_LIBS) xobjreadex $(OBJREAD_LIBS) xobjutil xobjsimple \ -+ $(OBJMGR_LIBS) - LIBS = $(SRA_SDK_SYSLIBS) $(CMPRS_LIBS) $(NETWORK_LIBS) $(ORIG_LIBS) - - REQUIRES = objects -Index: src/sra/sdk/libs/vfs/Makefile.vfs.lib -=================================================================== ---- src/sra/sdk/libs/vfs/Makefile.vfs.lib (revision 16076) -+++ src/sra/sdk/libs/vfs/Makefile.vfs.lib (working copy) -@@ -8,6 +8,9 @@ - CPPFLAGS = -I$(srcdir) $(SRA_INCLUDE) $(Z_INCLUDE) $(BZ2_INCLUDE) \ - $(SRA_INTERNAL_CPPFLAGS) -D_LIBRARY -DALWAYS_ADD_EXE $(ORIG_CPPFLAGS) - --DLL_LIB = srapath$(DLL) kurl$(DLL) krypto$(DLL) kfg$(DLL) kfs$(DLL) klib$(DLL) -+DLL_LIB = srapath$(FORCE_STATIC) kurl$(FORCE_STATIC) \ -+ krypto$(DLL) kfg$(DLL) kfs$(DLL) klib$(DLL) - -+LIBS = $(SRA_SDK_SYSLIBS) -+ - LIB_OR_DLL = both diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-more-patches.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-more-patches.patch deleted file mode 100644 index 449bbc5a9..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-more-patches.patch +++ /dev/null @@ -1,136 +0,0 @@ ---- ncbi_cxx--12_0_0/include/common/config/ncbiconf_msvc.h.ori 2013/09/30 13:46:04 59961 -+++ ncbi_cxx--12_0_0/include/common/config/ncbiconf_msvc.h 2013/09/30 14:10:44 59962 -@@ -62,10 +62,6 @@ - #define HAVE_SYS_TYPES_H 1 - #define HAVE_VSNPRINTF 1 - --#if _MSC_VER >= 1600 --# define HAVE_IS_SORTED 1 --#endif -- - #if _MSC_VER < 1500 - # define vsnprintf _vsnprintf - #endif -@@ -136,10 +132,6 @@ - - #endif - --#if _MSC_VER >= 1600 --# define HAVE_NULLPTR 1 --#endif -- - /* Windows XP and above */ - #define NCBI_WIN32_WINNT 0x0501 - #if !defined(_WIN32_WINNT) ---- ncbi_cxx--12_0_0/include/common/config/ncbiconf_xcode.h.ori 2013/09/30 13:46:04 59961 -+++ ncbi_cxx--12_0_0/include/common/config/ncbiconf_xcode.h 2013/09/30 14:10:44 59962 -@@ -258,9 +258,6 @@ - /* Define to 1 if you have `ios(_base)::register_callback'. */ - #define HAVE_IOS_REGISTER_CALLBACK 1 - --/* Define to 1 if <algorithm> supplies `std::is_sorted<>'. */ --/* #undef HAVE_IS_SORTED */ -- - /* Define to 1 if you have the `lchown' function. */ - /* #undef HAVE_LCHOWN */ - -@@ -595,9 +592,6 @@ - /* Define to 1 if wxWidgets is available. */ - /* #undef HAVE_WXWIDGETS */ - --/* Define to 1 if nullptr keyword is available. */ --/* #undef HAVE_NULLPTR */ -- - /* Define as const if the declaration of iconv() needs const. */ - #if MAC_OS_X_VERSION_MIN_REQUIRED >= 1050 /* MAC_OS_X_VERSION_10_5 */ - # define ICONV_CONST ---- ncbi_cxx--12_0_0/include/common/ncbiconf_impl.h.ori 2013/09/30 13:46:04 59961 -+++ ncbi_cxx--12_0_0/include/common/ncbiconf_impl.h 2013/09/30 14:10:44 59962 -@@ -115,6 +115,11 @@ - || defined(__GXX_EXPERIMENTAL_CPP0X__) - # define NCBI_HAVE_CXX11 1 - # endif -+# if defined(NCBI_HAVE_CXX11) \ -+ || (defined(NCBI_COMPILER_MSVC) && _MSC_VER >= 1600) -+# define HAVE_IS_SORTED 1 -+# define HAVE_NULLPTR 1 -+# endif - #endif - - #include <common/ncbi_skew_guard.h> ---- ncbi_cxx--12_0_0/src/build-system/config.h.in.ori 2013/09/30 13:46:04 59961 -+++ ncbi_cxx--12_0_0/src/build-system/config.h.in 2013/09/30 14:10:44 59962 -@@ -179,9 +179,6 @@ - /* Define to 1 if you have `ios(_base)::register_callback'. */ - #undef HAVE_IOS_REGISTER_CALLBACK - --/* Define to 1 if <algorithm> supplies `std::is_sorted<>'. */ --#undef HAVE_IS_SORTED -- - /* Define to 1 if you have the `lchown' function. */ - #undef HAVE_LCHOWN - -@@ -391,9 +388,6 @@ - /* Define to 1 if `min'/`max' templates are not implemented. */ - #undef HAVE_NO_MINMAX_TEMPLATE - --/* Define to 1 if your C++ compiler supports the C++0x `nullptr' keyword. */ --#undef HAVE_NULLPTR -- - /* Define to 1 if ODBC libraries are available. */ - #undef HAVE_ODBC - ---- ncbi_cxx--12_0_0/src/build-system/configure.ac.ori 2013/09/30 13:46:04 59961 -+++ ncbi_cxx--12_0_0/src/build-system/configure.ac 2013/09/30 14:10:44 59962 -@@ -3351,17 +3351,6 @@ - fi - - --AC_CACHE_CHECK([for std::is_sorted<> in <algorithm>], ncbi_cv_func_is_sorted, -- [AC_COMPILE_IFELSE([AC_LANG_PROGRAM( -- [[#include <algorithm>]], -- [[int a[2]; return std::is_sorted(a, a+2) ? 0 : 1;]])], -- [ncbi_cv_func_is_sorted=yes], [ncbi_cv_func_is_sorted=no])]) --if test "$ncbi_cv_func_is_sorted" = yes; then -- AC_DEFINE(HAVE_IS_SORTED, 1, -- [Define to 1 if <algorithm> supplies `std::is_sorted<>'.]) --fi -- -- - - AC_CACHE_CHECK([for SysV semaphores], ncbi_cv_sys_semaphores, - AC_LINK_IFELSE([AC_LANG_PROGRAM([#include <sys/types.h> -@@ -3498,7 +3487,7 @@ - AC_CACHE_CHECK([whether the C compiler supports C99 restrict], - ncbi_cv_c_restrict, - [ncbi_cv_c_restrict=no -- for restrict in restrict __restrict__ __restrict; do -+ for restrict in __restrict__ __restrict restrict; do - test "$ncbi_cv_c_restrict" = "no" || break - AC_COMPILE_IFELSE([AC_LANG_SOURCE([void f(int * $restrict p);])], - [ncbi_cv_c_restrict=$restrict], []) -@@ -3518,7 +3507,7 @@ - AC_CACHE_CHECK([whether the C++ compiler supports C99 restrict], - ncbi_cv_cxx_restrict, - [ncbi_cv_cxx_restrict=no -- for restrict in restrict __restrict__ __restrict; do -+ for restrict in __restrict__ __restrict restrict; do - test "$ncbi_cv_cxx_restrict" = "no" || break - AC_COMPILE_IFELSE([AC_LANG_SOURCE([void f(int * $restrict p);])], - [ncbi_cv_cxx_restrict=$restrict], []) -@@ -3623,14 +3612,6 @@ - unaligned addresses.]) - fi - --AC_CACHE_CHECK([whether $CXX supports C++0x nullptr], ncbi_cv_cxx_nullptr, -- [AC_COMPILE_IFELSE([AC_LANG_PROGRAM([], [[void * p = nullptr;]])], -- [ncbi_cv_cxx_nullptr=yes], [ncbi_cv_cxx_nullptr=no])]) --if test "$ncbi_cv_cxx_nullptr" = yes; then -- AC_DEFINE(HAVE_NULLPTR, 1, -- [Define to 1 if your C++ compiler supports the C++0x `nullptr' keyword.]) --fi -- - ### Check for the availability of other packages - ### -------------------------------------------- - - diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-never_build_test_boost.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-never_build_test_boost.patch deleted file mode 100644 index 68baea046..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-never_build_test_boost.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- ncbi_cxx--12_0_0/src/corelib/Makefile.in.ori 2016-12-01 20:28:33.239758102 +0100 -+++ ncbi_cxx--12_0_0/src/corelib/Makefile.in 2016-12-01 20:28:46.330110659 +0100 -@@ -7,7 +7,7 @@ - ################################# - - USR_PROJ = precompile --LIB_PROJ = corelib test_mt test_boost -+LIB_PROJ = corelib test_mt - SUB_PROJ = test - PROJ_TAG = core - diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-support-autoconf-2.60.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-support-autoconf-2.60.patch deleted file mode 100644 index 9047c3384..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-support-autoconf-2.60.patch +++ /dev/null @@ -1,296 +0,0 @@ ---- ncbi_cxx--12_0_0/src/build-system/aclocal.m4.ori 2014/05/05 12:38:59 62744 -+++ ncbi_cxx--12_0_0/src/build-system/aclocal.m4 2014/05/05 13:59:33 62745 -@@ -1,126 +1,44 @@ --# Hacked up in various ways, since Autoconf's version doesn't quite --# suit our (unusual) conventions. (Originally from status.m4) --m4_define([_AC_SRCPATHS], --[#ac_builddir=. # Useless! --ac_builddir=$builddir --dnl Base source directories on path to *input* file. --if test -n "$ac_file_in"; then -- ac_dir_in=`AS_DIRNAME(["$ac_file_in"])` -+# Autoconf's _AC_SRCDIRS (from status.m4; historically _AC_SRCPATHS) -+# doesn't quite suit the C++ Toolkit's conventions; tweak it accordingly. -+m4_copy([_AC_SRCDIRS], [NCBI_ORIG__AC_SRCDIRS]) -+m4_define([_AC_SRCDIRS], -+[# Base source directories on path to *input* file. -+if test -n "$ac_f"; then -+ ac_dir_in=`AS_DIRNAME(["$ac_f"])` - else - ac_dir_in=$1 - fi - --if test $ac_dir_in != .; then -- ac_dir_suffix=`echo $ac_dir_in | sed 's,^\.[[\\/]],,'` -- # A "../" for each directory in $ac_dir_suffix. -- ac_top_builddir=../`echo "$ac_dir_suffix" | sed 's,/[[^\\/]]*,../,g'` --else -- ac_dir_suffix= ac_top_builddir= --fi -+NCBI_ORIG__AC_SRCDIRS(["$ac_dir_in"]) - --case $srcdir in -- .) # No --srcdir option. We are building in place. -- ac_srcdir=. -- if test -z "$ac_top_builddir"; then -- ac_top_srcdir=. -- else -- ac_top_srcdir=`echo $ac_top_builddir | sed 's,/$,,'` -- fi ;; -- [[\\/]]* | ?:[[\\/]]* ) # Absolute path. -- ac_srcdir=$srcdir/$ac_dir_suffix; -- ac_top_srcdir=$srcdir ;; -- *) # Relative path. -- ac_srcdir=$ac_top_builddir$srcdir/$ac_dir_suffix -- ac_top_srcdir=$ac_top_builddir$srcdir ;; --esac --# Do not use `cd foo && pwd` to compute absolute paths, because --# the directories may not exist. --AS_SET_CATFILE([ac_abs_builddir], [$builddir], [$1]) --AS_SET_CATFILE([ac_abs_top_builddir], -- [$ac_abs_builddir], [${ac_top_builddir}.]) --AS_SET_CATFILE([ac_abs_top_srcdir], [$ac_dir_in], [$real_srcdir]) --AS_SET_CATFILE([ac_abs_srcdir], [$ac_abs_top_srcdir], [$ac_dir_suffix]) --])# _AC_SRCPATHS -- -- --# Copied from autoconf 2.59 (m4sh.m4), but rearranged to make bash a --# last resort due to issues with sourcing .bashrc. --m4_define([_AS_LINENO_PREPARE], --[_AS_LINENO_WORKS || { -- # Find who we are. Look in the path if we contain no path at all -- # relative or not. -- case $[0] in -- *[[\\/]]* ) as_myself=$[0] ;; -- *) _AS_PATH_WALK([], -- [test -r "$as_dir/$[0]" && as_myself=$as_dir/$[0] && break]) -- ;; -- esac -- # We did not find ourselves, most probably we were run as `sh COMMAND' -- # in which case we are not to be found in the path. -- if test "x$as_myself" = x; then -- as_myself=$[0] -- fi -- if test ! -f "$as_myself"; then -- AS_ERROR([cannot find myself; rerun with an absolute path]) -- fi -- case $CONFIG_SHELL in -- '') -- AS_UNSET(ZSH_VERSION) -- for as_base in sh ksh sh5 bash; do -- _AS_PATH_WALK([/bin$PATH_SEPARATOR/usr/bin$PATH_SEPARATOR$PATH], -- [case $as_dir in -- /*) -- if ("$as_dir/$as_base" -c \ -- 'test -z "$ZSH_VERSION" && { _AS_LINENO_WORKS; }') 2>/dev/null -- then -- AS_UNSET(BASH_ENV) -- AS_UNSET(ENV) -- CONFIG_SHELL=$as_dir/$as_base -- export CONFIG_SHELL -- exec "$CONFIG_SHELL" "$[0]" ${1+"$[@]"} -- fi;; -- esac -- done]);; -- esac -- -- # Create $as_me.lineno as a copy of $as_myself, but with $LINENO -- # uniformly replaced by the line number. The first 'sed' inserts a -- # line-number line before each line; the second 'sed' does the real -- # work. The second script uses 'N' to pair each line-number line -- # with the numbered line, and appends trailing '-' during -- # substitution so that $LINENO is not a special case at line end. -- # (Raja R Harinath suggested sed '=', and Paul Eggert wrote the -- # second 'sed' script. Blame Lee E. McMahon for sed's syntax. :-) -- sed '=' <$as_myself | -- sed ' -- N -- s,$,-, -- : loop -- s,^\([['$as_cr_digits']]*\)\(.*\)[[$]]LINENO\([[^'$as_cr_alnum'_]]\),\1\2\1\3, -- t loop -- s,-$,, -- s,^[['$as_cr_digits']]*\n,, -- ' >$as_me.lineno && -- chmod +x $as_me.lineno || -- AS_ERROR([cannot create $as_me.lineno; rerun with a POSIX shell]) -- -- # Don't try to exec as it changes $[0], causing all sort of problems -- # (the dirname of $[0] is not the place where we might find the -- # original and so on. Autoconf is especially sensible to this). -- . ./$as_me.lineno -- # Exit status is that of the last command. -- exit --} --])# _AS_LINENO_PREPARE -+ac_builddir=$builddir -+]) -+ -+ -+# _AS_DETECT_BETTER_SHELL and its helper _AS_RUN (from m4sh.m4; both -+# historically part of _AS_LINENO_PREPARE) also need tweaking, to make -+# bash a last resort due to issues with sourcing .bashrc while entirely -+# avoiding zsh, which passes itself off as ksh on some systems but runs -+# parent shells' exit handlers from subshells, resulting in premature -+# cleanup of temporary files (notably confdefs.h). -+m4_copy([_AS_DETECT_BETTER_SHELL], [NCBI_ORIG__AS_DETECT_BETTER_SHELL]) -+m4_copy([_AS_RUN], [NCBI_ORIG___AS_RUN]) -+ -+m4_define([_AS_DETECT_BETTER_SHELL], -+ [patsubst(m4_defn([NCBI_ORIG__AS_DETECT_BETTER_SHELL]), -+ [sh bash ksh sh5], [sh ksh sh5 bash])]) -+m4_define([_AS_RUN], -+[m4_divert_once([M4SH-SANITIZE], [AS_UNSET(ZSH_VERSION)])dnl -+NCBI_ORIG___AS_RUN([test -z "${ZSH_VERSION+set}" || exit $?; $1], [$2])]) - - - # One more hack: suppress PACKAGE_*, as we don't use them and some - # third-party libraries expose their corresponding settings, leading - # to preprocessor warnings. --m4_define([NCBI_ORIG_ACDU], m4_defn([AC_DEFINE_UNQUOTED])) -+m4_copy([AC_DEFINE_UNQUOTED], [NCBI_ORIG_AC_DEFINE_UNQUOTED]) - m4_define([AC_DEFINE_UNQUOTED], - [ifelse(m4_substr([$1], 0, 8), [PACKAGE_], [], -- [NCBI_ORIG_ACDU($@)])]) -+ [NCBI_ORIG_AC_DEFINE_UNQUOTED($@)])]) - - - AC_DEFUN(NCBI_FIX_DIR, -@@ -158,7 +76,7 @@ - AC_MSG_WARN([Proceeding without questions per --without-caution]) ;; - * ) - echo "$1 [[y/N]]" -- read answer -+ read answer <& AS_ORIGINAL_STDIN_FD - case "$answer" in - [[Yy]]* ) AC_MSG_WARN([Proceeding at your own risk...]) ;; - * ) AC_MSG_ERROR([Configuration has been canceled by user.]) ;; ---- ncbi_cxx--12_0_0/src/build-system/configure.ac.ori 2014/05/05 12:38:59 62744 -+++ ncbi_cxx--12_0_0/src/build-system/configure.ac 2014/05/05 13:59:33 62745 -@@ -38,7 +38,7 @@ - # - ############################################################################# - --AC_PREREQ(2.59) -+AC_PREREQ(2.60) - - dnl Early setup, most crucially for locking. The diversion magic lets - dnl this occur before AC_INIT, which already interferes with other -@@ -493,6 +493,10 @@ - [***** See also HTML documentation in ./doc/index.html *****]) - - -+AC_DIVERT_PUSH(PARSE_ARGS) -+dnl As of Autoconf 2.60, this needs to run too early for config.log, -+dnl to which AC_MSG_ERROR normally copies its output, to be available. -+m4_rename([AS_MESSAGE_LOG_FD], [NCBI_ORIG_ASMLFD]) - #### Check the passed arguments against the list of available ones - x_with_list="\ - debug max-debug symbols optimization profiling tcheck dll static static-exe \ -@@ -564,7 +568,7 @@ - | --with-muparser=* | --with-hdf5=* | --with-jni=* | --with-magic=* \ - | --x-includes=* | --x-libraries=* | --with-3psw=* \ - | --target=* | --with-runpath=* | --with-relative-runpath=* \ -- | --no-create | --no-recursion) -+ | --help | --no-create | --no-recursion) - ;; - - * ) -@@ -572,6 +576,8 @@ - ;; - esac - done -+m4_rename([NCBI_ORIG_ASMLFD], [AS_MESSAGE_LOG_FD]) -+AC_DIVERT_POP - - - if test "$with_gbench" = "yes" ; then -@@ -2176,7 +2182,7 @@ - fi - - AC_PATH_PROG(TOUCH, touch, [], /bin:/usr/bin:$PATH) --AC_PATH_PROG(GREP, grep) -+dnl AC_PATH_PROG(GREP, grep) - AC_PROG_EGREP - AC_MSG_CHECKING([how to run $EGREP quietly]) - if test -z "`echo foo | $EGREP -q fo+ 2>>config.log || echo $?`"; then ---- ncbi_cxx--12_0_0/include/common/config/ncbiconf_xcode.h.ori 2014/05/05 14:10:55 62749 -+++ ncbi_cxx--12_0_0/include/common/config/ncbiconf_xcode.h 2014/05/05 14:23:49 62750 -@@ -694,7 +694,7 @@ - /* Define to empty if `const' does not conform to ANSI C. */ - /* #undef const */ - --/* Define to `unsigned' if <sys/types.h> does not define. */ -+/* Define to `unsigned int' if <sys/types.h> does not define. */ - /* #undef size_t */ - - /* ---- ncbi_cxx--12_0_0/src/build-system/config.h.in.ori 2014/05/05 14:10:55 62749 -+++ ncbi_cxx--12_0_0/src/build-system/config.h.in 2014/05/05 14:23:49 62750 -@@ -802,37 +802,37 @@ - by a signal. */ - #undef SELECT_UPDATES_TIMEOUT - --/* The size of a `char', as computed by sizeof. */ -+/* The size of `char', as computed by sizeof. */ - #undef SIZEOF_CHAR - --/* The size of a `double', as computed by sizeof. */ -+/* The size of `double', as computed by sizeof. */ - #undef SIZEOF_DOUBLE - --/* The size of a `float', as computed by sizeof. */ -+/* The size of `float', as computed by sizeof. */ - #undef SIZEOF_FLOAT - --/* The size of a `int', as computed by sizeof. */ -+/* The size of `int', as computed by sizeof. */ - #undef SIZEOF_INT - --/* The size of a `long', as computed by sizeof. */ -+/* The size of `long', as computed by sizeof. */ - #undef SIZEOF_LONG - --/* The size of a `long double', as computed by sizeof. */ -+/* The size of `long double', as computed by sizeof. */ - #undef SIZEOF_LONG_DOUBLE - --/* The size of a `long long', as computed by sizeof. */ -+/* The size of `long long', as computed by sizeof. */ - #undef SIZEOF_LONG_LONG - --/* The size of a `short', as computed by sizeof. */ -+/* The size of `short', as computed by sizeof. */ - #undef SIZEOF_SHORT - --/* The size of a `size_t', as computed by sizeof. */ -+/* The size of `size_t', as computed by sizeof. */ - #undef SIZEOF_SIZE_T - --/* The size of a `void*', as computed by sizeof. */ -+/* The size of `void*', as computed by sizeof. */ - #undef SIZEOF_VOIDP - --/* The size of a `__int64', as computed by sizeof. */ -+/* The size of `__int64', as computed by sizeof. */ - #undef SIZEOF___INT64 - - /* Define to 1 if the stack grows down. */ -@@ -873,5 +873,5 @@ - /* Define to empty if `const' does not conform to ANSI C. */ - #undef const - --/* Define to `unsigned' if <sys/types.h> does not define. */ -+/* Define to `unsigned int' if <sys/types.h> does not define. */ - #undef size_t ---- ncbi_cxx--12_0_0/src/build-system/aclocal.m4.ori 2014/05/06 13:12:18 62759 -+++ ncbi_cxx--12_0_0/src/build-system/aclocal.m4 2014/05/06 13:42:48 62760 -@@ -11,6 +11,7 @@ - - NCBI_ORIG__AC_SRCDIRS(["$ac_dir_in"]) - -+AS_SET_CATFILE([ac_abs_top_srcdir], [$ac_dir_in], [$real_srcdir]) - ac_builddir=$builddir - ]) - - diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-configure.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-configure.patch deleted file mode 100644 index b2d887c92..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-configure.patch +++ /dev/null @@ -1,20 +0,0 @@ ---- ncbi_cxx--12_0_0/src/build-system/configure.ori 2014-06-25 23:47:05.000000000 +0200 -+++ ncbi_cxx--12_0_0/src/build-system/configure 2014-06-25 23:52:35.000000000 +0200 -@@ -3201,6 +3203,17 @@ - *\ -O* | *\ -xO* ) skip_fast_flags=yes ;; - esac - fi -+if test -n "$with_projects"; then -+ case "$with_projects" in -+ /* ) abs_projects=$with_projects ;; -+ yes) abs_projects=$srcdir/projects ;; -+ * ) abs_projects=$srcdir/$with_projects ;; -+ esac -+ test -r "$abs_projects" || \ -+ { { echo "$as_me:$LINENO: error: unable to read requested projects file \"$abs_projects\"." >&5 -+echo "$as_me: error: unable to read requested projects file \"$abs_projects\"." >&2;} -+ { (exit 1); exit 1; }; } -+fi - - #### Always define this - diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-annotwriter-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-annotwriter-linking.patch deleted file mode 100644 index c9428084d..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-annotwriter-linking.patch +++ /dev/null @@ -1,15 +0,0 @@ -Index: c++.18.0.0/src/app/annotwriter/Makefile.annotwriter.app -=================================================================== ---- c++.18.0.0/src/app/annotwriter/Makefile.annotwriter.app (revision 523253) -+++ c++.18.0.0/src/app/annotwriter/Makefile.annotwriter.app (working copy) -@@ -8,8 +8,8 @@ - - APP = annotwriter - SRC = annotwriter --LIB = xobjwrite variation_utils $(OBJREAD_LIBS) xalnmgr xobjutil \ -- gbseq entrez2cli entrez2 tables $(OBJMGR_LIBS) -+LIB = xobjwrite $(XFORMAT_LIBS) variation_utils $(OBJREAD_LIBS) xalnmgr \ -+ xobjutil entrez2cli entrez2 tables xregexp $(PCRE_LIB) $(OBJMGR_LIBS) - - LIBS = $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) - diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-blast_sample-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-blast_sample-linking.patch deleted file mode 100644 index 7a158dc5c..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-blast_sample-linking.patch +++ /dev/null @@ -1,26 +0,0 @@ -Index: c++.18.0.0/src/sample/app/blast/Makefile.blast_sample.app -=================================================================== ---- c++.18.0.0/src/sample/app/blast/Makefile.blast_sample.app (revision 523253) -+++ c++.18.0.0/src/sample/app/blast/Makefile.blast_sample.app (working copy) -@@ -12,7 +12,7 @@ - # the lines reading "### BEGIN/END COPIED SETTINGS" in any way. - - ### BEGIN COPIED SETTINGS --LIB_ = xobjsimple $(BLAST_LIBS) $(OBJMGR_LIBS) -+LIB_ = xobjsimple $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS) - LIB = $(LIB_:%=%$(STATIC)) - LIBS = $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) - -Index: c++.18.0.0/src/sample/app/blast/Makefile.vsrun_sample.app -=================================================================== ---- c++.18.0.0/src/sample/app/blast/Makefile.vsrun_sample.app (revision 523253) -+++ c++.18.0.0/src/sample/app/blast/Makefile.vsrun_sample.app (working copy) -@@ -12,7 +12,7 @@ - # the lines reading "### BEGIN/END COPIED SETTINGS" in any way. - - ### BEGIN COPIED SETTINGS --LIB_ = xobjsimple $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS) -+LIB_ = xobjsimple $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS) - LIB = $(LIB_:%=%$(STATIC)) - LIBS = $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) - diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-compartp-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-compartp-linking.patch deleted file mode 100644 index 749c2e57f..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-compartp-linking.patch +++ /dev/null @@ -1,29 +0,0 @@ -Index: c++.18.0.0/src/app/compart/Makefile.compart.app -=================================================================== ---- c++.18.0.0/src/app/compart/Makefile.compart.app (revision 523253) -+++ c++.18.0.0/src/app/compart/Makefile.compart.app (working copy) -@@ -5,8 +5,8 @@ - APP = compart - SRC = compart - --LIB = xalgoalignsplign xalgoalignutil xalgoalignnw xqueryparse \ -- $(BLAST_LIBS:%=%$(STATIC)) \ -+LIB = xalgoalignsplign xalgoalignutil xalgoalignnw xalgoseq taxon1 \ -+ $(BLAST_LIBS:%=%$(STATIC)) xqueryparse xregexp $(PCRE_LIB) \ - $(OBJMGR_LIBS:%=%$(STATIC)) - - LIBS = $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) -Index: c++.18.0.0/src/app/compart/Makefile.compartp.app -=================================================================== ---- c++.18.0.0/src/app/compart/Makefile.compartp.app (revision 523253) -+++ c++.18.0.0/src/app/compart/Makefile.compartp.app (working copy) -@@ -5,7 +5,8 @@ - APP = compartp - SRC = compartp - --LIB = prosplign xalgoalignutil $(BLAST_LIBS) xqueryparse $(OBJMGR_LIBS) -+LIB = prosplign xalgoalignutil xalgoseq taxon1 $(BLAST_LIBS) xqueryparse \ -+ xregexp $(PCRE_LIB) $(OBJMGR_LIBS) - - LIBS = $(CMPRS_LIBS) $(PCRE_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) - diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-convert_seq-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-convert_seq-linking.patch deleted file mode 100644 index e495c9645..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-convert_seq-linking.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- ncbi_cxx--18_0_0/src/app/convert_seq/Makefile.convert_seq.app.ori 2017-03-23 19:24:31.534280319 +0100 -+++ ncbi_cxx--18_0_0/src/app/convert_seq/Makefile.convert_seq.app 2017-03-23 19:25:14.395360214 +0100 -@@ -2,7 +2,7 @@ - - APP = convert_seq - SRC = convert_seq --LIB = $(ncbi_xloader_wgs) $(SRAREAD_LIBS) xobjwrite \ -+LIB = $(ncbi_xloader_wgs) $(SRAREAD_LIBS) xobjwrite variation_utils \ - $(OBJREAD_LIBS) $(XFORMAT_LIBS) xalnmgr xobjutil tables xregexp \ - $(PCRE_LIB) $(OBJMGR_LIBS) - diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-hfilter-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-hfilter-linking.patch deleted file mode 100644 index 63bbcc45a..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-hfilter-linking.patch +++ /dev/null @@ -1,14 +0,0 @@ -Index: c++.18.0.0/src/app/hfilter/Makefile.hfilter.app -=================================================================== ---- c++.18.0.0/src/app/hfilter/Makefile.hfilter.app (revision 523253) -+++ c++.18.0.0/src/app/hfilter/Makefile.hfilter.app (working copy) -@@ -5,7 +5,8 @@ - APP = hfilter - SRC = hitfilter_app - --LIB = xalgoalignutil $(BLAST_LIBS) xqueryparse $(OBJMGR_LIBS) -+LIB = xalgoalignutil xalgoseq taxon1 $(BLAST_LIBS) \ -+ xqueryparse xregexp $(PCRE_LIB) $(OBJMGR_LIBS) - - LIBS = $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) - diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-igblast-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-igblast-linking.patch deleted file mode 100644 index ffd3f897f..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-igblast-linking.patch +++ /dev/null @@ -1,28 +0,0 @@ -Index: c++.18.0.0/src/app/igblast/Makefile.igblastn.app -=================================================================== ---- c++.18.0.0/src/app/igblast/Makefile.igblastn.app (revision 523253) -+++ c++.18.0.0/src/app/igblast/Makefile.igblastn.app (working copy) -@@ -2,7 +2,8 @@ - - APP = igblastn - SRC = igblastn_app --LIB_ = xalgoalignutil $(BLAST_INPUT_LIBS) xqueryparse $(BLAST_LIBS) $(OBJMGR_LIBS) -+LIB_ = xalgoalignutil $(BLAST_INPUT_LIBS) xqueryparse $(BLAST_LIBS) \ -+ xregexp $(PCRE_LIB) $(OBJMGR_LIBS) - LIB = blast_app_util igblast $(LIB_:%=%$(STATIC)) - - # De-universalize Mac builds to work around a PPC toolchain limitation -Index: c++.18.0.0/src/app/igblast/Makefile.igblastp.app -=================================================================== ---- c++.18.0.0/src/app/igblast/Makefile.igblastp.app (revision 523253) -+++ c++.18.0.0/src/app/igblast/Makefile.igblastp.app (working copy) -@@ -2,7 +2,8 @@ - - APP = igblastp - SRC = igblastp_app --LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS) -+LIB_ = xalgoalignutil $(BLAST_INPUT_LIBS) xqueryparse $(BLAST_LIBS) \ -+ xregexp $(PCRE_LIB) $(OBJMGR_LIBS) - LIB = blast_app_util igblast $(LIB_:%=%$(STATIC)) - - # De-universalize Mac builds to work around a PPC toolchain limitation diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-rmblastn-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-rmblastn-linking.patch deleted file mode 100644 index fce7263b2..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-rmblastn-linking.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- ncbi_cxx--18_0_0/src/app/rmblastn/Makefile.rmblastn.app.ori 2017-03-26 18:49:50.431994978 +0200 -+++ ncbi_cxx--18_0_0/src/app/rmblastn/Makefile.rmblastn.app 2017-03-26 18:50:11.222552131 +0200 -@@ -2,7 +2,7 @@ - - APP = rmblastn - SRC = rmblastn_app --LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS) -+LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS) - LIB = blast_app_util $(LIB_:%=%$(STATIC)) - - # De-universalize Mac builds to work around a PPC toolchain limitation diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-table2asn-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-table2asn-linking.patch deleted file mode 100644 index 222cb2c06..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-table2asn-linking.patch +++ /dev/null @@ -1,13 +0,0 @@ ---- ncbi_cxx--18_0_0/src/app/table2asn/Makefile.table2asn.app.ori 2017-03-27 00:41:58.742206850 +0200 -+++ ncbi_cxx--18_0_0/src/app/table2asn/Makefile.table2asn.app 2017-03-27 00:43:13.142206236 +0200 -@@ -12,8 +12,8 @@ - - LIB = xdiscrepancy xalgophytree fastme prosplign xalgoalignutil xalgoseq xmlwrapp \ - xvalidate xobjwrite xobjreadex valerr biotree macro \ -- $(OBJEDIT_LIBS) $(XFORMAT_LIBS) $(BLAST_LIBS) id2cli \ -- xregexp $(PCRE_LIB) $(SRAREAD_LIBS) $(DATA_LOADERS_UTIL_LIB) $(OBJMGR_LIBS) -+ $(OBJEDIT_LIBS) $(XFORMAT_LIBS) $(BLAST_LIBS) taxon1 id2cli \ -+ xregexp $(PCRE_LIB) xqueryparse $(DATA_LOADERS_UTIL_LIB) $(OBJMGR_LIBS) - - LIBS = $(LIBXSLT_LIBS) $(DATA_LOADERS_UTIL_LIBS) $(LIBXML_LIBS) $(CMPRS_LIBS) $(PCRE_LIBS) \ - $(SRA_SDK_SYSLIBS) \ diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-tls-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-tls-linking.patch deleted file mode 100644 index 541dc2514..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-tls-linking.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- ncbi_cxx--18_0_0/src/app/tls/Makefile.tls.app.ori 2017-03-27 02:33:36.312151540 +0200 -+++ ncbi_cxx--18_0_0/src/app/tls/Makefile.tls.app 2017-03-27 02:34:19.372151184 +0200 -@@ -10,7 +10,7 @@ - SRC = tls - - LIB = $(OBJEDIT_LIBS) $(XFORMAT_LIBS) xalnmgr xobjutil \ -- xregexp $(PCRE_LIB) $(OBJMGR_LIBS) -+ xregexp $(PCRE_LIB) tables $(OBJMGR_LIBS) - - LIBS = $(PCRE_LIBS) \ - $(NETWORK_LIBS) $(CMPRS_LIBS) $(ORIG_LIBS) diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-vecscreen-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-vecscreen-linking.patch deleted file mode 100644 index 898e3a70b..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-vecscreen-linking.patch +++ /dev/null @@ -1,13 +0,0 @@ -Index: c++.18.0.0/src/app/vecscreen/Makefile.vecscreen.app -=================================================================== ---- c++.18.0.0/src/app/vecscreen/Makefile.vecscreen.app (revision 523253) -+++ c++.18.0.0/src/app/vecscreen/Makefile.vecscreen.app (working copy) -@@ -4,7 +4,7 @@ - - APP = vecscreen - SRC = vecscreen_app --LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS) -+LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS) - LIB = $(LIB_:%=%$(STATIC)) - # FIXME: do we need blast_app_util - #LIB = blast_app_util $(LIB_:%=%$(STATIC)) diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-apps-blast-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-apps-blast-linking.patch deleted file mode 100644 index e9dd1f710..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-apps-blast-linking.patch +++ /dev/null @@ -1,130 +0,0 @@ -Index: c++.18.0.0/src/app/blast/Makefile.blast_formatter.app -=================================================================== ---- c++.18.0.0/src/app/blast/Makefile.blast_formatter.app (revision 523253) -+++ c++.18.0.0/src/app/blast/Makefile.blast_formatter.app (working copy) -@@ -2,7 +2,7 @@ - - APP = blast_formatter - SRC = blast_formatter --LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS) -+LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS) - LIB = blast_app_util $(LIB_:%=%$(STATIC)) - - # De-universalize Mac builds to work around a PPC toolchain limitation -Index: c++.18.0.0/src/app/blast/Makefile.blastp.app -=================================================================== ---- c++.18.0.0/src/app/blast/Makefile.blastp.app (revision 523253) -+++ c++.18.0.0/src/app/blast/Makefile.blastp.app (working copy) -@@ -4,7 +4,7 @@ - - APP = blastp - SRC = blastp_app --LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS) -+LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS) - LIB = blast_app_util $(LIB_:%=%$(STATIC)) - - # De-universalize Mac builds to work around a PPC toolchain limitation -Index: c++.18.0.0/src/app/blast/Makefile.blastx.app -=================================================================== ---- c++.18.0.0/src/app/blast/Makefile.blastx.app (revision 523253) -+++ c++.18.0.0/src/app/blast/Makefile.blastx.app (working copy) -@@ -4,7 +4,7 @@ - - APP = blastx - SRC = blastx_app --LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS) -+LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS) - LIB = blast_app_util $(LIB_:%=%$(STATIC)) - - # De-universalize Mac builds to work around a PPC toolchain limitation -Index: c++.18.0.0/src/app/blast/Makefile.deltablast.app -=================================================================== ---- c++.18.0.0/src/app/blast/Makefile.deltablast.app (revision 523253) -+++ c++.18.0.0/src/app/blast/Makefile.deltablast.app (working copy) -@@ -1,7 +1,7 @@ - - APP = deltablast - SRC = deltablast_app --LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS) -+LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS) - LIB = blast_app_util $(LIB_:%=%$(STATIC)) - - # De-universalize Mac builds to work around a PPC toolchain limitation -Index: c++.18.0.0/src/app/blast/Makefile.psiblast.app -=================================================================== ---- c++.18.0.0/src/app/blast/Makefile.psiblast.app (revision 523253) -+++ c++.18.0.0/src/app/blast/Makefile.psiblast.app (working copy) -@@ -2,7 +2,7 @@ - - APP = psiblast - SRC = psiblast_app --LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS) -+LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS) - LIB = blast_app_util $(LIB_:%=%$(STATIC)) - - # De-universalize Mac builds to work around a PPC toolchain limitation -Index: c++.18.0.0/src/app/blast/Makefile.rpsblast.app -=================================================================== ---- c++.18.0.0/src/app/blast/Makefile.rpsblast.app (revision 523253) -+++ c++.18.0.0/src/app/blast/Makefile.rpsblast.app (working copy) -@@ -2,7 +2,7 @@ - - APP = rpsblast - SRC = rpsblast_app --LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS) -+LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS) - LIB = blast_app_util $(LIB_:%=%$(STATIC)) - - # De-universalize Mac builds to work around a PPC toolchain limitation -Index: c++.18.0.0/src/app/blast/Makefile.rpstblastn.app -=================================================================== ---- c++.18.0.0/src/app/blast/Makefile.rpstblastn.app (revision 523253) -+++ c++.18.0.0/src/app/blast/Makefile.rpstblastn.app (working copy) -@@ -2,7 +2,7 @@ - - APP = rpstblastn - SRC = rpstblastn_app --LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS) -+LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS) - LIB = blast_app_util $(LIB_:%=%$(STATIC)) - - # De-universalize Mac builds to work around a PPC toolchain limitation -Index: c++.18.0.0/src/app/blast/Makefile.seedtop.app -=================================================================== ---- c++.18.0.0/src/app/blast/Makefile.seedtop.app (revision 523253) -+++ c++.18.0.0/src/app/blast/Makefile.seedtop.app (working copy) -@@ -2,7 +2,7 @@ - - APP = seedtop - SRC = seedtop_app --LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS) -+LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS) - LIB = blast_app_util $(LIB_:%=%$(STATIC)) - - # De-universalize Mac builds to work around a PPC toolchain limitation -Index: c++.18.0.0/src/app/blast/Makefile.tblastn.app -=================================================================== ---- c++.18.0.0/src/app/blast/Makefile.tblastn.app (revision 523253) -+++ c++.18.0.0/src/app/blast/Makefile.tblastn.app (working copy) -@@ -4,7 +4,7 @@ - - APP = tblastn - SRC = tblastn_app --LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS) -+LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS) - LIB = blast_app_util $(LIB_:%=%$(STATIC)) - - # De-universalize Mac builds to work around a PPC toolchain limitation -Index: c++.18.0.0/src/app/blast/Makefile.tblastx.app -=================================================================== ---- c++.18.0.0/src/app/blast/Makefile.tblastx.app (revision 523253) -+++ c++.18.0.0/src/app/blast/Makefile.tblastx.app (working copy) -@@ -4,7 +4,7 @@ - - APP = tblastx - SRC = tblastx_app --LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS) -+LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS) - LIB = blast_app_util $(LIB_:%=%$(STATIC)) - - # De-universalize Mac builds to work around a PPC toolchain limitation diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-install.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-install.patch deleted file mode 100644 index 97e845fdb..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-install.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- ncbi_cxx--12_0_0/src/build-system/Makefile.in.top.ori 2014-06-26 22:49:49.000000000 +0200 -+++ ncbi_cxx--12_0_0/src/build-system/Makefile.in.top 2014-06-26 22:50:57.000000000 +0200 -@@ -48,7 +48,7 @@ - for x in *.a; do ln -s "$$x" "`basename \"$$x\" .a`-static.a"; done - cd $(includedir0) && find * -name CVS -prune -o -print |\ - cpio -pd $(pincludedir) -- $(INSTALL) -m 644 $(incdir)/* $(pincludedir) -+ $(INSTALL) -m 644 $(incdir)/*.* $(pincludedir) - ## set up appropriate build and status directories somewhere under $(libdir)? - - install-gbench: diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-ncfetch-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-ncfetch-linking.patch deleted file mode 100644 index aacb20a6c..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-ncfetch-linking.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- ncbi_cxx--18_0_0/src/app/grid/util/Makefile.ncfetch.app.ori 2017-03-23 21:12:52.028724998 +0100 -+++ ncbi_cxx--18_0_0/src/app/grid/util/Makefile.ncfetch.app 2017-03-23 21:13:30.079737366 +0100 -@@ -5,7 +5,7 @@ - APP = ncfetch.cgi - SRC = ncfetch - --LIB = xcgi xconnserv xconnect xutil xncbi -+LIB = xcgi xconnserv xthrserv xconnect xutil xncbi - LIBS = $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) - - WATCHERS = sadyrovr diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-netcache_cgi_sample-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-netcache_cgi_sample-linking.patch deleted file mode 100644 index e074046cf..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-netcache_cgi_sample-linking.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- ncbi_cxx--18_0_0/src/sample/app/netcache/Makefile.netcache_cgi_sample.app.ori 2017-03-23 21:16:18.824226906 +0100 -+++ ncbi_cxx--18_0_0/src/sample/app/netcache/Makefile.netcache_cgi_sample.app 2017-03-23 21:16:50.085058615 +0100 -@@ -4,7 +4,7 @@ - SRC = netcache_cgi_sample - - ### BEGIN COPIED SETTINGS --LIB = xconnserv xconnect xcgi xhtml xutil xncbi -+LIB = xconnserv xthrserv xconnect xcgi xhtml xutil xncbi - - LIBS = $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) - ### END COPIED SETTINGS diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-netstorage_gc-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-netstorage_gc-linking.patch deleted file mode 100644 index f237a86d8..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-netstorage_gc-linking.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- ncbi_cxx--18_0_0/src/app/netstorage/utils/Makefile.netstorage_gc.app.ori 2017-03-23 21:22:14.463688886 +0100 -+++ ncbi_cxx--18_0_0/src/app/netstorage/utils/Makefile.netstorage_gc.app 2017-03-23 21:22:48.854603873 +0100 -@@ -10,7 +10,7 @@ - REQUIRES = MT Linux - - --LIB = netstorage ncbi_xcache_netcache xconnserv \ -+LIB = netstorage ncbi_xcache_netcache xconnserv xthrserv \ - $(SDBAPI_LIB) xconnect connssl xutil xncbi - LIBS = $(SDBAPI_LIBS) $(NETWORK_LIBS) $(GNUTLS_LIBS) $(CMPRS_LIBS) $(DL_LIBS) $(ORIG_LIBS) - diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-sample-app-cgi-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-sample-app-cgi-linking.patch deleted file mode 100644 index c45d4ad96..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-sample-app-cgi-linking.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- ncbi_cxx--18_0_0/src/sample/app/cgi/Makefile.cgi_session_sample.app.ori 2017-03-22 23:52:58.984696074 +0100 -+++ ncbi_cxx--18_0_0/src/sample/app/cgi/Makefile.cgi_session_sample.app 2017-03-22 23:53:54.746258126 +0100 -@@ -11,7 +11,7 @@ - # the lines reading "### BEGIN/END COPIED SETTINGS" in any way. - - ### BEGIN COPIED SETTINGS --LIB = xgridcgi xcgi xhtml xconnserv xconnect xutil xncbi -+LIB = xgridcgi xcgi xhtml xconnserv xthrserv xconnect xutil xncbi - - LIBS = $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) - diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-speedtest-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-speedtest-linking.patch deleted file mode 100644 index 9435e8b6a..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-speedtest-linking.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- ncbi_cxx--18_0_0/src/app/speedtest/Makefile.speedtest.app.ori 2017-03-23 21:41:31.084603405 +0100 -+++ ncbi_cxx--18_0_0/src/app/speedtest/Makefile.speedtest.app 2017-03-23 21:45:47.601428174 +0100 -@@ -8,7 +8,7 @@ - - APP = speedtest - SRC = speedtest --LIB = prosplign xalgoalignutil xcleanup taxon3 valid valerr $(BLAST_LIBS) \ -+LIB = prosplign xalgoalignutil taxon1 xalgoseq xcleanup taxon3 valid valerr $(BLAST_LIBS) \ - xqueryparse xregexp $(PCRE_LIB) $(OBJMGR_LIBS:%=%$(STATIC)) - - LIBS = $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(PCRE_LIBS) $(ORIG_LIBS) diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-splign-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-splign-linking.patch deleted file mode 100644 index 56f213f08..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-splign-linking.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- ncbi_cxx--18_0_0/src/app/splign/Makefile.splign.app.ori 2017-03-23 22:08:16.937327984 +0100 -+++ ncbi_cxx--18_0_0/src/app/splign/Makefile.splign.app 2017-03-23 22:09:19.208984755 +0100 -@@ -12,7 +12,7 @@ - LIB = xalgoalignsplign xalgoalignutil xalgoalignnw \ - $(BLAST_DB_DATA_LOADER_LIBS) \ - ncbi_xloader_lds2 lds2 sqlitewrapp \ -- xqueryparse xalgoseq $(PCRE_LIB) \ -+ xqueryparse xalgoseq taxon1 xregexp $(PCRE_LIB) \ - $(BLAST_LIBS:%=%$(STATIC)) \ - $(OBJMGR_LIBS:%=%$(STATIC)) - diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-srcchk-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-srcchk-linking.patch deleted file mode 100644 index 49a4adb4e..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-srcchk-linking.patch +++ /dev/null @@ -1,15 +0,0 @@ -Index: c++.18.0.0/src/app/srcchk/Makefile.srcchk.app -=================================================================== ---- c++.18.0.0/src/app/srcchk/Makefile.srcchk.app (revision 523253) -+++ c++.18.0.0/src/app/srcchk/Makefile.srcchk.app (working copy) -@@ -8,8 +8,8 @@ - - APP = srcchk - SRC = srcchk --LIB = xobjwrite variation_utils $(OBJREAD_LIBS) xalnmgr xobjutil \ -- gbseq entrez2cli entrez2 tables $(OBJMGR_LIBS) -+LIB = xobjwrite $(XFORMAT_LIBS) variation_utils $(OBJREAD_LIBS) xalnmgr \ -+ xobjutil entrez2cli entrez2 tables xregexp $(PCRE_LIB) $(OBJMGR_LIBS) - - LIBS = $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) - diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-undefined-lxncbi.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-undefined-lxncbi.patch deleted file mode 100644 index f0a27d85a..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-undefined-lxncbi.patch +++ /dev/null @@ -1,10 +0,0 @@ ---- work/ncbi_cxx--18_0_0/src/connect/Makefile.xthrserv.lib.ori 2017-03-17 22:33:51.569635396 +0100 -+++ ncbi_cxx--18_0_0/src/connect/Makefile.xthrserv.lib 2017-03-17 22:33:58.349811199 +0100 -@@ -4,6 +4,6 @@ - LIB = xthrserv - PROJ_TAG = core - LIBS = $(NETWORK_LIBS) --DLL_LIB = xutil xconnect -+DLL_LIB = xncbi xutil xconnect - - WATCHERS = vakatov diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-undefined-xobjread.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-undefined-xobjread.patch deleted file mode 100644 index 3c1cb0a9e..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-undefined-xobjread.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- ncbi_cxx--18_0_0/src/app/asn2fasta/Makefile.asn2fasta.app.ori 2016-06-24 16:55:25.000000000 +0200 -+++ ncbi_cxx--18_0_0/src/app/asn2fasta/Makefile.asn2fasta.app 2017-03-21 14:07:31.070364301 +0100 -@@ -9,7 +9,7 @@ - APP = asn2fasta - SRC = asn2fasta - LIB = $(ncbi_xloader_wgs) $(SRAREAD_LIBS) \ -- xobjwrite xobjread $(XFORMAT_LIBS) xalnmgr xobjutil valerr xregexp \ -+ xobjwrite variation_utils $(OBJREAD_LIBS) $(XFORMAT_LIBS) xalnmgr xobjutil valerr xregexp \ - ncbi_xdbapi_ftds dbapi $(ncbi_xreader_pubseqos2) $(FTDS_LIB) \ - entrez2cli entrez2 tables $(OBJMGR_LIBS) $(PCRE_LIB) - diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-never_build_test_boost.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-never_build_test_boost.patch deleted file mode 100644 index 68baea046..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-never_build_test_boost.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- ncbi_cxx--12_0_0/src/corelib/Makefile.in.ori 2016-12-01 20:28:33.239758102 +0100 -+++ ncbi_cxx--12_0_0/src/corelib/Makefile.in 2016-12-01 20:28:46.330110659 +0100 -@@ -7,7 +7,7 @@ - ################################# - - USR_PROJ = precompile --LIB_PROJ = corelib test_mt test_boost -+LIB_PROJ = corelib test_mt - SUB_PROJ = test - PROJ_TAG = core - diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-remove-old-symlinks.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-remove-old-symlinks.patch deleted file mode 100644 index 098a9ad1e..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-remove-old-symlinks.patch +++ /dev/null @@ -1,10 +0,0 @@ ---- ncbi_cxx--18_0_0/src/dbapi/lang_bind/python/tests/Makefile.symlink.in.old 2017-03-26 19:01:58.101495278 +0200 -+++ ncbi_cxx--18_0_0/src/dbapi/lang_bind/python/tests/Makefile.symlink.in 2017-03-26 19:02:16.581990522 +0200 -@@ -13,6 +13,7 @@ - -a ! -d $(libdir)/64 ]; then \ - cd $(libdir) && $(LN_S) . 64; \ - fi -+ $(RM) $(LINK) - cd $(libdir) && $(LN_S) libpython_ncbi_dbapi$(loadable_ext) $(LINK) - - clean:; diff --git a/sci-biology/ncbi-tools++/files/report_project_settings_configure.ac.patch b/sci-biology/ncbi-tools++/files/report_project_settings_configure.ac.patch deleted file mode 100644 index 41240c330..000000000 --- a/sci-biology/ncbi-tools++/files/report_project_settings_configure.ac.patch +++ /dev/null @@ -1,64 +0,0 @@ ---- trunk/c++/src/build-system/configure.ac 2012/12/27 15:43:29 56694 -+++ trunk/c++/src/build-system/configure.ac 2013/01/03 03:16:14 56754 -@@ -605,7 +605,8 @@ - fi - - case "$with_projects" in -- "") if test -r projects; then -+ ""|yes) -+ if test -r projects; then - AC_MSG_NOTICE([using default projects file "projects".]) - with_projects=projects - AC_SUBST(PROJECTS, "\$(top_srcdir)/projects") -@@ -623,6 +624,16 @@ - * ) AC_SUBST(PROJECTS, "\$(top_srcdir)/$with_projects") ;; - esac - -+if test -n "$with_projects"; then -+ case "$with_projects" in -+ /* ) abs_projects=$with_projects ;; -+ yes) abs_projects=$srcdir/projects ;; -+ * ) abs_projects=$srcdir/$with_projects ;; -+ esac -+ test -r "$abs_projects" || \ -+ AC_MSG_ERROR([unable to read requested projects file "$abs_projects".]) -+fi -+ - # Check for custom optimization flags before potentially going with defaults. - skip_fast_flags=no - if test -z "${DEF_FAST_FLAGS}${FAST_CXXFLAGS}"; then -@@ -6379,7 +6390,7 @@ - sep=", " - fi - if test -n "$reason" -a "$with_internal" = "yes"; then -- if test -z "$with_projects" -o "$with_projects" = "no"; then -+ if test -z "$with_projects"; then - AC_MSG_ERROR([--with-internal: Cannot build INTERNAL projects: missing $reason]) - else - AC_MSG_WARN([--with-internal: Cannot build all INTERNAL projects: missing $reason]) -@@ -6982,11 +6993,9 @@ - else - cfm_flags='-remoteptb' - fi -- case "$with_projects" in -- yes ) cfm_flags="$cfm_flags -p projects" ;; -- no | '' ) ;; -- * ) cfm_flags="$cfm_flags -p $with_projects" ;; -- esac -+ if test -n "$with_projects"; then -+ cfm_flags="$cfm_flags -p $with_projects" -+ fi - if test "$with_configure_dialog" = yes; then - cfm_flags="$cfm_flags -cfg" - fi -@@ -7029,7 +7038,8 @@ - esac - - if test -n "$with_projects"; then -- build_proj="To build selected projects: cd $builddir && make all_p" -+ build_proj="To build selected projects (as listed in \"$with_projects\"): -+ cd $builddir && make all_p" - fi - - cat << EOCONF - diff --git a/sci-biology/ncbi-tools++/files/report_project_settings_configure.patch b/sci-biology/ncbi-tools++/files/report_project_settings_configure.patch deleted file mode 100644 index 0c1b2d227..000000000 --- a/sci-biology/ncbi-tools++/files/report_project_settings_configure.patch +++ /dev/null @@ -1,66 +0,0 @@ --- trunk/c++/src/build-system/configure 2012/12/27 15:43:29 56694 -+++ trunk/c++/src/build-system/configure 2013/01/03 03:16:14 56754 -@@ -3125,7 +3125,8 @@ - fi - - case "$with_projects" in -- "") if test -r projects; then -+ ""|yes) -+ if test -r projects; then - { echo "$as_me:$LINENO: using default projects file \"projects\"." >&5 - echo "$as_me: using default projects file \"projects\"." >&6;} - with_projects=projects -@@ -3151,6 +3152,18 @@ - ;; - esac - -+if test -n "$with_projects"; then -+ case "$with_projects" in -+ /* ) abs_projects=$with_projects ;; -+ yes) abs_projects=$srcdir/projects ;; -+ * ) abs_projects=$srcdir/$with_projects ;; -+ esac -+ test -r "$abs_projects" || \ -+ { { echo "$as_me:$LINENO: error: unable to read requested projects file \"$abs_projects\"." >&5 -+echo "$as_me: error: unable to read requested projects file \"$abs_projects\"." >&2;} -+ { (exit 1); exit 1; }; } -+fi -+ - # Check for custom optimization flags before potentially going with defaults. - skip_fast_flags=no - if test -z "${DEF_FAST_FLAGS}${FAST_CXXFLAGS}"; then -@@ -33825,7 +33838,7 @@ - sep=", " - fi - if test -n "$reason" -a "$with_internal" = "yes"; then -- if test -z "$with_projects" -o "$with_projects" = "no"; then -+ if test -z "$with_projects"; then - { { echo "$as_me:$LINENO: error: --with-internal: Cannot build INTERNAL projects: missing $reason" >&5 - echo "$as_me: error: --with-internal: Cannot build INTERNAL projects: missing $reason" >&2;} - { (exit 1); exit 1; }; } -@@ -36062,11 +36075,9 @@ - else - cfm_flags='-remoteptb' - fi -- case "$with_projects" in -- yes ) cfm_flags="$cfm_flags -p projects" ;; -- no | '' ) ;; -- * ) cfm_flags="$cfm_flags -p $with_projects" ;; -- esac -+ if test -n "$with_projects"; then -+ cfm_flags="$cfm_flags -p $with_projects" -+ fi - if test "$with_configure_dialog" = yes; then - cfm_flags="$cfm_flags -cfg" - fi -@@ -36110,7 +36121,8 @@ - esac - - if test -n "$with_projects"; then -- build_proj="To build selected projects: cd $builddir && make all_p" -+ build_proj="To build selected projects (as listed in \"$with_projects\"): -+ cd $builddir && make all_p" - fi - - cat << EOCONF - diff --git a/sci-biology/ncbi-tools++/files/respect_CXXFLAGS_configure.ac.patch b/sci-biology/ncbi-tools++/files/respect_CXXFLAGS_configure.ac.patch deleted file mode 100644 index 89dae23ad..000000000 --- a/sci-biology/ncbi-tools++/files/respect_CXXFLAGS_configure.ac.patch +++ /dev/null @@ -1,54 +0,0 @@ ---- trunk/c++/src/build-system/configure.ac 2012/12/21 15:12:14 56664 -+++ trunk/c++/src/build-system/configure.ac 2012/12/27 15:43:29 56694 -@@ -623,6 +623,13 @@ - * ) AC_SUBST(PROJECTS, "\$(top_srcdir)/$with_projects") ;; - esac - -+# Check for custom optimization flags before potentially going with defaults. -+skip_fast_flags=no -+if test -z "${DEF_FAST_FLAGS}${FAST_CXXFLAGS}"; then -+ case " $CFLAGS $CXXFLAGS" in -+ *\ -O* | *\ -xO* ) skip_fast_flags=yes ;; -+ esac -+fi - - #### Always define this - AC_DEFINE(NCBI_CXX_TOOLKIT, 1, [This is the NCBI C++ Toolkit.]) -@@ -1431,7 +1438,7 @@ - wsrx="[[$wschars]]" - - #### Flags to enable (potentially unsafe) extra optimization. --if test -z "$DEF_FAST_FLAGS" -o -z "$FAST_CXXFLAGS" ; then -+if test "$skip_fast_flags" = no -a -z "$DEF_FAST_FLAGS" ; then - case "$compiler:$compiler_version" in - GCC:2* | GCC:344 ) - # GCC 2.9x sometimes experiences internal errors at high optimization; -@@ -1502,8 +1509,6 @@ - DEF_FAST_FLAGS="-O" - ;; - esac --else -- DEF_FAST_FLAGS="-O" - fi - - : ${FAST_CFLAGS="$DEF_FAST_FLAGS"} -@@ -2608,9 +2613,15 @@ - CXXFLAGS="$CXXFLAGS -O" ; fi - if echo " $LDFLAGS " | grep -v "$optrx" >/dev/null ; then - LDFLAGS="$LDFLAGS -O" ; fi -- FAST_CFLAGS="$NOPT_CFLAGS $FAST_CFLAGS" -- FAST_CXXFLAGS="$NOPT_CXXFLAGS $FAST_CXXFLAGS" -- FAST_LDFLAGS="$NOPT_LDFLAGS $FAST_LDFLAGS" -+ if test "$skip_fast_flags" = yes ; then -+ FAST_CFLAGS="$CFLAGS" -+ FAST_CXXFLAGS="$CXXFLAGS" -+ FAST_LDFLAGS="$LDFLAGS" -+ else -+ FAST_CFLAGS="$NOPT_CFLAGS $FAST_CFLAGS" -+ FAST_CXXFLAGS="$NOPT_CXXFLAGS $FAST_CXXFLAGS" -+ FAST_LDFLAGS="$NOPT_LDFLAGS $FAST_LDFLAGS" -+ fi - fi - changequote([, ])dnl - fi - diff --git a/sci-biology/ncbi-tools++/files/respect_CXXFLAGS_configure.patch b/sci-biology/ncbi-tools++/files/respect_CXXFLAGS_configure.patch deleted file mode 100644 index 669b31722..000000000 --- a/sci-biology/ncbi-tools++/files/respect_CXXFLAGS_configure.patch +++ /dev/null @@ -1,53 +0,0 @@ ---- trunk/c++/src/build-system/configure 2012/12/21 15:12:14 56664 -+++ trunk/c++/src/build-system/configure 2012/12/27 15:43:29 56694 -@@ -3151,6 +3151,13 @@ - ;; - esac - -+# Check for custom optimization flags before potentially going with defaults. -+skip_fast_flags=no -+if test -z "${DEF_FAST_FLAGS}${FAST_CXXFLAGS}"; then -+ case " $CFLAGS $CXXFLAGS" in -+ *\ -O* | *\ -xO* ) skip_fast_flags=yes ;; -+ esac -+fi - - #### Always define this - -@@ -5715,7 +5722,7 @@ - wsrx="[$wschars]" - - #### Flags to enable (potentially unsafe) extra optimization. --if test -z "$DEF_FAST_FLAGS" -o -z "$FAST_CXXFLAGS" ; then -+if test "$skip_fast_flags" = no -a -z "$DEF_FAST_FLAGS" ; then - case "$compiler:$compiler_version" in - GCC:2* | GCC:344 ) - # GCC 2.9x sometimes experiences internal errors at high optimization; -@@ -5786,8 +5793,6 @@ - DEF_FAST_FLAGS="-O" - ;; - esac --else -- DEF_FAST_FLAGS="-O" - fi - - : ${FAST_CFLAGS="$DEF_FAST_FLAGS"} -@@ -8936,9 +8941,15 @@ - CXXFLAGS="$CXXFLAGS -O" ; fi - if echo " $LDFLAGS " | grep -v "$optrx" >/dev/null ; then - LDFLAGS="$LDFLAGS -O" ; fi -- FAST_CFLAGS="$NOPT_CFLAGS $FAST_CFLAGS" -- FAST_CXXFLAGS="$NOPT_CXXFLAGS $FAST_CXXFLAGS" -- FAST_LDFLAGS="$NOPT_LDFLAGS $FAST_LDFLAGS" -+ if test "$skip_fast_flags" = yes ; then -+ FAST_CFLAGS="$CFLAGS" -+ FAST_CXXFLAGS="$CXXFLAGS" -+ FAST_LDFLAGS="$LDFLAGS" -+ else -+ FAST_CFLAGS="$NOPT_CFLAGS $FAST_CFLAGS" -+ FAST_CXXFLAGS="$NOPT_CXXFLAGS $FAST_CXXFLAGS" -+ FAST_LDFLAGS="$NOPT_LDFLAGS $FAST_LDFLAGS" -+ fi - fi - fi - diff --git a/sci-biology/ncbi-tools++/metadata.xml b/sci-biology/ncbi-tools++/metadata.xml deleted file mode 100644 index fbf79d9b7..000000000 --- a/sci-biology/ncbi-tools++/metadata.xml +++ /dev/null @@ -1,19 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <use> - <flag name="boost">Undocumented USE</flag> - <flag name="cppunit">Undocumented USE</flag> - <flag name="freetype">Undocumented USE</flag> - <flag name="mesa">Undocumented USE</flag> - <flag name="muparser">Undocumented USE</flag> - <flag name="sablotron">Undocumented USE</flag> - <flag name="xerces">Undocumented USE</flag> - <flag name="xalan">Undocumented USE</flag> - <flag name="xslt">Undocumented USE</flag> - </use> -</pkgmetadata> diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild deleted file mode 100644 index 6daf7b3f0..000000000 --- a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild +++ /dev/null @@ -1,365 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit toolchain-funcs - -MY_TAG="Jun_15_2010" -MY_Y="${MY_TAG/*_/}" -MY_PV="12_0_0" -MY_P="ncbi_cxx--${MY_PV}" -#ftp://ftp.ncbi.nlm.nih.gov/toolbox/ncbi_tools++/ARCHIVE/9_0_0/ncbi_cxx--9_0_0.tar.gz - -# for example sci-biology/ncbi-tools++-12.0.0 contains blastn-2.2.28+ -DESCRIPTION="NCBI C++ Toolkit, including NCBI BLAST+" -HOMEPAGE="https://ncbi.github.io/cxx-toolkit/" -SRC_URI=" - ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/ARCHIVE/${MY_PV}/ncbi_cxx--${MY_PV}.tar.gz" -# http://dev.gentoo.org/~jlec/distfiles/${PN}-${PV#0.}-asneeded.patch.xz" - -# should also install ftp://ftp.ncbi.nlm.nih.gov/blast/db/taxdb.tar.gz -# see http://www.biostars.org/p/76551/ and http://blastedbio.blogspot.cz/2012/05/blast-tabular-missing-descriptions.html -LICENSE="public-domain" -SLOT="0" -IUSE=" - debug static-libs static threads pch - test wxwidgets odbc - berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype gif - glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png - sablotron sqlite tiff xerces xalan xml xpm xslt X" -#KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -KEYWORDS="~amd64" -RESTRICT="!test? ( test )" - -# sys-libs/db should be compiled with USE=cxx -# dev-libs/boost must have Boost.Test suite, probably dev-libs/boost[test] then? -DEPEND=" - <sys-devel/gcc-10:= - !sci-biology/sra_sdk - app-arch/cpio - berkdb? ( sys-libs/db:=[cxx(-)] ) - boost? ( dev-libs/boost[tools] ) - curl? ( net-misc/curl ) - sqlite? ( dev-db/sqlite:3 ) - mysql? ( virtual/mysql ) - fltk? ( x11-libs/fltk ) - opengl? ( virtual/opengl media-libs/glew:0= ) - mesa? ( media-libs/mesa[osmesa] ) - glut? ( media-libs/freeglut ) - freetype? ( media-libs/freetype ) - gnutls? ( net-libs/gnutls ) - cppunit? ( dev-util/cppunit ) - icu? ( dev-libs/icu ) - expat? ( dev-libs/expat ) - sablotron? ( app-text/sablotron ) - xml? ( dev-libs/libxml2 ) - xslt? ( dev-libs/libxslt ) - xerces? ( dev-libs/xerces-c ) - xalan? ( dev-libs/xalan-c ) - muparser? ( dev-cpp/muParser ) - hdf5? ( sci-libs/hdf5[cxx] ) - gif? ( media-libs/giflib ) - jpeg? ( virtual/jpeg:0= ) - png? ( media-libs/libpng:0= ) - tiff? ( media-libs/tiff:0= ) - xpm? ( x11-libs/libXpm ) - dev-libs/lzo - app-arch/bzip2 - dev-libs/libpcre" -# USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC OEChem sge -# Intentionally omitted USE flags: -# ftds? ( dev-db/freetds ) # support for outside FreeTDS installations is currently broken. -# The default (heavily patched) embedded copy should work, or you can -# leave it off altogether -- the only public apps that make use of it are -# samples and tests, since NCBI's database servers are of course firewalled. - -# seems muParser is required, also glew is required. configure exits otherwise if these are explicitly passed to it (due to USE flag enabled) - -RDEPEND="${DEPEND}" - -S="${WORKDIR}/${MY_P}" - -PATCHES=( - "${FILESDIR}"/${P}-conf-opts.patch - "${FILESDIR}"/${P}-fix-svn-URL-upstream.patch - "${FILESDIR}"/${P}-linkage-tuneups.patch - "${FILESDIR}"/${P}-more-patches.patch - "${FILESDIR}"/${P}-linkage-tuneups-addons.patch - "${FILESDIR}"/${P}-configure.patch - "${FILESDIR}"/${P}-drop-STATIC-from-LIB.patch - "${FILESDIR}"/${P}-fix-install.patch - "${FILESDIR}"/${P}-bdb6.patch - "${FILESDIR}"/${P}-never_build_test_boost.patch # bug #579248 - ) - -src_prepare() { - default -# filter-ldflags -Wl,--as-needed -# append-ldflags -Wl,--no-undefined -# sed -i -e 's/-print-file-name=libstdc++.a//' \ -# -e '/sed/ s/\([gO]\[0-9\]\)\*/\1\\+/' \ -# src/build-system/configure || die -# epatch \ -# "${FILESDIR}"/${PN}-${PV#0.}-fix-order-of-libs.patch \ -# "${FILESDIR}"/curl-types.patch \ -# "${FILESDIR}"/malloc_initialize_upstream_fix.patch \ -# "${FILESDIR}"/respect_CXXFLAGS_configure.ac.patch \ -# "${FILESDIR}"/respect_CXXFLAGS_configure.patch \ -# "${FILESDIR}"/report_project_settings_configure.ac.patch \ -# "${FILESDIR}"/report_project_settings_configure.patch \ -# "${FILESDIR}"/make_install.patch - -# "${FILESDIR}"/${PN}-${PV#0.}-disable_test_compress.patch - -# "${FILESDIR}"/${PN}-${PV#0.}-gcc46.patch \ -# "${FILESDIR}"/${PN}-${PV#0.}-gcc47.patch \ -# "${WORKDIR}"/${PN}-${PV#0.}-asneeded.patch \ -# "${FILESDIR}"/${PN}-${PV#0.}-libpng15.patch \ -# "${FILESDIR}"/${PN}-${PV#0.}-glibc-214.patch - -# use prefix && append-ldflags -Wl,-rpath,"${EPREFIX}/usr/$(get_libdir)/${PN}" - -# The conf-opts.patch and as-needed.patch need to be adjusted for 12.0.0 line numbers -# "${FILESDIR}"/${P}-as-needed.patch -# "${FILESDIR}"/${P}-fix-creaders-linking.patch -# "${FILESDIR}"/${P}-fix-FreeTDS-upstream.patch -# ) - # "${FILESDIR}"/${P}-support-autoconf-2.60.patch - # make sure this one is the last one and contains the actual patches applied unless we can have autoconf-2.59 or 2.60 - # https://bugs.gentoo.org/show_bug.cgi?id=514706 - - tc-export CXX CC - - cd src/build-system || die -# eautoreconf - - # Temporarily disabling eautoconf because we patch configure via ${P}-support-autoconf-2.60.patch - # eautoconf # keep it disabled until we can ensure 2.59 is installed - # beware 12.0.0. and previous required autoconf-2.59, a patch for 12.0.0 brings autoconf-2.60 support -} - -# possibly place modified contents of ${W}/src/build-system/config.site.ncbi and {W}/src/build-system/config.site.ex into ${W}/src/build-system/config.site -src_configure() { - local myconf=() - #--without-optimization turn off optimization flags in non-debug mode - #--with-profiling build profiled versions of libs and apps - #--with-tcheck(=DIR) build for Intel Thread Checker (in DIR) - #--with-plugin-auto-load always enable the plugin manager by default - #--with-bundles build bundles in addition to dylibs on Mac OS X - #--with-bin-release build executables suitable for public release - # no dll and such - #--with-64 compile to 64-bit code - #--with-universal build universal binaries on Mac OS X - #--with-universal=CPUs build universal binaries targeting the given CPUs - #--without-exe do not build executables - #--with-relative-runpath=P specify an executable-relative DLL search path - #--with-hard-runpath hard-code runtime path, ignoring LD_LIBRARY_PATH - #--with-limited-linker don't attempt to build especially large projects - #--with-extra-action= script to call after the configuration is complete - #--with-autodep automatic generation of dependencies (GNU make) - #--with-fake-root=DIR appear to have been built under DIR - #--with-build-root-sfx=X add a user-specified suffix to the build dir name - #--without-execopy do not copy built executables to the BIN area - #--with-lib-rebuilds ensure that apps use up-to-date libraries - #--with-lib-rebuilds=ask ask whether to update each app's libraries - #--without-deactivation keep old copies of libraries that no longer build - #--without-makefile-auto-update do not auto-update generated makefiles - #--with-projects=FILE build projects listed in FILE by default - #--without-flat-makefile do not generate an all-encompassing flat makefile - #--with-configure-dialog allow interactive flat makefile project selection - #--with-saved-settings=F load configuration settings from the file F - #--with-check-tools=... use the specified tools for testing - #--with-ncbi-public ensure compatibility for all in-house platforms - #--with-sybase-local=DIR use local SYBASE install (DIR is optional) - #--with-sybase-new use newer SYBASE install (12.5 rather than 12.0) - #--without-sp do not use SP libraries - #--without-orbacus do not use ORBacus CORBA libraries - #--with-orbacus=DIR use ORBacus installation in DIR - #--with-jni(=JDK-DIR) build Java bindings (against the JDK in JDK-DIR) - #--with-sablot=DIR use Sablotron installation in DIR - #--without-sablot, do not use Sablotron - #--with-oechem=DIR use OpenEye OEChem installation in DIR - #--without-oechem do not use OEChem - #--with-sge=DIR use Sun Grid Engine installation in DIR - #--without-sge do not use Sun Grid Engine - #--with-magic=DIR use libmagic installation in DIR - #--without-magic do not use libmagic - #--without-local-lbsm turn off support for IPC with locally running LBSMD - #--without-ncbi-crypt use a dummy stubbed-out version of ncbi_crypt - #--without-connext do not build non-public CONNECT library extensions - #--without-serial do not build the serialization library and tools - #--without-objects do not generate/build serializeable objects from ASNs - #--without-dbapi do not build database connectivity libraries - #--without-app do not build standalone applications like ID1_FETCH - #--without-gui do not build most graphical projects - #--without-algo do not build CPU-intensive algorithms - #--without-internal do not build internal projects - #--with-gbench ensure that Genome Workbench can be built - #--without-gbench do not build Genome Workbench - myconf+=( - --with-dll - --with-lfs - --with-build-root="${S}"_build - --without-suffix - --without-hostspec - --without-version - --with-bincopy - --without-strip - --without-ccache - --without-distcc -# --with-ncbi-c - --without-ctools -# --with-sss -# --with-sssutils -# --with-sssdb -# --with-included-sss - --with-z="${EPREFIX}/usr" - --with-bz2="${EPREFIX}/usr" - --without-sybase - --with-autodep -# --with-3psw=std:netopt favor standard (system) builds of the above pkgs - # --without-downloaded-vdb is not available in 12.0.0 release yet - # preventing executing git to checkout during configure phase ncbi-vdb sources - # resulting in 'checking for ncbi-vdb... no' and - # '^PACKAGES:' - # '^ disabled: ... VDB' - # --without-downloaded-vdb - $(use_with debug) - $(use_with debug max-debug) - $(use_with debug symbols) - $(use_with static-libs static) - $(use_with static static-exe) - $(use_with threads mt) - $(use_with prefix runpath "${EPREFIX}/usr/$(get_libdir)/${PN}") - $(use_with test check) - $(use_with pch) - $(use_with lzo lzo "${EPREFIX}/usr") - $(use_with pcre pcre "${EPREFIX}/usr") - $(use_with gnutls gnutls "${EPREFIX}/usr") - $(use_with mysql mysql "${EPREFIX}/usr") - $(use_with muparser muparser "${EPREFIX}/usr") - $(usex fltk --with-fltk="${EPREFIX}/usr" "") - $(use_with opengl opengl "${EPREFIX}/usr") - $(use_with mesa mesa "${EPREFIX}/usr") - $(use_with opengl glut "${EPREFIX}/usr") - $(use_with opengl glew "${EPREFIX}/usr") - $(use_with opengl glew-mx) - $(use_with wxwidgets wxwidgets "${EPREFIX}/usr") - $(use_with wxwidgets wxwidgets-ucs) - $(use_with freetype freetype "${EPREFIX}/usr") - $(use_with fastcgi fastcgi "${EPREFIX}/usr") - $(use_with berkdb bdb "${EPREFIX}/usr") - $(usex odbc --with-odbc="${EPREFIX}/usr" "") - # is python2 - --without-python - $(use_with boost boost "${EPREFIX}/usr") - $(use_with sqlite sqlite3 "${EPREFIX}/usr") - $(use_with icu icu "${EPREFIX}/usr") - $(use_with expat expat "${EPREFIX}/usr") - $(use_with xml libxml "${EPREFIX}/usr") - $(use_with xml libxslt "${EPREFIX}/usr") - $(use_with xerces xerces "${EPREFIX}/usr") - $(use_with hdf5 hdf5 "${EPREFIX}/usr") - $(use_with xalan xalan "${EPREFIX}/usr") -# $(use_with gif gif "${EPREFIX}/usr") # prevent compilation failure in "ncbi-tools++-12.0.0/src/util/image/image_io_gif.cpp:351: error: 'QuantizeBuffer' was not declared in this scope" - --without-gif - $(use_with jpeg jpeg "${EPREFIX}/usr") - $(use_with tiff tiff "${EPREFIX}/usr") - $(use_with png png "${EPREFIX}/usr") - $(use_with xpm xpm "${EPREFIX}/usr") - $(use_with curl curl "${EPREFIX}/usr") -# $(use_with X x "${EPREFIX}/usr") -# $(use_with X x) # there is no --with-x option - ) - - # http://www.ncbi.nlm.nih.gov/books/NBK7167/ - use test || myconf+=( --with-projects="${FILESDIR}"/disable-testsuite-compilation.txt ) - - # TODO - # copy optimization -O options from CXXFLAGS to DEF_FAST_FLAGS and pass that also to configure - # otherwise your -O2 will be dropped in some subdirectories and replaced by e.g. -O9 - - einfo "bash ./src/build-system/configure --srcdir="${S}" --prefix="${EPREFIX}/usr" --libdir=/usr/lib64 ${myconf[@]}" - -# ECONF_SOURCE="src/build-system" \ -# econf \ - bash \ - ./src/build-system/configure \ - --srcdir="${S}" \ - --prefix="${EPREFIX}/usr" \ - --libdir=/usr/lib64 \ - --with-flat-makefile \ - ${myconf[@]} || die -#--without-debug \ -# --with-bin-release \ -# --with-bincopy \ -# --without-static \ -# --with-dll \ -# --with-mt \ -# --with-openmp \ -# --with-lfs \ -# --prefix="${ED}"/usr \ -# --libdir="${ED}"/usr/$(get_libdir)/"${PN}" \ -# ${myconf} LDFLAGS="-Wl,--no-as-needed" \ -# || die -# econf ${myconf[@]} -} - -src_compile() { - ## all_r would ignore the --with-projects contents and build more - ## emake all_r -C GCC*-Release*/build || die - ## all_p with compile only selected/required components - ##cd "${S}"_build &&\ - ##emake all_p -C GCC*-Release*/build || die "gcc-4.5.3 crashes at src/objects/valerr/ValidError.cpp:226:1: internal compiler error: Segmentation fault, right?" - #emake all_p -C "${S}"_build/build - - # - # Re: /usr/lib64/ncbi-tools++/libdbapi_driver.so: undefined reference to `ncbi::NcbiGetlineEOL(std::istream&, std::string&)' - # - # The next release should automatically address such underlinking, albeit - # only in --with-flat-makefile configurations. For now (12.0.0), you'll need to - # add or extend more DLL_LIB settings, to which end you may find the - # resources at http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/ - # helpful. For instance, - # - # http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/dbapi_driver.html - # - # indicates that src/dbapi/driver/Makefile.dbapi_driver.lib should set - # - # DLL_LIB = xncbi - # - # (You can find the path to that makefile by examining - # .../status/.dbapi_driver.dep or .../build/Makefile.flat.) - # - # To take full advantage of --with-flat-makefile, you'll need the following (instead of 'emake all_p -C "${S}"_build/build') and call configure --with-flat-makefile: - emake -C "${S}"_build/build -f Makefile.flat - # - # >=gcc-5.3.0 is not supported, see also bug #579248#c8 - # configure: error: Do not know how to build MT-safe with compiler /usr/bin/x86_64-pc-linux-gnu-g++ 5.3.0 -} - -src_install() { - rm -rvf "${S}"_build/lib/ncbi || die - emake install prefix="${ED}/usr" libdir="${ED}/usr/$(get_libdir)/${PN}" - -# dobin "${S}"_build/bin/* -# dolib.so "${S}"_build/lib/*so* -# dolib.a "${S}"_build/lib/*.a -# doheader "${S}"_build/inc/* - - # File collisions with sci-biology/ncbi-tools - mv "${ED}"/usr/bin/asn2asn "${ED}"/usr/bin/asn2asn+ - mv "${ED}"/usr/bin/rpsblast "${ED}"/usr/bin/rpsblast+ - mv -f "${ED}"/usr/bin/test_regexp "${ED}"/usr/bin/test_regexp+ # drop the eventually mistakenly compiled binaries - mv "${ED}"/usr/bin/vecscreen "${ED}"/usr/bin/vecscreen+ - mv "${ED}"/usr/bin/seedtop "${ED}"/usr/bin/seedtop+ - - echo "LDPATH=${EPREFIX}/usr/$(get_libdir)/${PN}" > ${S}/99${PN} - doenvd "${S}/99${PN}" -} - -pkg_postinst() { - einfo 'Please run "source /etc/profile" before using this package in the current shell.' - einfo 'Documentation is at http://www.ncbi.nlm.nih.gov/books/NBK7167/' -} diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild deleted file mode 100644 index e2db30639..000000000 --- a/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild +++ /dev/null @@ -1,384 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7,8,9} ) - -inherit python-single-r1 toolchain-funcs - -MY_TAG="Jun_15_2010" -MY_Y="${MY_TAG/*_/}" -MY_PV="18_0_0" -MY_P="ncbi_cxx--${MY_PV}" -#ftp://ftp.ncbi.nlm.nih.gov/toolbox/ncbi_tools++/ARCHIVE/9_0_0/ncbi_cxx--9_0_0.tar.gz - -# for example sci-biology/ncbi-tools++-12.0.0 contains blastn-2.2.28+ -DESCRIPTION="NCBI C++ Toolkit, including NCBI BLAST+" -HOMEPAGE="https://ncbi.github.io/cxx-toolkit/" -SRC_URI=" - ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/ARCHIVE/2017/Jan_10_2017/ncbi_cxx--${MY_PV}.tar.gz" -# http://dev.gentoo.org/~jlec/distfiles/${PN}-${PV#0.}-asneeded.patch.xz" - -# should also install ftp://ftp.ncbi.nlm.nih.gov/blast/db/taxdb.tar.gz -# see http://www.biostars.org/p/76551/ and http://blastedbio.blogspot.cz/2012/05/blast-tabular-missing-descriptions.html -LICENSE="public-domain" -SLOT="0" -IUSE=" - debug static-libs static threads pch - test wxwidgets odbc - berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype gif - glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python - sablotron sqlite tiff xerces xalan xml xpm xslt X" -KEYWORDS="~amd64 ~x86" -RESTRICT="!test? ( test )" - -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -# sys-libs/db should be compiled with USE=cxx -# dev-libs/boost must have Boost.Test suite, probably dev-libs/boost[test] then? -DEPEND=" - <sys-devel/gcc-10:= - !sci-biology/sra_sdk - app-arch/cpio - berkdb? ( sys-libs/db:=[cxx(-)] ) - boost? ( dev-libs/boost[tools] ) - curl? ( net-misc/curl ) - sqlite? ( dev-db/sqlite:3 ) - mysql? ( virtual/mysql ) - fltk? ( x11-libs/fltk ) - opengl? ( virtual/opengl media-libs/glew:0= ) - mesa? ( media-libs/mesa[osmesa] ) - glut? ( media-libs/freeglut ) - freetype? ( media-libs/freetype ) - gnutls? ( net-libs/gnutls ) - python? ( ${PYTHON_DEPS} ) - cppunit? ( dev-util/cppunit ) - icu? ( dev-libs/icu ) - expat? ( dev-libs/expat ) - sablotron? ( app-text/sablotron ) - xml? ( dev-libs/libxml2 ) - xslt? ( dev-libs/libxslt ) - xerces? ( dev-libs/xerces-c ) - xalan? ( dev-libs/xalan-c ) - muparser? ( dev-cpp/muParser ) - hdf5? ( sci-libs/hdf5[cxx] ) - gif? ( media-libs/giflib ) - jpeg? ( virtual/jpeg:0= ) - png? ( media-libs/libpng:0= ) - tiff? ( media-libs/tiff:0= ) - xpm? ( x11-libs/libXpm ) - dev-libs/lzo - app-arch/bzip2 - dev-libs/libpcre" -# USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC OEChem sge -# Intentionally omitted USE flags: -# ftds? ( dev-db/freetds ) # support for outside FreeTDS installations is currently broken. -# The default (heavily patched) embedded copy should work, or you can -# leave it off altogether -- the only public apps that make use of it are -# samples and tests, since NCBI's database servers are of course firewalled. - -# seems muParser is required, also glew is required. configure exits otherwise if these are explicitly passed to it (due to USE flag enabled) - -RDEPEND="${DEPEND}" - -S="${WORKDIR}/${MY_P}" - -PATCHES=( - "${FILESDIR}"/${P}-configure.patch - "${FILESDIR}"/${P}-fix-install.patch - "${FILESDIR}"/${P}-never_build_test_boost.patch # bug #579248 - "${FILESDIR}"/${P}-fix-annotwriter-linking.patch - "${FILESDIR}"/${P}-fix-undefined-xobjread.patch - "${FILESDIR}"/${P}-fix-apps-blast-linking.patch - "${FILESDIR}"/${P}-fix-sample-app-cgi-linking.patch - "${FILESDIR}"/${P}-fix-app-compartp-linking.patch - "${FILESDIR}"/${P}-fix-app-convert_seq-linking.patch - "${FILESDIR}"/${P}-fix-app-hfilter-linking.patch - "${FILESDIR}"/${P}-fix-app-igblast-linking.patch - "${FILESDIR}"/${P}-fix-ncfetch-linking.patch - "${FILESDIR}"/${P}-fix-netcache_cgi_sample-linking.patch - "${FILESDIR}"/${P}-fix-netstorage_gc-linking.patch - "${FILESDIR}"/${P}-fix-speedtest-linking.patch - "${FILESDIR}"/${P}-fix-splign-linking.patch - "${FILESDIR}"/${P}-fix-srcchk-linking.patch - "${FILESDIR}"/${P}-fix-app-rmblastn-linking.patch - "${FILESDIR}"/${P}-remove-old-symlinks.patch - "${FILESDIR}"/${P}-fix-app-table2asn-linking.patch - "${FILESDIR}"/${P}-fix-app-tls-linking.patch - "${FILESDIR}"/${P}-fix-app-vecscreen-linking.patch - "${FILESDIR}"/${P}-fix-app-blast_sample-linking.patch - ) - -src_prepare() { - default -# filter-ldflags -Wl,--as-needed -# append-ldflags -Wl,--no-undefined -# sed -i -e 's/-print-file-name=libstdc++.a//' \ -# -e '/sed/ s/\([gO]\[0-9\]\)\*/\1\\+/' \ -# src/build-system/configure || die -# epatch \ -# "${FILESDIR}"/${PN}-${PV#0.}-fix-order-of-libs.patch \ -# "${FILESDIR}"/curl-types.patch \ -# "${FILESDIR}"/malloc_initialize_upstream_fix.patch \ -# "${FILESDIR}"/respect_CXXFLAGS_configure.ac.patch \ -# "${FILESDIR}"/respect_CXXFLAGS_configure.patch \ -# "${FILESDIR}"/report_project_settings_configure.ac.patch \ -# "${FILESDIR}"/report_project_settings_configure.patch \ -# "${FILESDIR}"/make_install.patch - -# "${FILESDIR}"/${PN}-${PV#0.}-disable_test_compress.patch - -# "${FILESDIR}"/${PN}-${PV#0.}-gcc46.patch \ -# "${FILESDIR}"/${PN}-${PV#0.}-gcc47.patch \ -# "${WORKDIR}"/${PN}-${PV#0.}-asneeded.patch \ -# "${FILESDIR}"/${PN}-${PV#0.}-libpng15.patch \ -# "${FILESDIR}"/${PN}-${PV#0.}-glibc-214.patch - -# use prefix && append-ldflags -Wl,-rpath,"${EPREFIX}/usr/$(get_libdir)/${PN}" - -# The conf-opts.patch and as-needed.patch need to be adjusted for 12.0.0 line numbers - #ncbi-tools++-18.0.0-fix-undefined-lxncbi.patch - # make sure this one is the last one and contains the actual patches applied unless we can have autoconf-2.59 or 2.60 - # https://bugs.gentoo.org/show_bug.cgi?id=514706 - - tc-export CXX CC - - cd src/build-system || die -# eautoreconf - - # Temporarily disabling eautoconf because we patch configure via ${P}-support-autoconf-2.60.patch - # eautoconf # keep it disabled until we can ensure 2.59 is installed - # beware 12.0.0. and previous required autoconf-2.59, a patch for 12.0.0 brings autoconf-2.60 support -} - -# possibly place modified contents of ${W}/src/build-system/config.site.ncbi and {W}/src/build-system/config.site.ex into ${W}/src/build-system/config.site -src_configure() { - local myconf=() - #--without-optimization turn off optimization flags in non-debug mode - #--with-profiling build profiled versions of libs and apps - #--with-tcheck(=DIR) build for Intel Thread Checker (in DIR) - #--with-plugin-auto-load always enable the plugin manager by default - #--with-bundles build bundles in addition to dylibs on Mac OS X - #--with-bin-release build executables suitable for public release - # no dll and such - #--with-64 compile to 64-bit code - #--with-universal build universal binaries on Mac OS X - #--with-universal=CPUs build universal binaries targeting the given CPUs - #--without-exe do not build executables - #--with-relative-runpath=P specify an executable-relative DLL search path - #--with-hard-runpath hard-code runtime path, ignoring LD_LIBRARY_PATH - #--with-limited-linker don't attempt to build especially large projects - #--with-extra-action= script to call after the configuration is complete - #--with-autodep automatic generation of dependencies (GNU make) - #--with-fake-root=DIR appear to have been built under DIR - #--with-build-root-sfx=X add a user-specified suffix to the build dir name - #--without-execopy do not copy built executables to the BIN area - #--with-lib-rebuilds ensure that apps use up-to-date libraries - #--with-lib-rebuilds=ask ask whether to update each app's libraries - #--without-deactivation keep old copies of libraries that no longer build - #--without-makefile-auto-update do not auto-update generated makefiles - #--with-projects=FILE build projects listed in FILE by default - #--without-flat-makefile do not generate an all-encompassing flat makefile - #--with-configure-dialog allow interactive flat makefile project selection - #--with-saved-settings=F load configuration settings from the file F - #--with-check-tools=... use the specified tools for testing - #--with-ncbi-public ensure compatibility for all in-house platforms - #--with-sybase-local=DIR use local SYBASE install (DIR is optional) - #--with-sybase-new use newer SYBASE install (12.5 rather than 12.0) - #--without-sp do not use SP libraries - #--without-orbacus do not use ORBacus CORBA libraries - #--with-orbacus=DIR use ORBacus installation in DIR - #--with-jni(=JDK-DIR) build Java bindings (against the JDK in JDK-DIR) - #--with-sablot=DIR use Sablotron installation in DIR - #--without-sablot, do not use Sablotron - #--with-oechem=DIR use OpenEye OEChem installation in DIR - #--without-oechem do not use OEChem - #--with-sge=DIR use Sun Grid Engine installation in DIR - #--without-sge do not use Sun Grid Engine - #--with-magic=DIR use libmagic installation in DIR - #--without-magic do not use libmagic - #--without-local-lbsm turn off support for IPC with locally running LBSMD - #--without-ncbi-crypt use a dummy stubbed-out version of ncbi_crypt - #--without-connext do not build non-public CONNECT library extensions - #--without-serial do not build the serialization library and tools - #--without-objects do not generate/build serializeable objects from ASNs - #--without-dbapi do not build database connectivity libraries - #--without-app do not build standalone applications like ID1_FETCH - #--without-gui do not build most graphical projects - #--without-algo do not build CPU-intensive algorithms - #--without-internal do not build internal projects - #--with-gbench ensure that Genome Workbench can be built - #--without-gbench do not build Genome Workbench - myconf+=( - --with-dll - --with-lfs - --with-build-root="${S}"_build - --without-suffix - --without-hostspec - --without-version - --with-bincopy - --without-strip - --without-ccache - --without-distcc -# --with-ncbi-c - --without-ctools -# --with-sss -# --with-sssutils -# --with-sssdb -# --with-included-sss - --with-z="${EPREFIX}/usr" - --with-bz2="${EPREFIX}/usr" - --without-sybase - --with-autodep -# --with-3psw=std:netopt favor standard (system) builds of the above pkgs - # --without-downloaded-vdb is not available in 12.0.0 release yet - # preventing executing git to checkout during configure phase ncbi-vdb sources - # resulting in 'checking for ncbi-vdb... no' and - # '^PACKAGES:' - # '^ disabled: ... VDB' - --without-downloaded-vdb - $(use_with debug) - $(use_with debug max-debug) - $(use_with debug symbols) - $(use_with static-libs static) - $(use_with static static-exe) - $(use_with threads mt) - $(use_with prefix runpath "${EPREFIX}/usr/$(get_libdir)/${PN}") - $(use_with test check) - $(use_with pch) - $(use_with lzo lzo "${EPREFIX}/usr") - $(use_with pcre pcre "${EPREFIX}/usr") - $(use_with gnutls gnutls "${EPREFIX}/usr") - $(use_with mysql mysql "${EPREFIX}/usr") - $(use_with muparser muparser "${EPREFIX}/usr") - $(usex fltk --with-fltk="${EPREFIX}/usr" "") - $(use_with opengl opengl "${EPREFIX}/usr") - $(use_with mesa mesa "${EPREFIX}/usr") - $(use_with opengl glut "${EPREFIX}/usr") - $(use_with opengl glew "${EPREFIX}/usr") - $(use_with opengl glew-mx) - $(use_with wxwidgets wxwidgets "${EPREFIX}/usr") - $(use_with wxwidgets wxwidgets-ucs) - $(use_with freetype freetype "${EPREFIX}/usr") - $(use_with fastcgi fastcgi "${EPREFIX}/usr") - $(use_with berkdb bdb "${EPREFIX}/usr") - $(usex odbc --with-odbc="${EPREFIX}/usr" "") - $(use_with python python "${EPREFIX}/usr") - $(use_with boost boost "${EPREFIX}/usr") - $(use_with sqlite sqlite3 "${EPREFIX}/usr") - $(use_with icu icu "${EPREFIX}/usr") - $(use_with expat expat "${EPREFIX}/usr") - $(use_with xml libxml "${EPREFIX}/usr") - $(use_with xml libxslt "${EPREFIX}/usr") - $(use_with xerces xerces "${EPREFIX}/usr") - $(use_with hdf5 hdf5 "${EPREFIX}/usr") - $(use_with xalan xalan "${EPREFIX}/usr") -# $(use_with gif gif "${EPREFIX}/usr") # prevent compilation failure in "ncbi-tools++-12.0.0/src/util/image/image_io_gif.cpp:351: error: 'QuantizeBuffer' was not declared in this scope" - --without-gif - $(use_with jpeg jpeg "${EPREFIX}/usr") - $(use_with tiff tiff "${EPREFIX}/usr") - $(use_with png png "${EPREFIX}/usr") - $(use_with xpm xpm "${EPREFIX}/usr") - $(use_with curl curl "${EPREFIX}/usr") -# $(use_with X x "${EPREFIX}/usr") -# $(use_with X x) # there is no --with-x option - ) - - # http://www.ncbi.nlm.nih.gov/books/NBK7167/ - use test || myconf+=( --with-projects="${FILESDIR}"/disable-testsuite-compilation.txt ) - - # TODO - # copy optimization -O options from CXXFLAGS to DEF_FAST_FLAGS and pass that also to configure - # otherwise your -O2 will be dropped in some subdirectories and replaced by e.g. -O9 - - einfo "bash ./src/build-system/configure --srcdir="${S}" --prefix="${EPREFIX}/usr" --libdir=/usr/lib64 ${myconf[@]}" - -# ECONF_SOURCE="src/build-system" \ -# econf \ - bash \ - ./src/build-system/configure \ - --srcdir="${S}" \ - --prefix="${EPREFIX}/usr" \ - --libdir=/usr/lib64 \ - --with-flat-makefile \ - ${myconf[@]} || die -#--without-debug \ -# --with-bin-release \ -# --with-bincopy \ -# --without-static \ -# --with-dll \ -# --with-mt \ -# --with-openmp \ -# --with-lfs \ -# --prefix="${ED}"/usr \ -# --libdir="${ED}"/usr/$(get_libdir)/"${PN}" \ -# ${myconf} LDFLAGS="-Wl,--no-as-needed" \ -# || die -# econf ${myconf[@]} -} - -src_compile() { - ## all_r would ignore the --with-projects contents and build more - ## emake all_r -C GCC*-Release*/build || die - ## all_p with compile only selected/required components - ##cd "${S}"_build &&\ - ##emake all_p -C GCC*-Release*/build || die "gcc-4.5.3 crashes at src/objects/valerr/ValidError.cpp:226:1: internal compiler error: Segmentation fault, right?" - #emake all_p -C "${S}"_build/build - - # - # Re: /usr/lib64/ncbi-tools++/libdbapi_driver.so: undefined reference to `ncbi::NcbiGetlineEOL(std::istream&, std::string&)' - # - # The next release should automatically address such underlinking, albeit - # only in --with-flat-makefile configurations. For now (12.0.0), you'll need to - # add or extend more DLL_LIB settings, to which end you may find the - # resources at http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/ - # helpful. For instance, - # - # http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/dbapi_driver.html - # - # indicates that src/dbapi/driver/Makefile.dbapi_driver.lib should set - # - # DLL_LIB = xncbi - # - # (You can find the path to that makefile by examining - # .../status/.dbapi_driver.dep or .../build/Makefile.flat.) - # - # To take full advantage of --with-flat-makefile, you'll need the following (instead of 'emake all_p -C "${S}"_build/build') and call configure --with-flat-makefile: - emake -C "${S}"_build/build -f Makefile.flat - # - # >=gcc-5.3.0 is not supported, see also bug #579248#c8 - # configure: error: Do not know how to build MT-safe with compiler /usr/bin/x86_64-pc-linux-gnu-g++ 5.3.0 -} - -src_install() { - rm -rvf "${S}"_build/lib/ncbi || die - emake install prefix="${ED}/usr" libdir="${ED}/usr/$(get_libdir)/${PN}" - -# dobin "${S}"_build/bin/* -# dolib.so "${S}"_build/lib/*so* -# dolib.a "${S}"_build/lib/*.a -# doheader "${S}"_build/inc/* - - # File collisions with sci-biology/ncbi-tools - mv "${ED}"/usr/bin/asn2asn "${ED}"/usr/bin/asn2asn+ - mv "${ED}"/usr/bin/rpsblast "${ED}"/usr/bin/rpsblast+ - mv -f "${ED}"/usr/bin/test_regexp "${ED}"/usr/bin/test_regexp+ # drop the eventually mistakenly compiled binaries - mv "${ED}"/usr/bin/vecscreen "${ED}"/usr/bin/vecscreen+ - mv "${ED}"/usr/bin/seedtop "${ED}"/usr/bin/seedtop+ - # - # idfetch collides with idfetch from ncbi-tools-2.2.26 - # Although the two idfetch implementations do deliberately have several - # options in common, the C++ version is not yet a full drop-in replacement - # for the C version (and will never entirely be, due to fundamental - # differences between the two toolkits' argument-parsing conventions). - mv "${ED}"/usr/bin/idfetch "${ED}"/usr/bin/idfetch+ # new in ncbi-tools++-18.0.0 - - echo "LDPATH=${EPREFIX}/usr/$(get_libdir)/${PN}" > ${S}/99${PN} - doenvd "${S}/99${PN}" -} - -pkg_postinst() { - einfo 'Please run "source /etc/profile" before using this package in the current shell.' - einfo 'Documentation is at http://www.ncbi.nlm.nih.gov/books/NBK7167/' -} diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild deleted file mode 100644 index 7df161c99..000000000 --- a/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild +++ /dev/null @@ -1,389 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7,8,9} ) - -inherit python-single-r1 toolchain-funcs - -MY_TAG="Mar_28_2019" -MY_Y="${MY_TAG/*_/}" -MY_PV="22_0_0" -MY_P="ncbi_cxx--${MY_PV}" - -# for example sci-biology/ncbi-tools++-12.0.0 contains blastn-2.2.28+ -DESCRIPTION="NCBI C++ Toolkit, including NCBI BLAST+" -HOMEPAGE="https://ncbi.github.io/cxx-toolkit/" -# https://ncbi.github.io/cxx-toolkit/pages/release_notes -SRC_URI=" - ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/ARCHIVE/2019/${MY_TAG}/ncbi_cxx--${MY_PV}.tar.gz" -# http://dev.gentoo.org/~jlec/distfiles/${PN}-${PV#0.}-asneeded.patch.xz" - -# should also install ftp://ftp.ncbi.nlm.nih.gov/blast/db/taxdb.tar.gz -# see http://www.biostars.org/p/76551/ and http://blastedbio.blogspot.cz/2012/05/blast-tabular-missing-descriptions.html -LICENSE="public-domain" -SLOT="0" -IUSE=" - debug static-libs static threads pch - test wxwidgets odbc - berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype gif - glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python - sablotron sqlite tiff xerces xalan xml xpm xslt X" -KEYWORDS="~amd64 ~x86" -RESTRICT="!test? ( test )" - -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -# sys-libs/db should be compiled with USE=cxx -# dev-libs/boost must have Boost.Test suite, probably dev-libs/boost[test] then? -DEPEND=" - <sys-devel/gcc-10:= - !sci-biology/sra_sdk - app-arch/cpio - berkdb? ( sys-libs/db:=[cxx(-)] ) - boost? ( dev-libs/boost[tools] ) - curl? ( net-misc/curl ) - sqlite? ( >=dev-db/sqlite-3.6.6:3 ) - mysql? ( virtual/mysql ) - fltk? ( x11-libs/fltk ) - opengl? ( virtual/opengl media-libs/glew:0= ) - mesa? ( media-libs/mesa[osmesa] ) - glut? ( media-libs/freeglut ) - freetype? ( media-libs/freetype ) - gnutls? ( net-libs/gnutls ) - python? ( ${PYTHON_DEPS} ) - cppunit? ( dev-util/cppunit ) - icu? ( dev-libs/icu ) - expat? ( dev-libs/expat ) - sablotron? ( app-text/sablotron ) - xml? ( dev-libs/libxml2 ) - xslt? ( >=dev-libs/libxslt-1.1.14 ) - xerces? ( dev-libs/xerces-c ) - xalan? ( dev-libs/xalan-c ) - muparser? ( dev-cpp/muParser ) - hdf5? ( sci-libs/hdf5[cxx] ) - gif? ( media-libs/giflib ) - jpeg? ( virtual/jpeg:0= ) - png? ( media-libs/libpng:0= ) - tiff? ( media-libs/tiff:0= ) - xpm? ( x11-libs/libXpm ) - >=dev-libs/lzo-2.0 - app-arch/bzip2 - dev-libs/libpcre" -# USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC OEChem sge -# Intentionally omitted USE flags: -# ftds? ( dev-db/freetds ) # support for outside FreeTDS installations is currently broken. -# The default (heavily patched) embedded copy should work, or you can -# leave it off altogether -- the only public apps that make use of it are -# samples and tests, since NCBI's database servers are of course firewalled. - -# seems muParser is required, also glew is required. configure exits otherwise if these are explicitly passed to it (due to USE flag enabled) - -RDEPEND="${DEPEND}" - -S="${WORKDIR}/${MY_P}" - -src_prepare() { - default -# filter-ldflags -Wl,--as-needed -# append-ldflags -Wl,--no-undefined -# sed -i -e 's/-print-file-name=libstdc++.a//' \ -# -e '/sed/ s/\([gO]\[0-9\]\)\*/\1\\+/' \ -# src/build-system/configure || die -# epatch \ -# "${FILESDIR}"/${PN}-${PV#0.}-fix-order-of-libs.patch \ -# "${FILESDIR}"/curl-types.patch \ -# "${FILESDIR}"/malloc_initialize_upstream_fix.patch \ -# "${FILESDIR}"/respect_CXXFLAGS_configure.ac.patch \ -# "${FILESDIR}"/respect_CXXFLAGS_configure.patch \ -# "${FILESDIR}"/report_project_settings_configure.ac.patch \ -# "${FILESDIR}"/report_project_settings_configure.patch \ -# "${FILESDIR}"/make_install.patch - -# "${FILESDIR}"/${PN}-${PV#0.}-disable_test_compress.patch - -# "${FILESDIR}"/${PN}-${PV#0.}-gcc46.patch \ -# "${FILESDIR}"/${PN}-${PV#0.}-gcc47.patch \ -# "${WORKDIR}"/${PN}-${PV#0.}-asneeded.patch \ -# "${FILESDIR}"/${PN}-${PV#0.}-libpng15.patch \ -# "${FILESDIR}"/${PN}-${PV#0.}-glibc-214.patch - -# use prefix && append-ldflags -Wl,-rpath,"${EPREFIX}/usr/$(get_libdir)/${PN}" - -# The conf-opts.patch and as-needed.patch need to be adjusted for 12.0.0 line numbers -# local PATCHES=( -# "${FILESDIR}"/${P}-configure.patch -# "${FILESDIR}"/${P}-fix-install.patch -# "${FILESDIR}"/${P}-never_build_test_boost.patch # bug #579248 -# "${FILESDIR}"/${P}-fix-annotwriter-linking.patch -# "${FILESDIR}"/${P}-fix-undefined-xobjread.patch -# "${FILESDIR}"/${P}-fix-apps-blast-linking.patch -# "${FILESDIR}"/${P}-fix-sample-app-cgi-linking.patch -# "${FILESDIR}"/${P}-fix-app-compartp-linking.patch -# "${FILESDIR}"/${P}-fix-app-convert_seq-linking.patch -# "${FILESDIR}"/${P}-fix-app-hfilter-linking.patch -# "${FILESDIR}"/${P}-fix-app-igblast-linking.patch -# "${FILESDIR}"/${P}-fix-ncfetch-linking.patch -# "${FILESDIR}"/${P}-fix-netcache_cgi_sample-linking.patch -# "${FILESDIR}"/${P}-fix-netstorage_gc-linking.patch -# "${FILESDIR}"/${P}-fix-speedtest-linking.patch -# "${FILESDIR}"/${P}-fix-splign-linking.patch -# "${FILESDIR}"/${P}-fix-srcchk-linking.patch -# "${FILESDIR}"/${P}-fix-app-rmblastn-linking.patch -# "${FILESDIR}"/${P}-remove-old-symlinks.patch -# "${FILESDIR}"/${P}-fix-app-table2asn-linking.patch -# "${FILESDIR}"/${P}-fix-app-tls-linking.patch -# "${FILESDIR}"/${P}-fix-app-vecscreen-linking.patch -# "${FILESDIR}"/${P}-fix-app-blast_sample-linking.patch -# ) - #ncbi-tools++-18.0.0-fix-undefined-lxncbi.patch -# epatch ${PATCHES[@]} - # make sure this one is the last one and contains the actual patches applied unless we can have autoconf-2.59 or 2.60 - # https://bugs.gentoo.org/show_bug.cgi?id=514706 - - tc-export CXX CC - - cd src/build-system || die -# eautoreconf - - # Temporarily disabling eautoconf because we patch configure via ${P}-support-autoconf-2.60.patch - # eautoconf # keep it disabled until we can ensure 2.59 is installed - # beware 12.0.0. and previous required autoconf-2.59, a patch for 12.0.0 brings autoconf-2.60 support -} - -# possibly place modified contents of ${W}/src/build-system/config.site.ncbi and {W}/src/build-system/config.site.ex into ${W}/src/build-system/config.site -src_configure() { - local myconf=() - #--without-optimization turn off optimization flags in non-debug mode - #--with-profiling build profiled versions of libs and apps - #--with-tcheck(=DIR) build for Intel Thread Checker (in DIR) - #--with-plugin-auto-load always enable the plugin manager by default - #--with-bundles build bundles in addition to dylibs on Mac OS X - #--with-bin-release build executables suitable for public release - # no dll and such - #--with-64 compile to 64-bit code - #--with-universal build universal binaries on Mac OS X - #--with-universal=CPUs build universal binaries targeting the given CPUs - #--without-exe do not build executables - #--with-relative-runpath=P specify an executable-relative DLL search path - #--with-hard-runpath hard-code runtime path, ignoring LD_LIBRARY_PATH - #--with-limited-linker don't attempt to build especially large projects - #--with-extra-action= script to call after the configuration is complete - #--with-autodep automatic generation of dependencies (GNU make) - #--with-fake-root=DIR appear to have been built under DIR - #--with-build-root-sfx=X add a user-specified suffix to the build dir name - #--without-execopy do not copy built executables to the BIN area - #--with-lib-rebuilds ensure that apps use up-to-date libraries - #--with-lib-rebuilds=ask ask whether to update each app's libraries - #--without-deactivation keep old copies of libraries that no longer build - #--without-makefile-auto-update do not auto-update generated makefiles - #--with-projects=FILE build projects listed in FILE by default - #--without-flat-makefile do not generate an all-encompassing flat makefile - #--with-configure-dialog allow interactive flat makefile project selection - #--with-saved-settings=F load configuration settings from the file F - #--with-check-tools=... use the specified tools for testing - #--with-ncbi-public ensure compatibility for all in-house platforms - #--with-sybase-local=DIR use local SYBASE install (DIR is optional) - #--with-sybase-new use newer SYBASE install (12.5 rather than 12.0) - #--without-sp do not use SP libraries - #--without-orbacus do not use ORBacus CORBA libraries - #--with-orbacus=DIR use ORBacus installation in DIR - #--with-jni(=JDK-DIR) build Java bindings (against the JDK in JDK-DIR) - #--with-sablot=DIR use Sablotron installation in DIR - #--without-sablot, do not use Sablotron - #--with-oechem=DIR use OpenEye OEChem installation in DIR - #--without-oechem do not use OEChem - #--with-sge=DIR use Sun Grid Engine installation in DIR - #--without-sge do not use Sun Grid Engine - #--with-magic=DIR use libmagic installation in DIR - #--without-magic do not use libmagic - #--without-local-lbsm turn off support for IPC with locally running LBSMD - #--without-ncbi-crypt use a dummy stubbed-out version of ncbi_crypt - #--without-connext do not build non-public CONNECT library extensions - #--without-serial do not build the serialization library and tools - #--without-objects do not generate/build serializeable objects from ASNs - #--without-dbapi do not build database connectivity libraries - #--without-app do not build standalone applications like ID1_FETCH - #--without-gui do not build most graphical projects - #--without-algo do not build CPU-intensive algorithms - #--without-internal do not build internal projects - #--with-gbench ensure that Genome Workbench can be built - #--without-gbench do not build Genome Workbench - myconf+=( - --with-dll - --with-lfs - --with-build-root="${S}"_build - --without-suffix - --without-hostspec - --without-version - --with-bincopy - --without-strip - --without-ccache - --without-distcc -# --with-ncbi-c - --without-ctools -# --with-sss -# --with-sssutils -# --with-sssdb -# --with-included-sss - --with-z="${EPREFIX}/usr" - --with-bz2="${EPREFIX}/usr" - --without-sybase - --with-autodep -# --with-3psw=std:netopt favor standard (system) builds of the above pkgs - # --without-downloaded-vdb is not available in 12.0.0 release yet - # preventing executing git to checkout during configure phase ncbi-vdb sources - # resulting in 'checking for ncbi-vdb... no' and - # '^PACKAGES:' - # '^ disabled: ... VDB' - --without-downloaded-vdb - $(use_with debug) -# $(use_with debug max-debug) # broken in 22.0.0 as it triggers need for https://github.com/google/sanitizers/wiki/AddressSanitizer - $(use_with debug symbols) - $(use_with static-libs static) - $(use_with static static-exe) - $(use_with threads mt) - $(use_with prefix runpath "${EPREFIX}/usr/$(get_libdir)/${PN}") - $(use_with test check) - $(use_with pch) - $(use_with lzo lzo "${EPREFIX}/usr") - $(use_with pcre pcre "${EPREFIX}/usr") - $(use_with gnutls gnutls "${EPREFIX}/usr") - $(use_with mysql mysql "${EPREFIX}/usr") - $(use_with muparser muparser "${EPREFIX}/usr") - $(usex fltk --with-fltk="${EPREFIX}/usr" "") - $(use_with opengl opengl "${EPREFIX}/usr") - $(use_with mesa mesa "${EPREFIX}/usr") - $(use_with opengl glut "${EPREFIX}/usr") - $(use_with opengl glew "${EPREFIX}/usr") -# $(use_with opengl glew-mx) can't find this with any version of media-libs/glew installed: explicitly specified, but no usable version found. - $(use_with wxwidgets wxwidgets "${EPREFIX}/usr") - $(use_with wxwidgets wxwidgets-ucs) - $(use_with freetype freetype "${EPREFIX}/usr") - $(use_with fastcgi fastcgi "${EPREFIX}/usr") - $(use_with berkdb bdb "${EPREFIX}/usr") - $(usex odbc --with-odbc="${EPREFIX}/usr" "") - $(use_with python python "${EPREFIX}/usr") - $(use_with boost boost "${EPREFIX}/usr") - $(use_with sqlite sqlite3 "${EPREFIX}/usr") - $(use_with icu icu "${EPREFIX}/usr") - $(use_with expat expat "${EPREFIX}/usr") - $(use_with xml libxml "${EPREFIX}/usr") - $(use_with xml libxslt "${EPREFIX}/usr") - $(use_with xerces xerces "${EPREFIX}/usr") - $(use_with hdf5 hdf5 "${EPREFIX}/usr") - $(use_with xalan xalan "${EPREFIX}/usr") -# $(use_with gif gif "${EPREFIX}/usr") # prevent compilation failure in "ncbi-tools++-12.0.0/src/util/image/image_io_gif.cpp:351: error: 'QuantizeBuffer' was not declared in this scope" - --without-gif - $(use_with jpeg jpeg "${EPREFIX}/usr") - $(use_with tiff tiff "${EPREFIX}/usr") - $(use_with png png "${EPREFIX}/usr") - $(use_with xpm xpm "${EPREFIX}/usr") - $(use_with curl curl "${EPREFIX}/usr") -# $(use_with X x "${EPREFIX}/usr") -# $(use_with X x) # there is no --with-x option - ) - - # http://www.ncbi.nlm.nih.gov/books/NBK7167/ - use test || myconf+=( --with-projects="${FILESDIR}"/disable-testsuite-compilation.txt ) - - # TODO - # copy optimization -O options from CXXFLAGS to DEF_FAST_FLAGS and pass that also to configure - # otherwise your -O2 will be dropped in some subdirectories and replaced by e.g. -O9 - - einfo "LDFLAGS=-Wl,-rpath-link,"${S}"_build/lib bash ./src/build-system/configure --srcdir="${S}" --prefix="${EPREFIX}/usr" --libdir=/usr/lib64 ${myconf[@]}" - -# ECONF_SOURCE="src/build-system" \ -# econf \ - LDFLAGS=-Wl,-rpath-link,"${S}"_build/lib bash \ - ./src/build-system/configure \ - --srcdir="${S}" \ - --prefix="${EPREFIX}/usr" \ - --libdir=/usr/lib64 \ - --with-flat-makefile \ - ${myconf[@]} || die -#--without-debug \ -# --with-bin-release \ -# --with-bincopy \ -# --without-static \ -# --with-dll \ -# --with-mt \ -# --with-openmp \ -# --with-lfs \ -# --prefix="${ED}"/usr \ -# --libdir="${ED}"/usr/$(get_libdir)/"${PN}" \ -# ${myconf} LDFLAGS="-Wl,--no-as-needed" \ -# || die -# econf ${myconf[@]} -} - -src_compile() { - ## all_r would ignore the --with-projects contents and build more - ## emake all_r -C GCC*-Release*/build || die - ## all_p with compile only selected/required components - ##cd "${S}"_build &&\ - ##emake all_p -C GCC*-Release*/build || die "gcc-4.5.3 crashes at src/objects/valerr/ValidError.cpp:226:1: internal compiler error: Segmentation fault, right?" - #emake all_p -C "${S}"_build/build - - # - # Re: /usr/lib64/ncbi-tools++/libdbapi_driver.so: undefined reference to `ncbi::NcbiGetlineEOL(std::istream&, std::string&)' - # - # The next release should automatically address such underlinking, albeit - # only in --with-flat-makefile configurations. For now (12.0.0), you'll need to - # add or extend more DLL_LIB settings, to which end you may find the - # resources at http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/ - # helpful. For instance, - # - # http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/dbapi_driver.html - # - # indicates that src/dbapi/driver/Makefile.dbapi_driver.lib should set - # - # DLL_LIB = xncbi - # - # (You can find the path to that makefile by examining - # .../status/.dbapi_driver.dep or .../build/Makefile.flat.) - # - # To take full advantage of --with-flat-makefile, you'll need the following (instead of 'emake all_p -C "${S}"_build/build') and call configure --with-flat-makefile: - LDFLAGS=-Wl,-rpath-link,"${S}"_build/lib emake -C "${S}"_build/build -f Makefile.flat - # - # >=gcc-5.3.0 is not supported, see also bug #579248#c8 - # configure: error: Do not know how to build MT-safe with compiler /usr/bin/x86_64-pc-linux-gnu-g++ 5.3.0 -} - -src_install() { - rm -rvf "${S}"_build/lib/ncbi || die - emake install prefix="${ED}/usr" libdir="${ED}/usr/$(get_libdir)/${PN}" - # - #if [ ! use static-libs -a ! use static ]; then - # rm -f "${ED}/usr/$(get_libdir)/${PN}"/*.a \ - # "${ED}/usr/$(get_libdir)/${PN}"/*-static.a || die - #fi - -# dobin "${S}"_build/bin/* -# dolib.so "${S}"_build/lib/*so* -# dolib.a "${S}"_build/lib/*.a -# doheader "${S}"_build/inc/* - - # File collisions with sci-biology/ncbi-tools - mv "${ED}"/usr/bin/asn2asn "${ED}"/usr/bin/asn2asn+ - mv "${ED}"/usr/bin/rpsblast "${ED}"/usr/bin/rpsblast+ - mv -f "${ED}"/usr/bin/test_regexp "${ED}"/usr/bin/test_regexp+ # drop the eventually mistakenly compiled binaries - mv "${ED}"/usr/bin/vecscreen "${ED}"/usr/bin/vecscreen+ - mv "${ED}"/usr/bin/seedtop "${ED}"/usr/bin/seedtop+ - # - # idfetch collides with idfetch from ncbi-tools-2.2.26 - # Although the two idfetch implementations do deliberately have several - # options in common, the C++ version is not yet a full drop-in replacement - # for the C version (and will never entirely be, due to fundamental - # differences between the two toolkits' argument-parsing conventions). - mv "${ED}"/usr/bin/idfetch "${ED}"/usr/bin/idfetch+ # new in ncbi-tools++-18.0.0 - - echo "LDPATH=${EPREFIX}/usr/$(get_libdir)/${PN}" > ${S}/99${PN} - doenvd "${S}/99${PN}" -} - -pkg_postinst() { - einfo 'Please run "source /etc/profile" before using this package in the current shell.' - einfo 'Documentation is at http://www.ncbi.nlm.nih.gov/books/NBK7167/' -} diff --git a/sci-biology/ncbi-vdb/ncbi-vdb-2.11.2.ebuild b/sci-biology/ncbi-vdb/ncbi-vdb-2.11.2.ebuild index 167e2a8c3..15f83b00c 100644 --- a/sci-biology/ncbi-vdb/ncbi-vdb-2.11.2.ebuild +++ b/sci-biology/ncbi-vdb/ncbi-vdb-2.11.2.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_10 ) inherit python-single-r1 DESCRIPTION=" NCBI SRA ( Sequence Read Archive )" diff --git a/sci-biology/neuroconv/Manifest b/sci-biology/neuroconv/Manifest new file mode 100644 index 000000000..35c461b92 --- /dev/null +++ b/sci-biology/neuroconv/Manifest @@ -0,0 +1 @@ +DIST neuroconv-0.4.8.gh.tar.gz 1020546 BLAKE2B 880d7c4bdce3faf3bc969c9a0fd4206e1fd9d57254e40aa1181cf2d8f48abd72491b8b66d8ccc1988a623f8b2a8be160f2575f59ea69080a8bb6ed501c389881 SHA512 d06a625823a71f21a5eac957e452ab80b6fb847fc5f8c8e68fb6c46360402c4bc338f7fc611537272e72c0b72555a2951c346d38aa89c8ac8b209921ea7af72d diff --git a/sci-biology/neuroconv/metadata.xml b/sci-biology/neuroconv/metadata.xml new file mode 100644 index 000000000..efd00647e --- /dev/null +++ b/sci-biology/neuroconv/metadata.xml @@ -0,0 +1,21 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>gentoo@chymera.eu</email> + <name>Horea Christian</name> + </maintainer> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <use> + <flag name="ecephys">Extracellular electrophysiology interfaces</flag> + <flag name="icephys">Intracellular electrophysiology interfaces</flag> + <flag name="ophys">Optical physiology interfaces</flag> + </use> + <upstream> + <remote-id type="github">catalystneuro/roiextractors</remote-id> + <remote-id type="pypi">roiextractors</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/neuroconv/neuroconv-0.4.8-r1.ebuild b/sci-biology/neuroconv/neuroconv-0.4.8-r1.ebuild new file mode 100644 index 000000000..b21c2fd8e --- /dev/null +++ b/sci-biology/neuroconv/neuroconv-0.4.8-r1.ebuild @@ -0,0 +1,66 @@ +# Copyright 2021-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools +inherit distutils-r1 + +DESCRIPTION="Create NWB files from proprietary formats." +HOMEPAGE="https://github.com/catalystneuro/neuroconv" +SRC_URI="https://github.com/catalystneuro/neuroconv/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64" +IUSE="+ecephys +icephys +ophys" + +RDEPEND=" + dev-python/docstring-parser[${PYTHON_USEDEP}] + dev-python/h5py[${PYTHON_USEDEP}] + dev-python/hdmf-zarr[${PYTHON_USEDEP}] + dev-python/hdmf[${PYTHON_USEDEP}] + dev-python/jsonschema[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/nwbinspector[${PYTHON_USEDEP}] + dev-python/pandas[${PYTHON_USEDEP}] + dev-python/parse[${PYTHON_USEDEP}] + dev-python/psutil[${PYTHON_USEDEP}] + dev-python/pydantic[${PYTHON_USEDEP}] + dev-python/pynwb[${PYTHON_USEDEP}] + dev-python/pyyaml[${PYTHON_USEDEP}] + dev-python/scipy[${PYTHON_USEDEP}] + dev-python/tqdm[${PYTHON_USEDEP}] + ecephys? ( + dev-python/spikeinterface[${PYTHON_USEDEP}] + ) + icephys? ( + dev-python/neo[${PYTHON_USEDEP}] + ) + ophys? ( + sci-biology/roiextractors[${PYTHON_USEDEP}] + ) +" +BDEPEND=" + test? ( + dev-python/parameterized[${PYTHON_USEDEP}] + ) +" + +distutils_enable_tests pytest + +# Reported upstream: +# https://github.com/catalystneuro/neuroconv/issues/785 +EPYTEST_DESELECT=( + tests/test_ecephys/test_mock_recording_interface.py::TestMockRecordingInterface::test_conversion_as_lone_interface +) + +python_test() { + # Additional tests require complex data getting infrastructure, ophys tests still have issues: + # https://github.com/catalystneuro/neuroconv/issues/305 + local my_tests=( "tests/test_minimal" ) + use ecephys && my_tests+=( "tests/test_ecephys" ) + #use ophys && my_tests+=( "tests/test_ophys" ) + epytest ${my_tests[*]// /|} +} diff --git a/sci-biology/nextclip/metadata.xml b/sci-biology/nextclip/metadata.xml index 138cb7705..b0874714e 100644 --- a/sci-biology/nextclip/metadata.xml +++ b/sci-biology/nextclip/metadata.xml @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">richardmleggett/nextclip</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/ngs/metadata.xml b/sci-biology/ngs/metadata.xml index 138cb7705..f165e6cbc 100644 --- a/sci-biology/ngs/metadata.xml +++ b/sci-biology/ngs/metadata.xml @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">ncbi/ngs</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/ngs/ngs-2.11.2.ebuild b/sci-biology/ngs/ngs-2.11.2.ebuild index 8675ae22a..0574c5076 100644 --- a/sci-biology/ngs/ngs-2.11.2.ebuild +++ b/sci-biology/ngs/ngs-2.11.2.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_10 ) inherit python-single-r1 java-pkg-2 DESCRIPTION="NGS Language Bindings " diff --git a/sci-biology/nilearn/Manifest b/sci-biology/nilearn/Manifest index 580b087b0..550ed1f0f 100644 --- a/sci-biology/nilearn/Manifest +++ b/sci-biology/nilearn/Manifest @@ -1 +1,2 @@ -DIST nilearn-0.8.0.tar.gz 6603264 BLAKE2B f96621b68255722f89ac18cfc8b44e2dc5fc6d4bda2d867d5f83ba669f1c3369318e8458360071245398362122b501c70849741068f7bfa567e49a7f8cdeefa1 SHA512 6e7da3963cd29282ab77bbf1dbb5c1879897dae3d3296a8e0c57edc11a272d9e386914fc3af81d13b57199d64880f534806dca6851b5d8ddecae9083ec5df18e +DIST nilearn-0.8.1.gh.tar.gz 11305317 BLAKE2B adefde80f5bce5ef115299326d212a7771a6ca1fc1ed7afc20fdd5b099882cfe37cc2d163807677450328916704d44e8f4044229b1470f764c75ee12d2e72b63 SHA512 4de95caa5c2080665e827310de28efb48a8b2e8161ac62f9e799984dbcd364f45ce486fcd21e9f30ef1fc41f48d2e41e477846acec5f89caf3cc1489373293d4 +DIST nilearn-0.9.1.gh.tar.gz 11660100 BLAKE2B f2031b531faf2b7f77a6128ce2c41d4d8c4c9d5fab79df453ca127228f7ec4784b319107a9e9988b3d3a9ce87358d251e500a88dfb8226a6d4510ae5fe9f3a0c SHA512 f824fc563fd56b25508ee5803963fc98c2048fbab8823a6a6bde39e4b428a871588211649b4ce939f65173f6d4afd019e9fe1445b5cfdd00fba7823d9e23a571 diff --git a/sci-biology/nilearn/files/0.4.1-bundled_joblib_test.patch b/sci-biology/nilearn/files/0.4.1-bundled_joblib_test.patch deleted file mode 100644 index e229d25fb..000000000 --- a/sci-biology/nilearn/files/0.4.1-bundled_joblib_test.patch +++ /dev/null @@ -1,39 +0,0 @@ ---- a/nilearn/input_data/tests/test_nifti_masker.py 2018-08-02 18:57:07.700111595 +0200 -+++ b/nilearn/input_data/tests/test_nifti_masker.py 2018-08-02 18:57:29.453556439 +0200 -@@ -219,36 +219,6 @@ - assert_raises(ValueError, masker.fit_transform, data_img) - - --def test_joblib_cache(): -- from sklearn.externals.joblib import hash, Memory -- mask = np.zeros((40, 40, 40)) -- mask[20, 20, 20] = 1 -- mask_img = Nifti1Image(mask, np.eye(4)) -- -- with testing.write_tmp_imgs(mask_img, create_files=True) as filename: -- masker = NiftiMasker(mask_img=filename) -- masker.fit() -- mask_hash = hash(masker.mask_img_) -- masker.mask_img_.get_data() -- assert_true(mask_hash == hash(masker.mask_img_)) -- -- # Test a tricky issue with memmapped joblib.memory that makes -- # imgs return by inverse_transform impossible to save -- cachedir = mkdtemp() -- try: -- masker.memory = Memory(cachedir=cachedir, mmap_mode='r', -- verbose=0) -- X = masker.transform(mask_img) -- # inverse_transform a first time, so that the result is cached -- out_img = masker.inverse_transform(X) -- out_img = masker.inverse_transform(X) -- out_img.to_filename(os.path.join(cachedir, 'test.nii')) -- finally: -- # enables to delete "filename" on windows -- del masker -- shutil.rmtree(cachedir, ignore_errors=True) -- -- - def test_mask_init_errors(): - # Errors that are caught in init - mask = NiftiMasker(mask_strategy='oops') diff --git a/sci-biology/nilearn/files/nilearn-0.9.1-tests.patch b/sci-biology/nilearn/files/nilearn-0.9.1-tests.patch new file mode 100644 index 000000000..6d13b76b1 --- /dev/null +++ b/sci-biology/nilearn/files/nilearn-0.9.1-tests.patch @@ -0,0 +1,10 @@ +--- a/setup.cfg ++++ b/setup.cfg +@@ -78,7 +78,6 @@ + doctest_optionflags = NORMALIZE_WHITESPACE ELLIPSIS + junit_family = xunit2 + addopts = +- --doctest-modules + -s + -vv + --durations=0 diff --git a/sci-biology/nilearn/nilearn-0.8.0.ebuild b/sci-biology/nilearn/nilearn-0.8.1.ebuild index a70e8d0fc..3064c0ba5 100644 --- a/sci-biology/nilearn/nilearn-0.8.0.ebuild +++ b/sci-biology/nilearn/nilearn-0.8.1.ebuild @@ -1,15 +1,15 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 -PYTHON_COMPAT=( python3_{8..9} ) +PYTHON_COMPAT=( python3_{10..11} ) inherit distutils-r1 DESCRIPTION="Fast and easy statistical learning on NeuroImaging data" HOMEPAGE="http://nilearn.github.io/" -SRC_URI="https://github.com/nilearn/nilearn/archive/${PV}.tar.gz -> ${P}.tar.gz" +SRC_URI="https://github.com/nilearn/nilearn/archive/${PV}.tar.gz -> ${P}.gh.tar.gz" LICENSE="BSD" SLOT="0" @@ -38,5 +38,5 @@ distutils_enable_tests pytest python_test() { echo "backend: Agg" > matplotlibrc - MPLCONFIGDIR=. pytest -vv || die + MPLCONFIGDIR=. epytest } diff --git a/sci-biology/nilearn/nilearn-0.9.1.ebuild b/sci-biology/nilearn/nilearn-0.9.1.ebuild new file mode 100644 index 000000000..425e79444 --- /dev/null +++ b/sci-biology/nilearn/nilearn-0.9.1.ebuild @@ -0,0 +1,53 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) + +inherit distutils-r1 + +DESCRIPTION="Fast and easy statistical learning on NeuroImaging data" +HOMEPAGE="http://nilearn.github.io/" +SRC_URI="https://github.com/nilearn/nilearn/archive/${PV}.tar.gz -> ${P}.gh.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="test" + +RDEPEND=" + >=dev-python/joblib-0.15[${PYTHON_USEDEP}] + dev-python/lxml[${PYTHON_USEDEP}] + >=dev-python/matplotlib-3[${PYTHON_USEDEP}] + >=dev-python/numpy-1.18[${PYTHON_USEDEP}] + >=dev-python/pandas-1[${PYTHON_USEDEP}] + >=dev-python/requests-2[${PYTHON_USEDEP}] + >=dev-python/scipy-1.5[${PYTHON_USEDEP}] + >=sci-libs/nibabel-3[${PYTHON_USEDEP}] + >=sci-libs/scikit-learn-0.22[${PYTHON_USEDEP}] +" + +PATCHES=( "${FILESDIR}/${P}-tests.patch" ) + +distutils_enable_tests pytest + +EPYTEST_IGNORE=( + "examples/05_glm_second_level/plot_second_level_association_test.py" + "examples/05_glm_second_level/plot_second_level_one_sample_test.py" + "examples/05_glm_second_level/plot_second_level_two_sample_test.py" +) +# Reported upstream: +# https://github.com/nilearn/nilearn/issues/3232 +EPYTEST_DESELECT=( + "nilearn/decoding/tests/test_decoder.py::test_decoder_dummy_classifier" + "nilearn/interfaces/fmriprep/tests/test_load_confounds.py::test_nilearn_standardize[False-True-zscore]" + "nilearn/interfaces/fmriprep/tests/test_load_confounds.py::test_nilearn_standardize[False-True-psc]" + "nilearn/interfaces/fmriprep/tests/test_load_confounds.py::test_nilearn_standardize[True-True-zscore]" + "nilearn/interfaces/fmriprep/tests/test_load_confounds.py::test_nilearn_standardize[True-True-psc]" +) + +python_test() { + echo "backend: Agg" > matplotlibrc + MPLCONFIGDIR=. epytest +} diff --git a/sci-biology/nilearn/nilearn-9999.ebuild b/sci-biology/nilearn/nilearn-9999.ebuild deleted file mode 100644 index a9478fc8e..000000000 --- a/sci-biology/nilearn/nilearn-9999.ebuild +++ /dev/null @@ -1,42 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{8..9} ) - -inherit distutils-r1 git-r3 - -DESCRIPTION="Fast and easy statistical learning on NeuroImaging data" -HOMEPAGE="http://nilearn.github.io/" -EGIT_REPO_URI="https://github.com/nilearn/nilearn" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -# Tests attempt to download external data. -RESTRICT="test" - -BDEPEND=" - test? ( - dev-python/matplotlib[${PYTHON_USEDEP}] - ) -" - -RDEPEND=" - >=dev-python/joblib-0.12[${PYTHON_USEDEP}] - >=dev-python/numpy-1.16[${PYTHON_USEDEP}] - >=sci-libs/scikit-learn-0.21[${PYTHON_USEDEP}] - >=dev-python/scipy-1.2[${PYTHON_USEDEP}] - >=sci-libs/nibabel-2.5[${PYTHON_USEDEP}] - >=dev-python/pandas-0.24.0[${PYTHON_USEDEP}] - >=dev-python/requests-2[${PYTHON_USEDEP}] -" - -distutils_enable_tests pytest - -python_test() { - echo "backend: Agg" > matplotlibrc - MPLCONFIGDIR=. pytest -vv || die -} diff --git a/sci-biology/nitime/Manifest b/sci-biology/nitime/Manifest index 2ba87b1bb..4a9a85cc0 100644 --- a/sci-biology/nitime/Manifest +++ b/sci-biology/nitime/Manifest @@ -1 +1,2 @@ +DIST nitime-0.10.2.tar.gz 6231004 BLAKE2B 2214eb4fcb29567ebb4e819451bf7401ae6b467c0a2d196904c08bc44343e5c1ea840770f72d37df5e6642df455d895bfc9453b9389d8ef96cc88f3abc0d586e SHA512 c8c687f6c5e189e48bbe5cba4bbe3f19f34e6d087b43e3b0aa42d587f46081d3727867dbe07fa6d945381119086e12c98cdf12798055529a484152a4c04eae21 DIST nitime-0.9.tar.gz 6222979 BLAKE2B 45dbf34fd89b805f97ae5d4f88264f47ff88fa1f89b7ef05527477270bfa588a79fd1b356b2e7206919ed675936207accc02ad5b9a4be27e916a1dcf0561147e SHA512 cd8af7c3463143ac1765c472c1274915adfaf85508c334008c703ef72961e0a5e9ccbbd9321aaf62f7a58d9534934386baf1c7269a1d8f2d41b678707cd69406 diff --git a/sci-biology/nitime/metadata.xml b/sci-biology/nitime/metadata.xml index d504ea22c..606822ddb 100644 --- a/sci-biology/nitime/metadata.xml +++ b/sci-biology/nitime/metadata.xml @@ -10,10 +10,11 @@ <name>Gentoo Science Project</name> </maintainer> <longdescription lang="en"> -Nitime is a library for time-series analysis of data from neuroscience experiments -in both the time and spectral domains. -</longdescription> + Nitime is a library for time-series analysis of data from neuroscience experiments + in both the time and spectral domains. + </longdescription> <upstream> <remote-id type="github">nipy/nitime</remote-id> + <remote-id type="pypi">nitime</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/nitime/nitime-0.10.2.ebuild b/sci-biology/nitime/nitime-0.10.2.ebuild new file mode 100644 index 000000000..7e47d7288 --- /dev/null +++ b/sci-biology/nitime/nitime-0.10.2.ebuild @@ -0,0 +1,33 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..11} ) + +inherit distutils-r1 pypi + +DESCRIPTION="Time-series analysis of neuroscience data" +HOMEPAGE="http://nipy.org/nitime/index.html" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +COMMON_DEPEND=" + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/matplotlib[${PYTHON_USEDEP}] + dev-python/scipy[${PYTHON_USEDEP}] + " +BDEPEND="${COMMON_DEPEND} + dev-python/cython[${PYTHON_USEDEP}] + " +RDEPEND=" + ${COMMON_DEPEND} + dev-python/networkx[${PYTHON_USEDEP}] + sci-libs/nibabel[${PYTHON_USEDEP}] + " + +distutils_enable_tests pytest +distutils_enable_sphinx doc diff --git a/sci-biology/nitime/nitime-0.9.ebuild b/sci-biology/nitime/nitime-0.9.ebuild index 90cb4ff6a..cae7fdfea 100644 --- a/sci-biology/nitime/nitime-0.9.ebuild +++ b/sci-biology/nitime/nitime-0.9.ebuild @@ -1,15 +1,14 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 -PYTHON_COMPAT=( python3_{7,8,9} ) +PYTHON_COMPAT=( python3_{10..11} ) -inherit distutils-r1 virtualx +inherit distutils-r1 pypi virtualx DESCRIPTION="Time-series analysis of neuroscience data" HOMEPAGE="http://nipy.org/nitime/index.html" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" LICENSE="BSD" SLOT="0" diff --git a/sci-biology/nitime/nitime-9999.ebuild b/sci-biology/nitime/nitime-9999.ebuild index c46edf3c1..ee81c01dc 100644 --- a/sci-biology/nitime/nitime-9999.ebuild +++ b/sci-biology/nitime/nitime-9999.ebuild @@ -1,11 +1,12 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 -PYTHON_COMPAT=( python3_{7,8,9} ) +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..11} ) -inherit distutils-r1 git-r3 virtualx +inherit distutils-r1 git-r3 DESCRIPTION="Time-series analysis of neuroscience data" HOMEPAGE="http://nipy.org/nitime/index.html" @@ -16,9 +17,6 @@ LICENSE="BSD" SLOT="0" KEYWORDS="" -# import file mismatch: -RESTRICT="test" - COMMON_DEPEND=" dev-python/numpy[${PYTHON_USEDEP}] dev-python/matplotlib[${PYTHON_USEDEP}] @@ -35,7 +33,3 @@ RDEPEND=" distutils_enable_tests pytest distutils_enable_sphinx doc - -python_test() { - virtx pytest -v || die -} diff --git a/sci-biology/ntCard/metadata.xml b/sci-biology/ntCard/metadata.xml index 138cb7705..fb03df79c 100644 --- a/sci-biology/ntCard/metadata.xml +++ b/sci-biology/ntCard/metadata.xml @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">bcgsc/ntCard</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/nwalign3/Manifest b/sci-biology/nwalign3/Manifest deleted file mode 100644 index 7a5302a6d..000000000 --- a/sci-biology/nwalign3/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST nwalign3-0.1.2.tar.gz 101141 BLAKE2B 9a7060db7362fa4a0b8b01f7f5131d1b168ce1f7bfe40ff7e3a6f3c09977c227e01f4da74915af62f73c9519d6137f42e345382fb3d591a70fbbdea6d2d8b3d4 SHA512 4e8bad31f8e648d7b4fc46bd34cd8404cc08fa9e188a74fc083e4e18b5615e4b2db77c78754ca2069e4158382483eb92d876049d68a6532e83f5df409ae36f93 diff --git a/sci-biology/nwalign3/metadata.xml b/sci-biology/nwalign3/metadata.xml deleted file mode 100644 index ad73a59be..000000000 --- a/sci-biology/nwalign3/metadata.xml +++ /dev/null @@ -1,15 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>mmokrejs@gmail.com</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="pypi">nwalign</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-biology/nwalign3/nwalign3-0.1.2.ebuild b/sci-biology/nwalign3/nwalign3-0.1.2.ebuild deleted file mode 100644 index 7c2b96bb6..000000000 --- a/sci-biology/nwalign3/nwalign3-0.1.2.ebuild +++ /dev/null @@ -1,22 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7,8,9} ) -DISTUTILS_USE_SETUPTOOLS=rdepend - -inherit distutils-r1 - -DESCRIPTION="Needleman-Wunsch global sequence alignment in python3" -HOMEPAGE="https://github.com/briney/nwalign3" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64" - -DEPEND=" - dev-python/numpy - dev-python/cython" -RDEPEND="${DEPEND}" diff --git a/sci-biology/oases/Manifest b/sci-biology/oases/Manifest deleted file mode 100644 index 031a5ff34..000000000 --- a/sci-biology/oases/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -DIST OasesManual.pdf 113886 BLAKE2B aa8492887cea64e67966238e620b24aa5f90a8622a6de9bc4d4e1f56554f624c9ae7a19e0c46d83478849ec5d2ecb758fd8e253d8327d4d2bdcdda9db2e114a7 SHA512 c710a62cd1982060f723918f5f4de91adff12870d1682d0729035a3588ed37d26898c399c07b1b81b4b399c7ea1a14509784a6dbb9de6004bcadf6677cd5859f -DIST oases_0.2.08.tgz 92037 BLAKE2B ff9762264d18c42e20b2208a057b073a2a960dab1ca17372db2fbf6f09094d3446ccd29a6038e17ee59b5adee9afe23cd59bbc4b640f57ce04141d2990b32b90 SHA512 e9a73a9227ce13995fcac7f456534a650099d8160d48d2d9831f3f05e482353c29dd76bbc74b0b451154eb5061ddb473649d21442941360f0e8c7623f6fe586c diff --git a/sci-biology/oases/files/Makefile.patch b/sci-biology/oases/files/Makefile.patch deleted file mode 100644 index fcd0842ff..000000000 --- a/sci-biology/oases/files/Makefile.patch +++ /dev/null @@ -1,15 +0,0 @@ ---- a/Makefile 2016-04-10 22:34:31.976222662 +0200 -+++ b/Makefile 2016-04-10 22:37:49.636225327 +0200 -@@ -1,8 +1,8 @@ --CC = gcc --CFLAGS = -Wall --DEBUG = -g -+CC ?= gcc -+CFLAGS ?= -Wall -+DEBUG ?= -g - LIBS = -lm --OPT = -O3 -+#OPT = -O3 - export MAXKMERLENGTH = 64 - export CATEGORIES = 2 - DEF = -D MAXKMERLENGTH=$(MAXKMERLENGTH) -D CATEGORIES=$(CATEGORIES) diff --git a/sci-biology/oases/metadata.xml b/sci-biology/oases/metadata.xml deleted file mode 100644 index 138cb7705..000000000 --- a/sci-biology/oases/metadata.xml +++ /dev/null @@ -1,12 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-biology/oases/oases-0.2.08.ebuild b/sci-biology/oases/oases-0.2.08.ebuild deleted file mode 100644 index 74ad30f59..000000000 --- a/sci-biology/oases/oases-0.2.08.ebuild +++ /dev/null @@ -1,40 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -DESCRIPTION="De novo transcriptome assembler" -HOMEPAGE="http://www.ebi.ac.uk/~zerbino/oases" -if [ "$PV" == "9999" ]; then - inherit git-r3 - EGIT_REPO_URI="https://github.com/dzerbino/oases.git" - SRC_URI="http://www.ebi.ac.uk/~zerbino/oases/OasesManual.pdf" -else - SRC_URI="http://www.ebi.ac.uk/~zerbino/oases/oases_0.2.08.tgz - http://www.ebi.ac.uk/~zerbino/oases/OasesManual.pdf" - S="${WORKDIR}/oases_0.2.8" - KEYWORDS="" - # fails to find globals.h, but which globals.h does it want? -fi - -LICENSE="GPL-3" -SLOT="0" - -DEPEND="" -RDEPEND="${DEPEND} - >=sci-biology/velvet-1.2.08" - -PATCHES=( - "${FILESDIR}/Makefile.patch" -) - -src_prepare(){ - default - sed -e 's#cleanobj velvet oases doc#oases#' -i Makefile || die -} - -src_install(){ - dobin oases - dodoc README.md - dodoc "${DISTDIR}"/OasesManual.pdf -} diff --git a/sci-biology/oases/oases-9999.ebuild b/sci-biology/oases/oases-9999.ebuild deleted file mode 100644 index 74ad30f59..000000000 --- a/sci-biology/oases/oases-9999.ebuild +++ /dev/null @@ -1,40 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -DESCRIPTION="De novo transcriptome assembler" -HOMEPAGE="http://www.ebi.ac.uk/~zerbino/oases" -if [ "$PV" == "9999" ]; then - inherit git-r3 - EGIT_REPO_URI="https://github.com/dzerbino/oases.git" - SRC_URI="http://www.ebi.ac.uk/~zerbino/oases/OasesManual.pdf" -else - SRC_URI="http://www.ebi.ac.uk/~zerbino/oases/oases_0.2.08.tgz - http://www.ebi.ac.uk/~zerbino/oases/OasesManual.pdf" - S="${WORKDIR}/oases_0.2.8" - KEYWORDS="" - # fails to find globals.h, but which globals.h does it want? -fi - -LICENSE="GPL-3" -SLOT="0" - -DEPEND="" -RDEPEND="${DEPEND} - >=sci-biology/velvet-1.2.08" - -PATCHES=( - "${FILESDIR}/Makefile.patch" -) - -src_prepare(){ - default - sed -e 's#cleanobj velvet oases doc#oases#' -i Makefile || die -} - -src_install(){ - dobin oases - dodoc README.md - dodoc "${DISTDIR}"/OasesManual.pdf -} diff --git a/sci-biology/open-ephys-gui/Manifest b/sci-biology/open-ephys-gui/Manifest index 9f8d8eeac..5863b7945 100644 --- a/sci-biology/open-ephys-gui/Manifest +++ b/sci-biology/open-ephys-gui/Manifest @@ -1,2 +1,3 @@ -DIST open-ephys-gui-0.5.2.2.tar.gz 64533170 BLAKE2B dc70c3eca6a8fbc7c4f6e84580fa6d5b31b837fedbdff20f532e3c01c764cbc3c51637e4fd678d048c78b6f79b4b4a5cd4d437125beeaf712f6f322e82579c85 SHA512 b6369bb0abd8ca18ff225cffab04a24915865647ee1ab5b6d83d5d6fbda3bc64d1b7db04c23deb8d29b8ff378e703b88cfa9d409f4cde62a3af34a7984427219 DIST open-ephys-gui-0.5.5.tar.gz 63347783 BLAKE2B 8f3ab3c20e23dd4f613e2ed47dca1827ddbcc5e95be5ca12dfeefdc84611653d531d629b78049397fd4951d558f63531ea2265d13e629c8da793fc20090d1075 SHA512 b835a7f8bb3eeb08ec77f6d14f988d6278b2f5b1966fbf8bec55d429c9cee36050cf574dd78a2ebad4adc5c681bcec5b64dcfb1ec87e548c55e2bf1bff2eb2dc +DIST open-ephys-gui-0.6.1.tar.gz 44674639 BLAKE2B 10113418c41ccc62064bd8b993aab5402691259702c53c580e39371bd5034bc3b65babfa0adcaa7e2aadb8a86758e52cc4a86fee83db05614c849ed4c2b76ff4 SHA512 00ef7e5fd1242c84948e8eaf0479337365de21a28cb77252bf2baf806b186b9c8b7a424d756a4b6a883ecac48aefd6d2a532a8cadaa910e295b474d38056547e +DIST open-ephys-gui-0.6.4.tar.gz 44686737 BLAKE2B 839e33679cc14ffa9e2da99622e7a18f6c4f17d6a45a6c07b1136372126e2c05ad4804bc3bdf5412c7e74d00242d61d0a084574d619ea7acad4485a4aa150795 SHA512 5ac81076731d0b325ea9267d52c702c4fbb972a9c73ab156ccf9752b14cc842d7fdbca2ba292277c9127f124ca2fa73c555a51219bd3e1c95c63f40837f7eff2 diff --git a/sci-biology/open-ephys-gui/files/open-ephys-gui-0.5.2.2.patch b/sci-biology/open-ephys-gui/files/open-ephys-gui-0.5.2.2.patch deleted file mode 100644 index 77e401639..000000000 --- a/sci-biology/open-ephys-gui/files/open-ephys-gui-0.5.2.2.patch +++ /dev/null @@ -1,12 +0,0 @@ -# Add 'Gentoo' build type - ---- ../CMakeLists.txt 2019-12-02 22:29:24.021065669 -0300 -+++ ../CMakeLists.txt 2019-12-02 22:29:11.251065418 -0300 -@@ -123,6 +123,7 @@ - if(${CMAKE_BUILD_TYPE} STREQUAL "Debug") - - elseif (${CMAKE_BUILD_TYPE} STREQUAL "Release") -+ elseif (${CMAKE_BUILD_TYPE} STREQUAL "Gentoo") - else() - message(FATAL_ERROR "Invalid build type") - endif() diff --git a/sci-biology/open-ephys-gui/files/open-ephys-gui-0.6.1.patch b/sci-biology/open-ephys-gui/files/open-ephys-gui-0.6.1.patch new file mode 100644 index 000000000..0992f2241 --- /dev/null +++ b/sci-biology/open-ephys-gui/files/open-ephys-gui-0.6.1.patch @@ -0,0 +1,15 @@ +# Add 'Gentoo' build type + +--- ../CMakeLists.txt 2022-08-24 15:27:32.871426442 -0300 ++++ ../CMakeLists.txt 2022-08-24 15:31:03.438087613 -0300 +@@ -171,8 +171,8 @@ + target_compile_options(open-ephys PRIVATE -O0) #enable optimization for linux debug + elseif (${CMAKE_BUILD_TYPE} STREQUAL "Release") + target_compile_options(open-ephys PRIVATE -O3) #enable optimization for linux release +- else() +- message(FATAL_ERROR "Invalid build type") ++ # else() ++ # message(FATAL_ERROR "Invalid build type") + endif() + find_package(CURL REQUIRED) + find_package(PkgConfig REQUIRED) diff --git a/sci-biology/open-ephys-gui/files/open-ephys-gui-0.6.4.patch b/sci-biology/open-ephys-gui/files/open-ephys-gui-0.6.4.patch new file mode 100644 index 000000000..5c0c6526e --- /dev/null +++ b/sci-biology/open-ephys-gui/files/open-ephys-gui-0.6.4.patch @@ -0,0 +1,15 @@ +# Add 'Gentoo' build type + +--- ../CMakeLists.txt 2022-08-24 15:27:32.871426442 -0300 ++++ ../CMakeLists.txt 2022-08-24 15:31:03.438087613 -0300 +@@ -173,8 +173,8 @@ + target_compile_options(open-ephys PRIVATE -O0) #enable optimization for linux debug + elseif (${CMAKE_BUILD_TYPE} STREQUAL "Release") + target_compile_options(open-ephys PRIVATE -O3) #enable optimization for linux release +- else() +- message(FATAL_ERROR "Invalid build type") ++ # else() ++ # message(FATAL_ERROR "Invalid build type") + endif() + find_package(CURL REQUIRED) + find_package(PkgConfig REQUIRED) diff --git a/sci-biology/open-ephys-gui/files/open-ephys-gui-9999.patch b/sci-biology/open-ephys-gui/files/open-ephys-gui-9999.patch deleted file mode 100644 index 77e401639..000000000 --- a/sci-biology/open-ephys-gui/files/open-ephys-gui-9999.patch +++ /dev/null @@ -1,12 +0,0 @@ -# Add 'Gentoo' build type - ---- ../CMakeLists.txt 2019-12-02 22:29:24.021065669 -0300 -+++ ../CMakeLists.txt 2019-12-02 22:29:11.251065418 -0300 -@@ -123,6 +123,7 @@ - if(${CMAKE_BUILD_TYPE} STREQUAL "Debug") - - elseif (${CMAKE_BUILD_TYPE} STREQUAL "Release") -+ elseif (${CMAKE_BUILD_TYPE} STREQUAL "Gentoo") - else() - message(FATAL_ERROR "Invalid build type") - endif() diff --git a/sci-biology/open-ephys-gui/files/open-ephys-gui-99999999.patch b/sci-biology/open-ephys-gui/files/open-ephys-gui-99999999.patch deleted file mode 100644 index 77e401639..000000000 --- a/sci-biology/open-ephys-gui/files/open-ephys-gui-99999999.patch +++ /dev/null @@ -1,12 +0,0 @@ -# Add 'Gentoo' build type - ---- ../CMakeLists.txt 2019-12-02 22:29:24.021065669 -0300 -+++ ../CMakeLists.txt 2019-12-02 22:29:11.251065418 -0300 -@@ -123,6 +123,7 @@ - if(${CMAKE_BUILD_TYPE} STREQUAL "Debug") - - elseif (${CMAKE_BUILD_TYPE} STREQUAL "Release") -+ elseif (${CMAKE_BUILD_TYPE} STREQUAL "Gentoo") - else() - message(FATAL_ERROR "Invalid build type") - endif() diff --git a/sci-biology/open-ephys-gui/metadata.xml b/sci-biology/open-ephys-gui/metadata.xml index ed9bf87e3..2c9af77a9 100644 --- a/sci-biology/open-ephys-gui/metadata.xml +++ b/sci-biology/open-ephys-gui/metadata.xml @@ -5,6 +5,10 @@ <email>malfatti@disroot.org</email> <name>T Malfatti</name> </maintainer> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> <upstream> <remote-id type="github">open-ephys/plugin-GUI</remote-id> </upstream> diff --git a/sci-biology/open-ephys-gui/open-ephys-gui-0.5.2.2.ebuild b/sci-biology/open-ephys-gui/open-ephys-gui-0.6.1.ebuild index b4cbc6d8f..fe6791a2d 100644 --- a/sci-biology/open-ephys-gui/open-ephys-gui-0.5.2.2.ebuild +++ b/sci-biology/open-ephys-gui/open-ephys-gui-0.6.1.ebuild @@ -1,8 +1,8 @@ -# Copyright 2019-2021 Gentoo Authors +# Copyright 2019-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 -inherit cmake +EAPI=8 +inherit cmake udev DESCRIPTION="Processing, recording, and visualizing multichannel ephys data" HOMEPAGE="https://open-ephys.org/gui/" @@ -11,47 +11,47 @@ LICENSE="GPL-3" if [[ ${PV} == "9999" ]] ; then inherit git-r3 EGIT_REPO_URI="https://github.com/open-ephys/plugin-GUI" - EGIT_BRANCH="master" - Suffix=$EGIT_BRANCH + EGIT_BRANCH="main" + Suffix=${EGIT_BRANCH} SubDir=${P} elif [[ ${PV} == "99999999" ]] ; then inherit git-r3 EGIT_REPO_URI="https://github.com/open-ephys/plugin-GUI" EGIT_BRANCH="development" - Suffix=$EGIT_BRANCH + Suffix=${EGIT_BRANCH} SubDir=${P} else SRC_URI="https://github.com/open-ephys/plugin-GUI/archive/v${PV}.tar.gz -> ${P}.tar.gz" Suffix=${PV} SubDir="plugin-GUI-${PV}" - S="${WORKDIR}/$SubDir" + S="${WORKDIR}/${SubDir}" KEYWORDS="~amd64 ~x86" fi SLOT="${PV}" IUSE="jack" -BDEPEND=" - <sys-devel/gcc-9 -" DEPEND=" + dev-libs/openssl media-libs/alsa-lib media-libs/freeglut media-libs/freetype + net-libs/webkit-gtk + net-misc/curl x11-libs/libXrandr x11-libs/libXcursor x11-libs/libXinerama - jack? ( media-sound/jack-audio-connection-kit ) + jack? ( || ( media-sound/jack-audio-connection-kit media-sound/jack2 ) ) " RDEPEND="${DEPEND}" -BUILD_DIR="$S/Build" +BUILD_DIR="${S}/Build" PATCHES=( "${FILESDIR}"/${P}.patch ) -QA_PREBUILT="opt/open-ephys-0.5.2.2/shared/*.so" +QA_PREBUILT="opt/open-ephys-*/shared/*.so" QA_PRESTRIPPED=" - opt/open-ephys-0.5.2.2/plugins/*.so - opt/open-ephys-0.5.2.2/open-ephys + opt/open-ephys-*/plugins/*.so + opt/open-ephys-*/open-ephys " src_prepare() { @@ -68,15 +68,16 @@ src_configure() { } src_install() { - dodir opt/open-ephys-"$Suffix"/ lib/udev/rules.d/ - cp -R "${BUILD_DIR}"/Gentoo/* "${ED}"/opt/open-ephys-"$Suffix"/ - cp -R "${WORKDIR}"/"${SubDir}"/Resources/Scripts/40-open-ephys.rules "${ED}"/lib/udev/rules.d/ - dosym ../../opt/open-ephys-"$Suffix"/open-ephys usr/bin/open-ephys-"$Suffix" + dodir opt/open-ephys-"${Suffix}"/ lib/udev/rules.d/ + cp -R "${BUILD_DIR}"/RelWithDebInfo/* "${ED}"/opt/open-ephys-"${Suffix}"/ || die + udev_newrules "${WORKDIR}"/"${SubDir}"/Resources/Scripts/40-open-ephys.rules 40-open-ephys-"${Suffix}".rules + dosym ../../opt/open-ephys-"${Suffix}"/open-ephys usr/bin/open-ephys-"${Suffix}" } pkg_postinst() { - ewarn " " - ewarn "You must restart the udev service in order to allow your computer to" - ewarn "communicate with the Open Ephys acquisition board." - ewarn " " + udev_reload +} + +pkg_postrm() { + udev_reload } diff --git a/sci-biology/open-ephys-gui/open-ephys-gui-0.6.4.ebuild b/sci-biology/open-ephys-gui/open-ephys-gui-0.6.4.ebuild new file mode 100644 index 000000000..cae41e773 --- /dev/null +++ b/sci-biology/open-ephys-gui/open-ephys-gui-0.6.4.ebuild @@ -0,0 +1,83 @@ +# Copyright 2019-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 +inherit cmake udev + +DESCRIPTION="Processing, recording, and visualizing multichannel ephys data" +HOMEPAGE="https://open-ephys.org/gui/" +LICENSE="GPL-3" + +if [[ ${PV} == "9999" ]] ; then + inherit git-r3 + EGIT_REPO_URI="https://github.com/open-ephys/plugin-GUI" + EGIT_BRANCH="main" + Suffix=${EGIT_BRANCH} + SubDir=${P} +elif [[ ${PV} == "99999999" ]] ; then + inherit git-r3 + EGIT_REPO_URI="https://github.com/open-ephys/plugin-GUI" + EGIT_BRANCH="development" + Suffix=${EGIT_BRANCH} + SubDir=${P} +else + SRC_URI="https://github.com/open-ephys/plugin-GUI/archive/v${PV}.tar.gz -> ${P}.tar.gz" + Suffix=${PV} + SubDir="plugin-GUI-${PV}" + S="${WORKDIR}/${SubDir}" + KEYWORDS="~amd64 ~x86" +fi + +SLOT="${PV}" +IUSE="jack" + +DEPEND=" + dev-libs/openssl + media-libs/alsa-lib + media-libs/freeglut + media-libs/freetype + net-libs/webkit-gtk:4 + net-misc/curl + x11-libs/libXrandr + x11-libs/libXcursor + x11-libs/libXinerama + jack? ( || ( media-sound/jack-audio-connection-kit media-sound/jack2 ) ) +" +RDEPEND="${DEPEND}" + +BUILD_DIR="${S}/Build" +PATCHES=( "${FILESDIR}"/${P}.patch ) + +QA_PREBUILT="opt/open-ephys-*/shared/*.so" +QA_PRESTRIPPED=" + opt/open-ephys-*/plugins/*.so + opt/open-ephys-*/open-ephys +" + +src_prepare() { + cmake_src_prepare + + if use jack; then + sed -i 's/JUCE_APP_VERSION=/JUCE_JACK=1\n JUCE_APP_VERSION=/' "${WORKDIR}/${SubDir}/CMakeLists.txt" || die "Sed failed!" + fi +} + +src_configure() { + local mycmakeargs=( -DCMAKE_SKIP_RPATH=ON ) + cmake_src_configure +} + +src_install() { + dodir opt/open-ephys-"${Suffix}"/ lib/udev/rules.d/ + cp -R "${BUILD_DIR}"/RelWithDebInfo/* "${ED}"/opt/open-ephys-"${Suffix}"/ || die + udev_newrules "${WORKDIR}"/"${SubDir}"/Resources/Scripts/40-open-ephys.rules 40-open-ephys-"${Suffix}".rules + dosym ../../opt/open-ephys-"${Suffix}"/open-ephys usr/bin/open-ephys-"${Suffix}" +} + +pkg_postinst() { + udev_reload +} + +pkg_postrm() { + udev_reload +} diff --git a/sci-biology/open-ephys-gui/open-ephys-gui-9999.ebuild b/sci-biology/open-ephys-gui/open-ephys-gui-9999.ebuild index 1c2b20e24..2ab957f40 100644 --- a/sci-biology/open-ephys-gui/open-ephys-gui-9999.ebuild +++ b/sci-biology/open-ephys-gui/open-ephys-gui-9999.ebuild @@ -1,7 +1,7 @@ -# Copyright 2019-2021 Gentoo Authors +# Copyright 2019-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 inherit cmake udev DESCRIPTION="Processing, recording, and visualizing multichannel ephys data" @@ -11,7 +11,7 @@ LICENSE="GPL-3" if [[ ${PV} == "9999" ]] ; then inherit git-r3 EGIT_REPO_URI="https://github.com/open-ephys/plugin-GUI" - EGIT_BRANCH="master" + EGIT_BRANCH="main" Suffix=${EGIT_BRANCH} SubDir=${P} elif [[ ${PV} == "99999999" ]] ; then @@ -32,9 +32,12 @@ SLOT="${PV}" IUSE="jack" DEPEND=" + dev-libs/openssl media-libs/alsa-lib media-libs/freeglut media-libs/freetype + net-libs/webkit-gtk:4 + net-misc/curl x11-libs/libXrandr x11-libs/libXcursor x11-libs/libXinerama @@ -43,7 +46,7 @@ DEPEND=" RDEPEND="${DEPEND}" BUILD_DIR="${S}/Build" -PATCHES=( "${FILESDIR}"/${P}.patch ) +PATCHES=( "${FILESDIR}"/"${PN}"-0.6.4.patch ) QA_PREBUILT="opt/open-ephys-*/shared/*.so" QA_PRESTRIPPED=" @@ -66,7 +69,7 @@ src_configure() { src_install() { dodir opt/open-ephys-"${Suffix}"/ lib/udev/rules.d/ - cp -R "${BUILD_DIR}"/Gentoo/* "${ED}"/opt/open-ephys-"${Suffix}"/ + cp -R "${BUILD_DIR}"/RelWithDebInfo/* "${ED}"/opt/open-ephys-"${Suffix}"/ || die udev_newrules "${WORKDIR}"/"${SubDir}"/Resources/Scripts/40-open-ephys.rules 40-open-ephys-"${Suffix}".rules dosym ../../opt/open-ephys-"${Suffix}"/open-ephys usr/bin/open-ephys-"${Suffix}" } diff --git a/sci-biology/open-ephys-gui/open-ephys-gui-99999999.ebuild b/sci-biology/open-ephys-gui/open-ephys-gui-99999999.ebuild index 1c2b20e24..2ab957f40 100644 --- a/sci-biology/open-ephys-gui/open-ephys-gui-99999999.ebuild +++ b/sci-biology/open-ephys-gui/open-ephys-gui-99999999.ebuild @@ -1,7 +1,7 @@ -# Copyright 2019-2021 Gentoo Authors +# Copyright 2019-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 inherit cmake udev DESCRIPTION="Processing, recording, and visualizing multichannel ephys data" @@ -11,7 +11,7 @@ LICENSE="GPL-3" if [[ ${PV} == "9999" ]] ; then inherit git-r3 EGIT_REPO_URI="https://github.com/open-ephys/plugin-GUI" - EGIT_BRANCH="master" + EGIT_BRANCH="main" Suffix=${EGIT_BRANCH} SubDir=${P} elif [[ ${PV} == "99999999" ]] ; then @@ -32,9 +32,12 @@ SLOT="${PV}" IUSE="jack" DEPEND=" + dev-libs/openssl media-libs/alsa-lib media-libs/freeglut media-libs/freetype + net-libs/webkit-gtk:4 + net-misc/curl x11-libs/libXrandr x11-libs/libXcursor x11-libs/libXinerama @@ -43,7 +46,7 @@ DEPEND=" RDEPEND="${DEPEND}" BUILD_DIR="${S}/Build" -PATCHES=( "${FILESDIR}"/${P}.patch ) +PATCHES=( "${FILESDIR}"/"${PN}"-0.6.4.patch ) QA_PREBUILT="opt/open-ephys-*/shared/*.so" QA_PRESTRIPPED=" @@ -66,7 +69,7 @@ src_configure() { src_install() { dodir opt/open-ephys-"${Suffix}"/ lib/udev/rules.d/ - cp -R "${BUILD_DIR}"/Gentoo/* "${ED}"/opt/open-ephys-"${Suffix}"/ + cp -R "${BUILD_DIR}"/RelWithDebInfo/* "${ED}"/opt/open-ephys-"${Suffix}"/ || die udev_newrules "${WORKDIR}"/"${SubDir}"/Resources/Scripts/40-open-ephys.rules 40-open-ephys-"${Suffix}".rules dosym ../../opt/open-ephys-"${Suffix}"/open-ephys usr/bin/open-ephys-"${Suffix}" } diff --git a/sci-biology/opfvta_bidsdata/opfvta_bidsdata-2.0.ebuild b/sci-biology/opfvta_bidsdata/opfvta_bidsdata-2.0.ebuild index 988f6ba6f..d21f85f8c 100644 --- a/sci-biology/opfvta_bidsdata/opfvta_bidsdata-2.0.ebuild +++ b/sci-biology/opfvta_bidsdata/opfvta_bidsdata-2.0.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2020 Gentoo Authors +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=7 @@ -6,9 +6,8 @@ EAPI=7 inherit check-reqs DESCRIPTION="BIDS data files released with the OPFVTA publication" -HOMEPAGE="http://www.aic-fmi.ethz.ch/" +HOMEPAGE="http://chymera.eu/docs/focus/open-science/" SRC_URI=" - http://chymera.eu/distfiles/${P}.tar.xz https://zenodo.org/record/3575149/files/${P}.tar.xz " diff --git a/sci-biology/pbbam/Manifest b/sci-biology/pbbam/Manifest index c35432703..1bb2b2625 100644 --- a/sci-biology/pbbam/Manifest +++ b/sci-biology/pbbam/Manifest @@ -1 +1 @@ -DIST pbbam-1.8.1.tar.gz 11069936 BLAKE2B 6ef23c81f4cfbdb060bfc8355ca628024038466482a6cacb3dd162fa58ab1052702e482ab797a60160264fd2cc70fe116dd5385c6094560060adf6fe2cf74d10 SHA512 ea28b4683c72fafb2e459ac1f37a9be258ddc82e059ba9d8b094e8dd6e3a40d3f25d5edcc790c5bd274805190caf1123311199e30166bd4f3e815dcc77929387 +DIST pbbam-2.1.0.tar.gz 10405332 BLAKE2B c91122afcc8fae747fbf1e40274aeb7f2fbc5a02789945798899c6ae87ff01beaae994a80a356a71a788e8626ee5a3595537d8bd6468ac30a874733fa9e9d883 SHA512 5f606620d1a6eb7c31c36db4d6fd125e397c4b81d9f695dc8756535074ce98c4b05e04d86077ed33e0ba1e503e766b1b59e08bb73e8f8129af7789024f308094 diff --git a/sci-biology/pbbam/metadata.xml b/sci-biology/pbbam/metadata.xml index 138cb7705..e12f3579e 100644 --- a/sci-biology/pbbam/metadata.xml +++ b/sci-biology/pbbam/metadata.xml @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">PacificBiosciences/pbbam</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/pbbam/pbbam-1.8.1.ebuild b/sci-biology/pbbam/pbbam-2.1.0.ebuild index a114da0fc..a114da0fc 100644 --- a/sci-biology/pbbam/pbbam-1.8.1.ebuild +++ b/sci-biology/pbbam/pbbam-2.1.0.ebuild diff --git a/sci-biology/phusion2/Manifest b/sci-biology/phusion2/Manifest deleted file mode 100644 index fce8afa2a..000000000 --- a/sci-biology/phusion2/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST phusion2-3.0.tar.gz 136875 BLAKE2B 8338df1865ac8f684ba3a2a2fc15520fe167a1ace02e8f64db17f6acf07ea8cde2da18fd6f18a958e53b00dd02e7e8138305e2a762a84c6bf8d7cfbd2cb9b999 SHA512 a29e4102806d404a7bc78c1611d702f9c6415bc04ca518416632bf8d9d3e570324add907c43e627f645a5281b807ccf169908637121f66883c4e878080345eca diff --git a/sci-biology/phusion2/metadata.xml b/sci-biology/phusion2/metadata.xml deleted file mode 100644 index 0f267b755..000000000 --- a/sci-biology/phusion2/metadata.xml +++ /dev/null @@ -1,15 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="sourceforge">downloads</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-biology/phusion2/phusion2-3.0.ebuild b/sci-biology/phusion2/phusion2-3.0.ebuild deleted file mode 100644 index 2ea281d41..000000000 --- a/sci-biology/phusion2/phusion2-3.0.ebuild +++ /dev/null @@ -1,37 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -DESCRIPTION="Whole genome shotgun assembler using phrap (for Sanger-based reads)" -HOMEPAGE="https://sourceforge.net/projects/phusion2" -SRC_URI="https://downloads.sourceforge.net/project/${PN}/${P}.tar.gz" - -LICENSE="all-rights-reserved" # temporarily placed value -# from http://genome.cshlp.org/content/13/1/81.full -# Availability -# Phusion is undergoing a rewrite of the code to make this a portable package. It will be made available free of charge to academic sites, but requires licensing for commercial use. For more information please contact the authors. -SLOT="0" -KEYWORDS="~amd64" - -DEPEND="app-shells/tcsh - sys-cluster/openmpi" -RDEPEND="${DEPEND} - sci-biology/phrap - dev-lang/perl" - -# contains bundled ssaha -# file collision with sci-biology/shrimp on /usr/bin/fasta2fastq - -S="${WORKDIR}" - -src_prepare(){ - default - rm -f phusion2 *.o - sed -e 's/^CFLAGS =/# CFLAGS =/' -i Makefile || die -} - -src_install(){ - dobin ctgreads.pl phusion2 - dodoc how_to_make_mates -} diff --git a/sci-biology/polyphen/Manifest b/sci-biology/polyphen/Manifest deleted file mode 100644 index 6b1d95704..000000000 --- a/sci-biology/polyphen/Manifest +++ /dev/null @@ -1,3 +0,0 @@ -DIST mafft-7.221-without-extensions-src.tgz 376075 BLAKE2B effe24080d453bad8ff4cd424e8ea592e64e254233cbaa245cc71edbeba293edb24d039f9bde3f54c000a1b1f5d966317020a546d8fc78f63494066b207624a9 SHA512 f5a79621a784ef8b054e93be70aa0ada8a366951349b4e4f9e6a42c287502ba60ec0722c199da2874098c6b5c6b9449dfb5071914770a8364007b779a6a601a2 -DIST polyphen-2.2.2r405d.tar.gz 2205380 BLAKE2B 5cb863b8b1626bfa2da264bfebfe5fea3932d13eac5f74fd76932c310fa20cbdd33905d8faa7bb82739d3d0b2bdbaea94c1470a4f28c8df1fd5accee23faef26 SHA512 e2418b0e18aeb1ebeaa31a743901e89b8b5cd670357ed8d78d7d22f414b8f5e98e80124bbea9d7ebf2fdc7a6ef33f050b67683740c1e4a4d01ac7a75d33dbaac -DIST weka-3-6-12.zip 24335916 BLAKE2B fe9b9406fce1f8ad5b4338e7cf18d8a6cf1fbc19e335f5fd66197c1aa45fdaf25859a191a0d99d32e06e6f84a6d9f900817a9d574fe447a2be1a818855787f10 SHA512 4301e1c2a751e26ff8d860e24e54e71511276f8cb90020c935595aaaab547f8614381ca8087b83a670d13ef0ff3fa13084f4984b9249e16042703ef9f43c0bd1 diff --git a/sci-biology/polyphen/metadata.xml b/sci-biology/polyphen/metadata.xml deleted file mode 100644 index 138cb7705..000000000 --- a/sci-biology/polyphen/metadata.xml +++ /dev/null @@ -1,12 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-biology/polyphen/polyphen-2.2.2.ebuild b/sci-biology/polyphen/polyphen-2.2.2.ebuild deleted file mode 100644 index 3100c6bbd..000000000 --- a/sci-biology/polyphen/polyphen-2.2.2.ebuild +++ /dev/null @@ -1,56 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -DESCRIPTION="Predict effect of aminoacid substitution on human protein function" -HOMEPAGE="http://genetics.bwh.harvard.edu/pph2/dokuwiki/start" -SRC_URI=" - http://genetics.bwh.harvard.edu/pph2/dokuwiki/_media/polyphen-${PV}r405d.tar.gz - http://mafft.cbrc.jp/alignment/software/mafft-7.221-without-extensions-src.tgz - http://prdownloads.sourceforge.net/weka/weka-3-6-12.zip -" - -LICENSE="polyphen" # for non-commercial use only -SLOT="0" -KEYWORDS="~amd64" - -DEPEND=" - dev-perl/CGI - sci-biology/ncbi-blast+ -" -RDEPEND="${DEPEND}" -BDEPEND="app-arch/unzip" - -# 3.7GB -# ftp://genetics.bwh.harvard.edu/pph2/bundled/polyphen-2.2.2-databases-2011_12.tar.bz2 - -# 2.4GB -# ftp://genetics.bwh.harvard.edu/pph2/bundled/polyphen-2.2.2-alignments-mlc-2011_12.tar.bz2 - -# 895MB -# ftp://genetics.bwh.harvard.edu/pph2/bundled/polyphen-2.2.2-alignments-multiz-2009_10.tar.bz2 - -src_unpack() { - unpack "polyphen-${PV}r405d.tar.gz" - cp "${DISTDIR}/mafft-7.221-without-extensions-src.tgz" "${S}/src" || die - cp "${DISTDIR}/weka-3-6-12.zip" "${S}/src" || die -} - -src_configure() { - # non-standard configure script - ./configure -} - -src_compile() { - pushd src - emake -j1 - popd -} - -src_install() { - pushd src - default - popd - einstalldocs -} diff --git a/sci-biology/primerD/Manifest b/sci-biology/primerD/Manifest deleted file mode 100644 index 063af78cf..000000000 --- a/sci-biology/primerD/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST primerD.tar.gz 58132 BLAKE2B 4fdf1126649ba3bddb92852dacd14a4e4bf652715166f7c6d9ba23aa3ebe8ab7419cf939131e6bde09190c65e5ed04222172757ff642d7af9eb34bfadd9875eb SHA512 9f70ccb2a8304fe9e3a3885f2607969ca00483c1f3bb70ea3b5da709db0c43979cdd6bbf2b9ef805c13d215000afab2053fdeda66dc48006cb50f536886b86b2 diff --git a/sci-biology/primerD/metadata.xml b/sci-biology/primerD/metadata.xml deleted file mode 100644 index 138cb7705..000000000 --- a/sci-biology/primerD/metadata.xml +++ /dev/null @@ -1,12 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-biology/primerD/primerD-1.0.0.ebuild b/sci-biology/primerD/primerD-1.0.0.ebuild deleted file mode 100644 index 6d46832a9..000000000 --- a/sci-biology/primerD/primerD-1.0.0.ebuild +++ /dev/null @@ -1,42 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit toolchain-funcs - -DESCRIPTION="Design degenerate primers" -HOMEPAGE="https://mblab.wustl.edu/software.html" -SRC_URI="primerD.tar.gz" -#SRC_URI="https://mblab.wustl.edu/software/download/primerD.tar.gz -> primerD-1.0.tar.gz" -# ERROR: cannot verify mblab.wustl.edu's certificate, issued by ‘CN=InCommon RSA Server CA,OU=InCommon,O=Internet2,L=Ann Arbor,ST=MI,C=US’: -# Unable to locally verify the issuer's authority. -# To connect to mblab.wustl.edu insecurely, use `--no-check-certificate'. -RESTRICT="fetch" - -LICENSE="LGPL-2.1" -SLOT="0" -# make: *** No rule to make target '/usr/include/linux/new.h', needed by 'Main.o'. Stop. -KEYWORDS="" - -S="${WORKDIR}"/primerD - -src_prepare(){ - default - sed -i -e "s:CC=g++:CC=$(tc-getCXX):; s:-Wall -g:${CFLAGS}:" \ - -e "s:/usr/include/g++-3/stl_algobase.h:/usr/lib/gcc/${CHOST}/$(gcc-fullversion)/include/g++-v$(gcc-major-version )/bits/stl_algobase.h:g" \ - -e "s:/usr/include/g++-3/stl_relops.h:/usr/lib/gcc/${CHOST}/$(gcc-fullversion)/include/g++-v$(gcc-major-version )/bits/stl_relops.h:g" \ - -e "s:/usr/include/g++-3/stl_pair.h:/usr/lib/gcc/${CHOST}/$(gcc-fullversion)/include/g++-v$(gcc-major-version )/bits/stl_pair.h:g" \ - -e "s:/usr/include/g++-3/type_traits.h:/usr/lib/gcc/${CHOST}/$(gcc-fullversion)/include/g++-v$(gcc-major-version )/ext/type_traits.h:g" \ - -e "s:/usr/include/g++-3/stl_config.h:/usr/lib/gcc/${CHOST}/$(gcc-fullversion)/include/g++-v$(gcc-major-version )/pstl/pstl_config.h:g" \ - -e "s:/usr/include/g++-3/:/usr/lib/gcc/${CHOST}/$(gcc-fullversion)/include/g++-v$(gcc-major-version )/:g" \ - -e "s:/usr/include/_G_config.h:/usr/include/stdio.h:g" \ - -e "s:/usr/lib/gcc-lib/i386-redhat-linux/2.96/include/:/usr/include/linux/:g" \ - Makefile || die - -} - -src_install(){ - dodoc README - dobin primerD -} diff --git a/sci-biology/prokka/Manifest b/sci-biology/prokka/Manifest deleted file mode 100644 index e0285e5de..000000000 --- a/sci-biology/prokka/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST prokka-1.14.6.tar.gz 112621657 BLAKE2B 3188d0a9dc6c62fa375a007950eaf91a7ff3fe6d610e89daaa8f8f911dd0035ac976cd3a2f4a14719b5c5e7d9a5bf7fdae64f838d5c54101ca8818cb2d0fd2c0 SHA512 96cc7490072d68242d4444c0842af7618f7ac132d00b008b8c4c1056d45a1f6f25c0599e7b74cd0477794bd88d88897cf57276d29c979ff1104f79f5bbf7c447 diff --git a/sci-biology/prokka/metadata.xml b/sci-biology/prokka/metadata.xml deleted file mode 100644 index 138cb7705..000000000 --- a/sci-biology/prokka/metadata.xml +++ /dev/null @@ -1,12 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-biology/prokka/prokka-1.14.6.ebuild b/sci-biology/prokka/prokka-1.14.6.ebuild deleted file mode 100644 index b56fd143f..000000000 --- a/sci-biology/prokka/prokka-1.14.6.ebuild +++ /dev/null @@ -1,36 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -DESCRIPTION="Prokaryotic whole genome annotation pipeline" -HOMEPAGE="https://vicbioinformatics.com/software.prokka.shtml" -SRC_URI="https://github.com/tseemann/prokka/archive/v${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="~amd64" - -RDEPEND=" - sys-process/parallel - sci-biology/bioperl - sci-biology/prodigal - || ( sci-biology/ncbi-tools++ sci-biology/ncbi-blast+ ) - sci-biology/hmmer:* - sci-biology/infernal - sci-biology/exonerate - sci-biology/barrnap" -DEPEND="${RDEPEND}" -# sci-biology/minced -# >=sci-biolohy/hmmer-3.1 -# Aragorn -# >=RNAmmer-1.2 -# >=HMMmmer-2.0 (that is not sci-biology/hmmer) -# SignalP >= 3.0 -# sequin -# tbl2asn >= 23.0 from wget --mirror -nH -nd ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/by_program/tbl2asn/linux64.tbl2asn.gz - -src_install() { - default - dobin bin/prokka -} diff --git a/sci-biology/proovread/Manifest b/sci-biology/proovread/Manifest deleted file mode 100644 index e6f75545a..000000000 --- a/sci-biology/proovread/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST proovread-2.14.1.tar.gz 21965507 BLAKE2B 5f9f3e6ae7f5b95a2cd9092f8ab8b53b70ac48733fe5f816fddd9b2e0957c3a8fe0bad74d317f780a628127e8a6674b238f9df9fb7908e705ff92ca7e21a8a4f SHA512 836c1da96fc90c24729d8e72610e48e6ccae5a9fc2d6fa94c32738537bbc95584c9d46b37659bbcf56cdc3c1412ca93b04c7c0a54a28a6e8cebeccd278a6f764 diff --git a/sci-biology/proovread/metadata.xml b/sci-biology/proovread/metadata.xml deleted file mode 100644 index 138cb7705..000000000 --- a/sci-biology/proovread/metadata.xml +++ /dev/null @@ -1,12 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-biology/proovread/proovread-2.14.1.ebuild b/sci-biology/proovread/proovread-2.14.1.ebuild deleted file mode 100644 index be1d610b0..000000000 --- a/sci-biology/proovread/proovread-2.14.1.ebuild +++ /dev/null @@ -1,51 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit perl-functions - -DESCRIPTION="Error correct PacBio subreads using Illumina reads" -HOMEPAGE="https://github.com/BioInf-Wuerzburg/proovread" -if [ "$PV" == "9999" ]; then - inherit git-r3 - EGIT_REPO_URI="https://github.com/BioInf-Wuerzburg/proovread" -else - SRC_URI="https://github.com/BioInf-Wuerzburg/${PN}/releases/download/${P}/${P}.tar.gz" - KEYWORDS="~amd64 ~x86" -fi - -LICENSE="Artistic-2 GPL-3 blasr" -SLOT="0" - -# TODO: package shrimp and update blasr -# blasr requires new dep libblasr, which -# I cannot get to compile successfully -RDEPEND=" - >=dev-lang/perl-5.10 - dev-perl/Log-Log4perl - dev-perl/File-Which - >=sci-biology/ncbi-tools++-2.2.24 - >=sci-biology/samtools-1.1 -" -DEPEND="${RDEPEND}" - -src_install(){ - cd bin || die - dobin ChimeraToSeqFilter.pl dazz2sam ccseq bam2cns test_cfg.pl siamaera samfilter sam2cns proovread-flex proovread - cd ../util/bwa || die - dobin bwa-proovread # xa2multi.pl qualfa2fq.pl libbwa.a bwa.1 - cd ../../util/SeqFilter || die - dobin bin/SeqFilter - cd ../../util/SeqChunker || die - dobin bin/* - cd ../../lib || die - perl_domodule -r -C ${PN} * - cd ../util/blasr-1.3.1 || die - dobin blasr -} - -pkg_postinst(){ - einfo "Proovread uses its own, modified version of bwa as bwa-proovread" - einfo "with linked in libbwa.a. It also bundles shrimp2 and blasr" -} diff --git a/sci-biology/proovread/proovread-9999.ebuild b/sci-biology/proovread/proovread-9999.ebuild deleted file mode 100644 index be1d610b0..000000000 --- a/sci-biology/proovread/proovread-9999.ebuild +++ /dev/null @@ -1,51 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit perl-functions - -DESCRIPTION="Error correct PacBio subreads using Illumina reads" -HOMEPAGE="https://github.com/BioInf-Wuerzburg/proovread" -if [ "$PV" == "9999" ]; then - inherit git-r3 - EGIT_REPO_URI="https://github.com/BioInf-Wuerzburg/proovread" -else - SRC_URI="https://github.com/BioInf-Wuerzburg/${PN}/releases/download/${P}/${P}.tar.gz" - KEYWORDS="~amd64 ~x86" -fi - -LICENSE="Artistic-2 GPL-3 blasr" -SLOT="0" - -# TODO: package shrimp and update blasr -# blasr requires new dep libblasr, which -# I cannot get to compile successfully -RDEPEND=" - >=dev-lang/perl-5.10 - dev-perl/Log-Log4perl - dev-perl/File-Which - >=sci-biology/ncbi-tools++-2.2.24 - >=sci-biology/samtools-1.1 -" -DEPEND="${RDEPEND}" - -src_install(){ - cd bin || die - dobin ChimeraToSeqFilter.pl dazz2sam ccseq bam2cns test_cfg.pl siamaera samfilter sam2cns proovread-flex proovread - cd ../util/bwa || die - dobin bwa-proovread # xa2multi.pl qualfa2fq.pl libbwa.a bwa.1 - cd ../../util/SeqFilter || die - dobin bin/SeqFilter - cd ../../util/SeqChunker || die - dobin bin/* - cd ../../lib || die - perl_domodule -r -C ${PN} * - cd ../util/blasr-1.3.1 || die - dobin blasr -} - -pkg_postinst(){ - einfo "Proovread uses its own, modified version of bwa as bwa-proovread" - einfo "with linked in libbwa.a. It also bundles shrimp2 and blasr" -} diff --git a/sci-biology/pufferfish/Manifest b/sci-biology/pufferfish/Manifest deleted file mode 100644 index 4ca8429dc..000000000 --- a/sci-biology/pufferfish/Manifest +++ /dev/null @@ -1,4 +0,0 @@ -DIST htslib-pufferfish-1.4.0.tar.gz 1262620 BLAKE2B 7fff233fadd4737e416058a24d9dc916e5ecf1fa10c456cfb15001df7c664daedecdbcef49469dffb6516c47e00937cbe399a68032fcf18ab9070768d40d3091 SHA512 52ae9099ddadb1d0136f1a62825ff0539baf754302c735ea81b8748a1c349107766b2022cc59814728d366b6df2c9f1b93edf926c1a6a7af78a4f40c4e821c4c -DIST pufferfish-1.4.0.tar.gz 3099274 BLAKE2B 65c26b02513840b3f7b6f381af674b59a21960fe56559b8d87dd22051fa02e7e5c06ab1ba1b9f81516f9831ea1b79492a9cc0e2d0b9258d9c21ddfb7ea162d69 SHA512 683bad5a5e3512c56c211af1270ea1e627d2483d601d20ef70f92087b37327463b36224eda38699231f8daa8c318d745757eed2a4190351ebb8b4a252fca6474 -DIST seqlib-pufferfish-1.4.0.tar.gz 315441 BLAKE2B b402f94837aeb43e4d443044c65d1c193ce7b24a8507b9a79da6cbfc5d7093d286ccd8573eca64c78bd3c65830dc11a18ec26dc619e7ab95d04a472c15ec70d7 SHA512 b3efa0511df9c39ed8021c1bf316f88fb6b51ebd745b7f799bc92edebf31ff7dbd466b83ba30a3381e411d36455f4074163267d4331c5fe16f2934762865d22f -DIST setcover-pufferfish-1.4.0.tar.gz 33911 BLAKE2B 690cfca7e271490ef8b7119fe9fb7df3e7c06897eab52346b485c22a8a7b8e75d344a07f24dbf44aa68919793f942c8f5d1bd1932d2ce1a21a18631e3e64aecf SHA512 8954b38a183f81fff36663c6cbbef25fbf003045d93462933d09f0384f6e17fa726d48e9d94daa5195052e6ff9650aba4a2c8a6f0691f50c360462f02760e2a1 diff --git a/sci-biology/pufferfish/files/pufferfish-do-not-fetch.patch b/sci-biology/pufferfish/files/pufferfish-do-not-fetch.patch deleted file mode 100644 index c86fe847f..000000000 --- a/sci-biology/pufferfish/files/pufferfish-do-not-fetch.patch +++ /dev/null @@ -1,31 +0,0 @@ -diff --git a/CMakeLists.txt b/CMakeLists.txt -index 7f1516a..90f7cdd 100644 ---- a/CMakeLists.txt -+++ b/CMakeLists.txt -@@ -282,12 +282,9 @@ message("TBB_LIBRARIES = ${TBB_LIBRARIES}") - - - ExternalProject_Add(libseqlib --GIT_REPOSITORY https://github.com/COMBINE-lab/SeqLib.git --GIT_TAG master - UPDATE_COMMAND "" - UPDATE_DISCONNECTED 1 - BUILD_IN_SOURCE TRUE --DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/seqlib - SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/seqlib - INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install - CONFIGURE_COMMAND ./configure -@@ -300,13 +297,10 @@ INSTALL_COMMAND mkdir -p <INSTALL_DIR>/lib && mkdir -p <INSTALL_DIR>/include & - ) - - ExternalProject_Add(libSetCover -- GIT_REPOSITORY https://github.com/martin-steinegger/setcover.git -- GIT_TAG master - UPDATE_COMMAND "" - CONFIGURE_COMMAND "" - UPDATE_DISCONNECTED 1 - BUILD_IN_SOURCE TRUE -- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/setcover - SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/setcover - INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install - BUILD_COMMAND make -j8 diff --git a/sci-biology/pufferfish/metadata.xml b/sci-biology/pufferfish/metadata.xml deleted file mode 100644 index 7b582e896..000000000 --- a/sci-biology/pufferfish/metadata.xml +++ /dev/null @@ -1,11 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="github">COMBINE-lab/pufferfish</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-biology/pufferfish/pufferfish-1.4.0.ebuild b/sci-biology/pufferfish/pufferfish-1.4.0.ebuild deleted file mode 100644 index 588970e06..000000000 --- a/sci-biology/pufferfish/pufferfish-1.4.0.ebuild +++ /dev/null @@ -1,35 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit cmake - -SC_COMMIT="b1de7919c0a4d0e65c5cd0b6d78963516e44be25" -SL_COMMIT="340dad36dff67ca96815bd412fe65587d4d64479" -HL_COMMIT="be22a2a1082f6e570718439b9ace2db17a609eae" - -DESCRIPTION="Index for the colored, compacted, de Bruijn graph" -HOMEPAGE="https://github.com/COMBINE-lab/pufferfish" -SRC_URI="https://github.com/COMBINE-lab/pufferfish/archive/salmon-v${PV}.tar.gz -> ${P}.tar.gz - https://github.com/martin-steinegger/setcover/archive/${SC_COMMIT}.tar.gz -> setcover-${P}.tar.gz - https://github.com/COMBINE-lab/SeqLib/archive/${SL_COMMIT}.tar.gz -> seqlib-${P}.tar.gz - https://github.com/samtools/htslib/archive/${HL_COMMIT}.tar.gz -> htslib-${P}.tar.gz" - -LICENSE="GPL-3" -SLOT="0" -KEYWORDS="" - -DEPEND="dev-cpp/tbb" - -S="${WORKDIR}/${PN}-salmon-v${PV}" - -PATCHES=( "${FILESDIR}/${PN}-do-not-fetch.patch" ) - -src_prepare() { - mkdir -p external/{setcover,seqlib} - mv "../setcover-${SC_COMMIT}"/* external/setcover || die - mv "../SeqLib-${SL_COMMIT}"/* external/seqlib || die - mv "../htslib-${HL_COMMIT}"/* external/seqlib/htslib || die - cmake_src_prepare -} diff --git a/sci-biology/pybedtools/Manifest b/sci-biology/pybedtools/Manifest index 8cfd1985e..a952ac4b8 100644 --- a/sci-biology/pybedtools/Manifest +++ b/sci-biology/pybedtools/Manifest @@ -1 +1,2 @@ DIST pybedtools-0.8.2.tar.gz 12496355 BLAKE2B f1ff67f524a5a51a6f6a5450bb72ecd6602fe41232c77a38838b9b4051c528abadaa65d561bbef69cb595624a7f2edee8b98927ca0e7a55d5352e56e17f81d64 SHA512 4534c0ff4eeebbe8e3b1f126563700e4ba2b212581a76106d89fa8c61e043974b76649bf68d0b78f45923d66eb63c44bc69994de1f5a42e5069a761a93b8acbe +DIST pybedtools-0.9.0.tar.gz 12497249 BLAKE2B f43c94a7dae773b2ca46c0105d4de57f4e93a095f168b67771a568b64bc088b517e160da27ef68d81fea3df75689cad1a3db2b25dda36a37ed688e4e426fe43a SHA512 aa0cca035d560bd4e4d39f6eac74e677e3bac3266af5b69ceca1c4878742220d576d0db9ebf9c8da490d24259b1153e9999a78d2a5c46f1acb544fa3dba73a18 diff --git a/sci-biology/pybedtools/pybedtools-0.8.2.ebuild b/sci-biology/pybedtools/pybedtools-0.8.2.ebuild index 95bee9be2..bc02bda6f 100644 --- a/sci-biology/pybedtools/pybedtools-0.8.2.ebuild +++ b/sci-biology/pybedtools/pybedtools-0.8.2.ebuild @@ -1,9 +1,10 @@ -# Copyright 1999-2022 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools inherit distutils-r1 @@ -15,9 +16,6 @@ LICENSE="MIT" SLOT="0" KEYWORDS="~amd64 ~x86" -# ModuleNotFoundError: No module named 'pybedtools.cbedtools' -RESTRICT="test" - RDEPEND=" sci-biology/bedtools sci-biology/pysam[${PYTHON_USEDEP}] @@ -34,3 +32,12 @@ BDEPEND="dev-python/cython[${PYTHON_USEDEP}]" # even if pybedtools is installed #distutils_enable_sphinx docs/source distutils_enable_tests pytest + +python_test() { + # Requires network + local EPYTEST_DESELECT=( + test/test_helpers.py::test_chromsizes + ) + cd "${T}" || die + epytest --pyargs pybedtools +} diff --git a/sci-biology/pybedtools/pybedtools-0.9.0.ebuild b/sci-biology/pybedtools/pybedtools-0.9.0.ebuild new file mode 100644 index 000000000..bc02bda6f --- /dev/null +++ b/sci-biology/pybedtools/pybedtools-0.9.0.ebuild @@ -0,0 +1,43 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools + +inherit distutils-r1 + +DESCRIPTION="Use BED and GFF files from python using BEDtools" +HOMEPAGE="https://daler.github.io/pybedtools" +SRC_URI="https://github.com/daler/pybedtools/archive/v${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +RDEPEND=" + sci-biology/bedtools + sci-biology/pysam[${PYTHON_USEDEP}] + dev-python/six[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/pandas[${PYTHON_USEDEP}] + dev-python/matplotlib[${PYTHON_USEDEP}] +" + +BDEPEND="dev-python/cython[${PYTHON_USEDEP}]" + +# TODO: fix docs building +# ModuleNotFoundError: No module named 'pybedtools.cbedtools' +# even if pybedtools is installed +#distutils_enable_sphinx docs/source +distutils_enable_tests pytest + +python_test() { + # Requires network + local EPYTEST_DESELECT=( + test/test_helpers.py::test_chromsizes + ) + cd "${T}" || die + epytest --pyargs pybedtools +} diff --git a/sci-biology/pyfaidx/Manifest b/sci-biology/pyfaidx/Manifest index 7ce654125..0bb3b35f4 100644 --- a/sci-biology/pyfaidx/Manifest +++ b/sci-biology/pyfaidx/Manifest @@ -1 +1,2 @@ DIST pyfaidx-0.5.9.2.tar.gz 93438 BLAKE2B 3d3d225907f8bd04fdf4b20d608d02cd0e5a723f2a73df24b732992f139102e2a9042c37c5a73f762256fd007dd7e14bace910c0961e60870926c2ce1dca3ac3 SHA512 57b94421d6858fa2bd7b867b386d47d53d3afd75878b08e6e32fb7d8f4942f2a051e0123e6c4b4395abe656d639fa4f47afadbd8c4b2cbc001c5113cbbf96af4 +DIST pyfaidx-0.7.2.1.tar.gz 102951 BLAKE2B d8c76bb9f817a7f4a0f3aa58ef20344c1d5aa5e99a181f1171145264baab4603d772d7c37f8286654442ee0f6bf3b62f8d94d6e0495a65f54495e084403c0b92 SHA512 20833c2e11f942aa69b524170a0203ca4d035d058d1d8029c2fab50c4b60a4e947cbbdc0dc954e4ecdefbf07d095f861a86dbebdfdac4bdbecf65a691226e25c diff --git a/sci-biology/pyfaidx/metadata.xml b/sci-biology/pyfaidx/metadata.xml index fd0f24633..47cc39d79 100644 --- a/sci-biology/pyfaidx/metadata.xml +++ b/sci-biology/pyfaidx/metadata.xml @@ -11,5 +11,6 @@ </maintainer> <upstream> <remote-id type="pypi">pyfaidx</remote-id> + <remote-id type="github">mdshw5/pyfaidx</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/pyfaidx/pyfaidx-0.5.9.2.ebuild b/sci-biology/pyfaidx/pyfaidx-0.5.9.2.ebuild index be1990514..bec223f6c 100644 --- a/sci-biology/pyfaidx/pyfaidx-0.5.9.2.ebuild +++ b/sci-biology/pyfaidx/pyfaidx-0.5.9.2.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2020 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 -PYTHON_COMPAT=( python3_{7..9} ) +PYTHON_COMPAT=( python3_{10..11} ) DISTUTILS_USE_SETUPTOOLS=rdepend inherit distutils-r1 @@ -19,4 +19,4 @@ IUSE="" REPEND="dev-python/six[${PYTHON_USEDEP}]" -distutils_enable_tests nose +#distutils_enable_tests nose diff --git a/sci-biology/pyfaidx/pyfaidx-0.7.2.1.ebuild b/sci-biology/pyfaidx/pyfaidx-0.7.2.1.ebuild new file mode 100644 index 000000000..14f557869 --- /dev/null +++ b/sci-biology/pyfaidx/pyfaidx-0.7.2.1.ebuild @@ -0,0 +1,24 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools + +inherit distutils-r1 pypi + +DESCRIPTION="Efficient pythonic random access to fasta subsequences" +HOMEPAGE="https://pypi.python.org/pypi/pyfaidx https://github.com/mdshw5/pyfaidx" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" +# Test issues reported upstream: +# https://github.com/mdshw5/pyfaidx/issues/208 +RESTRICT="test" + +REPEND="dev-python/six[${PYTHON_USEDEP}]" + +distutils_enable_tests pytest diff --git a/sci-biology/pysamstats/Manifest b/sci-biology/pysamstats/Manifest deleted file mode 100644 index fb8a27ec1..000000000 --- a/sci-biology/pysamstats/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST pysamstats-1.1.2.tar.gz 251400 BLAKE2B 770a34d6f2c983aba78924dac2c42e26dd52113a2abd11dc6b7b416fc6c612104e263d3a62f869534f4ef2e06c4ce4c387d60575f7fb63c8f885f5ac05f9acde SHA512 d294aac0b8ed7144218d24209978e345bf89ba67c9786155c1826dd37c48fd820cda6467530d6b717ab4b84c6988fb65bec2ee679746c5782413babc45e600ef diff --git a/sci-biology/pysamstats/metadata.xml b/sci-biology/pysamstats/metadata.xml deleted file mode 100644 index cc923c1df..000000000 --- a/sci-biology/pysamstats/metadata.xml +++ /dev/null @@ -1,16 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="github">alimanfoo/pysamstats</remote-id> - <remote-id type="pypi">pysamstats</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-biology/pysamstats/pysamstats-1.1.2.ebuild b/sci-biology/pysamstats/pysamstats-1.1.2.ebuild deleted file mode 100644 index 445ec2162..000000000 --- a/sci-biology/pysamstats/pysamstats-1.1.2.ebuild +++ /dev/null @@ -1,30 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7,8,9} ) - -inherit distutils-r1 - -DESCRIPTION="Calculate stats against genome positions from SAM/BAM/CRAM file" -HOMEPAGE="https://github.com/alimanfoo/pysamstats - https://pypi.python.org/pypi/pysamstats" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -# TODO: fix this -# ModuleNotFoundError: No module named 'pysamstats.opt' -# happens even with the --install option -RESTRICT="test" - -BDEPEND="dev-python/cython[${PYTHON_USEDEP}]" -RDEPEND=" - dev-python/numpy[${PYTHON_USEDEP}] - sci-biology/pysam[${PYTHON_USEDEP}] -" - -distutils_enable_tests pytest diff --git a/sci-biology/quast/Manifest b/sci-biology/quast/Manifest deleted file mode 100644 index 200704ee2..000000000 --- a/sci-biology/quast/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST quast-5.0.2.tar.gz 34210765 BLAKE2B 6443e05586019bfe9b29feb2210194de69c7161fae4cbdadb7f16c72d03c3dbfd7f92c359b7d706786ae8fa42e0f59fc2263c5702f78a6b7b89ab6dbfafdc721 SHA512 eeb6f16435a1c8d1ed4c782b19b17557631d3cd129a4948da9355f71221ec1f6d12abe716557a239f736f94c36f1ced8922e5f8fec0b9bec5b447f8a354cda2b diff --git a/sci-biology/quast/metadata.xml b/sci-biology/quast/metadata.xml deleted file mode 100644 index c821b722e..000000000 --- a/sci-biology/quast/metadata.xml +++ /dev/null @@ -1,15 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="sourceforge">quast</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-biology/quast/quast-5.0.2.ebuild b/sci-biology/quast/quast-5.0.2.ebuild deleted file mode 100644 index eb49a803b..000000000 --- a/sci-biology/quast/quast-5.0.2.ebuild +++ /dev/null @@ -1,23 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7,8,9} ) - -inherit distutils-r1 - -DESCRIPTION="Compare quality of multiple genome assemblies to each other" -HOMEPAGE="http://bioinf.spbau.ru/QUAST" # no https -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -RDEPEND=" - dev-python/joblib[${PYTHON_USEDEP}] - dev-python/simplejson[${PYTHON_USEDEP}] -" - -distutils_enable_tests --install setup.py diff --git a/sci-biology/quicktree/metadata.xml b/sci-biology/quicktree/metadata.xml index 8417d1580..e3ce321ed 100644 --- a/sci-biology/quicktree/metadata.xml +++ b/sci-biology/quicktree/metadata.xml @@ -5,4 +5,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">khowe/quicktree</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/rat-brain-templates/metadata.xml b/sci-biology/rat-brain-templates/metadata.xml index ac271f806..5dacf4476 100644 --- a/sci-biology/rat-brain-templates/metadata.xml +++ b/sci-biology/rat-brain-templates/metadata.xml @@ -14,4 +14,7 @@ format oriented in the standard RAS space, with origin at bregma for use in magnetic resonance rat brain imaging. </longdescription> + <upstream> + <remote-id type="gitlab">FOS-FMI/rat-brain-templates_generator</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/rat-brain-templates/rat-brain-templates-0.2.ebuild b/sci-biology/rat-brain-templates/rat-brain-templates-0.2.ebuild index 20c923eb0..cab3dec4f 100644 --- a/sci-biology/rat-brain-templates/rat-brain-templates-0.2.ebuild +++ b/sci-biology/rat-brain-templates/rat-brain-templates-0.2.ebuild @@ -7,7 +7,7 @@ inherit check-reqs DESCRIPTION="A collection of rat brain templates in NIfTI format" HOMEPAGE="https://gitlab.com/FOS-FMI/rat-brain-templates_generator" -SRC_URI="http://chymera.eu/distfiles/${P}.tar.xz" +SRC_URI="https://resources.chymera.eu/distfiles/${P}.tar.xz" LICENSE="fairuse" SLOT="0" diff --git a/sci-biology/roche454ace2caf/Manifest b/sci-biology/roche454ace2caf/Manifest deleted file mode 100644 index 6711cecd3..000000000 --- a/sci-biology/roche454ace2caf/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST roche454ace2gap-2010-12-08.tgz 261317 BLAKE2B e00ba3b1d19c9856447c74d3943854e2c6556c14ef19a1abe73a6e0375b8e889c57b4c00beda2f9f9adf6cb76f6f89a12bfe9c9782b5668c0f883e914fa68204 SHA512 ce477ab88c45e947764d0dcb667f76de195db8f1ebc53ca6892f74017a79e231f77c458564a9ac682679bb6b486493ee6692157628401351de5a732894e5a732 diff --git a/sci-biology/roche454ace2caf/metadata.xml b/sci-biology/roche454ace2caf/metadata.xml deleted file mode 100644 index 138cb7705..000000000 --- a/sci-biology/roche454ace2caf/metadata.xml +++ /dev/null @@ -1,12 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-biology/roche454ace2caf/roche454ace2caf-20100812.ebuild b/sci-biology/roche454ace2caf/roche454ace2caf-20100812.ebuild deleted file mode 100644 index a3c4eee39..000000000 --- a/sci-biology/roche454ace2caf/roche454ace2caf-20100812.ebuild +++ /dev/null @@ -1,28 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -DESCRIPTION="ace to gap4 converter" -HOMEPAGE="https://genome.imb-jena.de/software/roche454ace2caf/" -SRC_URI="https://genome.imb-jena.de/software/roche454ace2caf/download/src/roche454ace2gap-2010-12-08.tgz" - -LICENSE="FLI-Jena" -SLOT="0" -KEYWORDS="~amd64" - -DEPEND="" -RDEPEND="${DEPEND} - sci-biology/align_to_scf - sci-biology/sff_dump - sci-biology/caftools - sci-biology/staden - dev-lang/perl - app-shells/ksh" - -S="${WORKDIR}/roche2gap" - -src_install(){ - dobin bin/*.pl bin/roche454ace2gap - einstalldocs -} diff --git a/sci-biology/roiextractors/Manifest b/sci-biology/roiextractors/Manifest new file mode 100644 index 000000000..4db78b7b8 --- /dev/null +++ b/sci-biology/roiextractors/Manifest @@ -0,0 +1 @@ +DIST roiextractors-0.5.1.gh.tar.gz 288765 BLAKE2B 5e1b1931f3da8c1157fc2668c203e3ea9812b94246b85e97848d25ff880b1b6d9433637b9847a28dc53c9d88746d1eaa472c7beffd2593d461a24f98eaddd997 SHA512 6f02decfca12f45c8e18ad9ee07931a5891a2099b046e56a7c415d179d93bc6b9a47a320e4ce500217b1f02abdbbdb59c7e85b4f0a773cbd44ba983f5b7595d6 diff --git a/sci-biology/roiextractors/metadata.xml b/sci-biology/roiextractors/metadata.xml new file mode 100644 index 000000000..000a44418 --- /dev/null +++ b/sci-biology/roiextractors/metadata.xml @@ -0,0 +1,16 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>gentoo@chymera.eu</email> + <name>Horea Christian</name> + </maintainer> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <upstream> + <remote-id type="github">catalystneuro/roiextractors</remote-id> + <remote-id type="pypi">roiextractors</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/roiextractors/roiextractors-0.5.1.ebuild b/sci-biology/roiextractors/roiextractors-0.5.1.ebuild new file mode 100644 index 000000000..1c2fba6ea --- /dev/null +++ b/sci-biology/roiextractors/roiextractors-0.5.1.ebuild @@ -0,0 +1,40 @@ +# Copyright 2021-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools +inherit distutils-r1 + +DESCRIPTION="Optical imaging data handling from several file formats" +HOMEPAGE="https://github.com/catalystneuro/roiextractors" +SRC_URI="https://github.com/catalystneuro/roiextractors/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64" +IUSE="" + +RDEPEND=" + dev-python/dill[${PYTHON_USEDEP}] + dev-python/h5py[${PYTHON_USEDEP}] + dev-python/lazy_ops[${PYTHON_USEDEP}] + dev-python/psutil[${PYTHON_USEDEP}] + dev-python/pynwb[${PYTHON_USEDEP}] + dev-python/pyyaml[${PYTHON_USEDEP}] + dev-python/scipy[${PYTHON_USEDEP}] + dev-python/tqdm[${PYTHON_USEDEP}] +" +BDEPEND=" + test? ( + dev-python/parameterized[${PYTHON_USEDEP}] + dev-python/spikeinterface[${PYTHON_USEDEP}] + ) +" + +distutils_enable_tests pytest + +python_test() { + epytest tests/test_internals +} diff --git a/sci-biology/rtg-tools/Manifest b/sci-biology/rtg-tools/Manifest deleted file mode 100644 index 4e0799efc..000000000 --- a/sci-biology/rtg-tools/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST rtg-tools-3.12.tar.gz 32484461 BLAKE2B 3fcee1db9ddcb0d04c34d1252fdf3564aeb255bff36501d0e0bdbe5f6c7d3564581b7fd8aacc90c1a818787c03c3da5478590402cda3cb691be90e816a7ee048 SHA512 2ab7c2a2203e48c74983e89a72b2cf0053e8810a7442931868489f71af6db5f22ca119a5924e7e03bc0f524e41bddff0b20ee8e3c811a21f9168a6b3d6b92d89 diff --git a/sci-biology/rtg-tools/metadata.xml b/sci-biology/rtg-tools/metadata.xml deleted file mode 100644 index 138cb7705..000000000 --- a/sci-biology/rtg-tools/metadata.xml +++ /dev/null @@ -1,12 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-biology/rtg-tools/rtg-tools-3.12.ebuild b/sci-biology/rtg-tools/rtg-tools-3.12.ebuild deleted file mode 100644 index a07f55539..000000000 --- a/sci-biology/rtg-tools/rtg-tools-3.12.ebuild +++ /dev/null @@ -1,63 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit java-pkg-2 java-ant-2 - -DESCRIPTION="Manipulate and analyze VCF files" -HOMEPAGE="https://github.com/RealTimeGenomics/rtg-tools" -SRC_URI="https://github.com/RealTimeGenomics/rtg-tools/archive/${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="BSD-2" -SLOT="0" -KEYWORDS="~amd64" - -DEPEND=" - >=virtual/jdk-1.8:* - >=dev-java/ant-core-1.9 - dev-java/jython" -RDEPEND="${DEPEND} - >=virtual/jre-1.8:*" - -src_compile(){ - ant zip-nojre || die -} - -# "${S}"/lib/sam-2.9.1.jar -# "${S}"/lib/findbugs-annotations.jar -# "${S}"/lib/findbugs-jsr305.jar -# "${S}"/lib/velocity-tools-generic.jar -# "${S}"/lib/RPlot.jar -# "${S}"/lib/commons-collections-3.2.1.jar -# "${S}"/lib/velocity-1.7.jar -# "${S}"/lib/commons-compress-1.4.1.jar -# "${S}"/lib/commons-lang-2.4.jar -# "${S}"/lib/jumble-annotations.jar -# "${S}"/lib/sam-2.9.1-src.jar -# "${S}"/lib/gzipfix.jar -# "${S}"/buildLib/ant-contrib-1.0b3.jar -# "${S}"/buildLib/handlechecker.jar -# "${S}"/testLib/hamcrest-core-1.3.jar -# "${S}"/testLib/junit.jar -# "${S}"/testLib/spelling.jar - -src_install(){ - dobin installer/rtg - insinto /usr/share/"${PN}" - doins build/rtg-tools.jar - doins lib/gzipfix.jar - dodoc installer/resources/tools/RTGOperationsManual.pdf - doins -r installer/resources/tools/RTGOperationsManual - dodoc installer/resources/tools/scripts/README.txt - dodoc installer/ReleaseNotes.txt - # TODO - # extract more files from the generated rtg-tools-3.11-39691f9f-base.zip - # file or better the installer/resources/ source directory - # - # install installer/resources/common/scripts/rtg-bash-completion -} - -src_test(){ - ant runalltests || die -} diff --git a/sci-biology/ruffus/Manifest b/sci-biology/ruffus/Manifest deleted file mode 100644 index 41e7eb0b2..000000000 --- a/sci-biology/ruffus/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST ruffus-2.8.4.tar.gz 12147217 BLAKE2B 742fdb060d9c7bad6ee9ce9c602c72d205f3442bb8d33b7b455198bca2c84cbc275098f17e103650b18f70ab624cd6f491f6138d6d3906e4697dd010bedc93c7 SHA512 5f38ad4ca5aca007e63b59be6117af85618bc27e8d98cc3b32add82ac48766c37b3fb2633a28c98941397ab3154553ba57509b321d2c80d01c753ac189f092e7 diff --git a/sci-biology/ruffus/metadata.xml b/sci-biology/ruffus/metadata.xml deleted file mode 100644 index 1a91c19c5..000000000 --- a/sci-biology/ruffus/metadata.xml +++ /dev/null @@ -1,15 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="pypi">ruffus</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-biology/ruffus/ruffus-2.8.4.ebuild b/sci-biology/ruffus/ruffus-2.8.4.ebuild deleted file mode 100644 index beda7db9a..000000000 --- a/sci-biology/ruffus/ruffus-2.8.4.ebuild +++ /dev/null @@ -1,26 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7,8,9} ) - -inherit distutils-r1 - -DESCRIPTION="Python module to support computational pipelines" -HOMEPAGE="http://www.ruffus.org.uk" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -# TODO: why does this not work: Duplicate pipeline -RESTRICT="test" - -RDEPEND=" - media-gfx/graphviz -" - -distutils_enable_sphinx doc dev-python/sphinx_rtd_theme -distutils_enable_tests pytest diff --git a/sci-biology/sailfish/Manifest b/sci-biology/sailfish/Manifest deleted file mode 100644 index 025cfe9ea..000000000 --- a/sci-biology/sailfish/Manifest +++ /dev/null @@ -1,5 +0,0 @@ -DIST jellyfish-2.2.5.tar.gz 1083486 BLAKE2B 545c110199cb2661656ddd558f5ee2b9715a78f6d33275f53aa5a9719247dff4421ef5dd37c3683a3423c8b79ff33395bf4e0ac86cade7480bc604a2b197e214 SHA512 7747030628f82562669c5021aeaca03d8dfc559dc9c3a407e2e4e8de633673f7cf9c60989c16f73deb8e88e7204a3fe84993209a2ebffcb34fd35eac7784e9ab -DIST quasi-mph.zip 414036 BLAKE2B 414ccd806fc11fdc949ecf107db079e4ab0dec8f443f4ba27df9c4273bc3e01f9d4e7c377651a930cf28c77198526a7ed52eb65419a9c29d6cf12a6ecf268b6c SHA512 65d420af549ce138e6d240438919cbfb76a6f137d2767ba45c099c9a946ca04686fedca609a5ebe4c9d371d2587379f35d9e5dd591abe1afc4b7d433bb4f61c9 -DIST sailfish-0.10.0.tar.gz 1621862 BLAKE2B d04d8db99e1d191ad1bea690bf43f31d23d6505bc3e80399cfafbbf4e1404edf8a4bbe0532e2c47ec59a5a26f50509342a7143bc0b0c41c3a8723ec0f6e53bd4 SHA512 ec66cff89dac037b84deaf997b7769802f594e69820d42915fb830bfcd527786c9c466a9476bdf2b29b9f7481e98905acf580f4a766765bccaa1b0ced22c4bb2 -DIST sparsehash-2.0.2.tar.gz 321951 BLAKE2B 057776f89fe3ca4b826eec7a142a18106561e4a20eaf907b3996f4dc52f484b84196c3bf9cf6d8bc31bd09aec34fc68b5992560c5fbe8c279c94d18062a96855 SHA512 e086b8beb45f2aa395b5ae49aed8ebaed1cafc9a59ece862f64f067098e2b9c28efc5cfac6b26eea46e5fe6b3db1bfa1afc0b9656c48adc01c3c3d05a5b327e8 -DIST v1.0.tar.gz 86404 BLAKE2B ce59ff034cbd70a504ed8c2e42e552489cc07a80a7130149234294aa2c75329f15ff5c4da4709a40712e18762e160355de67f4f68810856f8bc8218ceffb671d SHA512 ba4b395374da16f9ac22dd3cbf96ab5a67ab4d64a312f382ace883633199bbbd5f7602abe768ac84f6ddf2611eaf2db3d402893bd5dad135d598b4b9853ccd6b diff --git a/sci-biology/sailfish/files/sailfish-0.9.2-no-boost-static.patch b/sci-biology/sailfish/files/sailfish-0.9.2-no-boost-static.patch deleted file mode 100644 index 7ac3d0882..000000000 --- a/sci-biology/sailfish/files/sailfish-0.9.2-no-boost-static.patch +++ /dev/null @@ -1,20 +0,0 @@ -Do not force static and multithreaded boost libs, use what is available - -Patch by Michael Schubert - ---- a/CMakeLists.txt -+++ b/CMakeLists.txt -@@ -162,13 +162,6 @@ if ( DEFINED CUSTOM_BOOST_PATH ) - set (CMAKE_LIBRARY_PATH ${CUSTOM_BOOST_PATH}/lib ${CMAKE_LIBRARY_PATH}) - endif ( DEFINED CUSTOM_BOOST_PATH ) - --## --# We want static, multithreaded boost libraries --## --set (Boost_USE_STATIC_LIBS ON) --set (Boost_USE_MULTITHREADED ON) --#set (Boost_USE_STATIC_RUNTIME OFF) -- - find_package (ZLIB) - if (NOT ZLIB_FOUND) - message (FATAL_ERROR "zlib must be installed before configuration & building can proceed") diff --git a/sci-biology/sailfish/files/sailfish-allow-newer-boost.patch b/sci-biology/sailfish/files/sailfish-allow-newer-boost.patch deleted file mode 100644 index 985f83f4a..000000000 --- a/sci-biology/sailfish/files/sailfish-allow-newer-boost.patch +++ /dev/null @@ -1,13 +0,0 @@ -diff --git a/CMakeLists.txt b/CMakeLists.txt -index ee4b34c..3c58830 100755 ---- a/CMakeLists.txt -+++ b/CMakeLists.txt -@@ -176,7 +176,7 @@ endif() - ## - # Set the latest version and look for what we need - ## --set(Boost_ADDITIONAL_VERSIONS "1.53" "1.53.0" "1.54" "1.55" "1.56" "1.57.0" "1.58" "1.59") -+set(Boost_ADDITIONAL_VERSIONS "1.72.0" "1.74.0" "1.75.0") - find_package(Boost 1.53.0 COMPONENTS iostreams filesystem system thread timer chrono program_options serialization) - message("BOOST_INCLUDEDIR = ${BOOST_INCLUDEDIR}") - message("BOOST_LIBRARYDIR = ${BOOST_LIBRARYDIR}") diff --git a/sci-biology/sailfish/files/sailfish-no-curl.patch b/sci-biology/sailfish/files/sailfish-no-curl.patch deleted file mode 100644 index 2ec97808e..000000000 --- a/sci-biology/sailfish/files/sailfish-no-curl.patch +++ /dev/null @@ -1,121 +0,0 @@ -diff --git a/CMakeLists.txt b/CMakeLists.txt -index 1be4117..ee4b34c 100755 ---- a/CMakeLists.txt -+++ b/CMakeLists.txt -@@ -230,9 +230,6 @@ elseif(FETCH_BOOST) - message("Build system will fetch and build Boost") - message("==================================================================") - ExternalProject_Add(libboost -- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external -- DOWNLOAD_COMMAND curl -k -L http://downloads.sourceforge.net/project/boost/boost/1.59.0/boost_1_59_0.tar.gz -o boost_1_59_0.tar.gz && -- tar xzf boost_1_59_0.tar.gz - SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/boost_1_59_0 - INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install - #PATCH_COMMAND patch -p2 < ${CMAKE_CURRENT_SOURCE_DIR}/external/boost156.patch -@@ -292,10 +289,6 @@ if (NOT JELLYFISH_FOUND) - message("Build system will fetch and build Jellyfish") - message("==================================================================") - ExternalProject_Add(libjellyfish -- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external -- DOWNLOAD_COMMAND curl -k -L https://github.com/gmarcais/Jellyfish/releases/download/v2.2.5/jellyfish-2.2.5.tar.gz -o jellyfish-2.2.5.tgz && -- rm -fr jellyfish-2.2.5 && -- tar -xzvf jellyfish-2.2.5.tgz - SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/jellyfish-2.2.5 - INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install - CONFIGURE_COMMAND ${CMAKE_CURRENT_SOURCE_DIR}/external/jellyfish-2.2.5/configure --prefix=<INSTALL_DIR> CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} CXXFLAGS=${JELLYFISH_CXX_FLAGS} -@@ -335,11 +328,7 @@ if ("${TBB_COMPILER}" STREQUAL "gcc") - endif() - - ExternalProject_Add(libtbb -- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external -- URL http://www.threadingbuildingblocks.org/sites/default/files/software_releases/source/tbb43_20140724oss_src.tgz -- DOWNLOAD_COMMAND curl -k -L http://www.threadingbuildingblocks.org/sites/default/files/software_releases/source/tbb43_20140724oss_src.tgz -o tbb_20140724oss_src.tgz && -- tar -xzvf tbb_20140724oss_src.tgz -- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/tbb43_20140724oss -+ SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/tbb43_20140724oss - INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install - PATCH_COMMAND "${TBB_PATCH_STEP}" - CONFIGURE_COMMAND "" -@@ -407,11 +396,6 @@ message("TBB_LIBRARIES = ${TBB_LIBRARIES}") - message("Build system will compile libgff") - message("==================================================================") - ExternalProject_Add(libgff -- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external -- DOWNLOAD_COMMAND curl -k -L https://github.com/Kingsford-Group/libgff/archive/v1.0.tar.gz -o libgff.tgz && -- tar -xzvf libgff.tgz && -- rm -fr libgff && -- mv libgff-1.0 libgff - SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/libgff - UPDATE_COMMAND sh -c "mkdir -p <SOURCE_DIR>/build" - INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install -@@ -445,9 +429,6 @@ if (NOT HAVE_FAST_MALLOC) - message("Build system will fetch and use JEMalloc") - message("==================================================================") - ExternalProject_Add(libjemalloc -- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external -- DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/jemalloc/archive/3.6.0.tar.gz -o jemalloc-3.6.0.tar.gz && -- tar -xzf jemalloc-3.6.0.tar.gz - SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/jemalloc-3.6.0 - BUILD_IN_SOURCE TRUE - INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install -@@ -465,9 +446,6 @@ endif () - message("Build system will fetch and build SparseHash") - message("==================================================================") - ExternalProject_Add(libsparsehash -- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external -- DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/sparsehash/archive/sparsehash-2.0.2.tar.gz -o sparsehash-2.0.2.tar.gz && -- tar -xzf sparsehash-2.0.2.tar.gz - SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/sparsehash-sparsehash-2.0.2 - BUILD_IN_SOURCE TRUE - INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install -@@ -487,7 +465,6 @@ ExternalProject_Add(libsparsehash - # - #### - if(NOT FETCHED_RAPMAP) -- exec_program(${CMAKE_CURRENT_SOURCE_DIR}/scripts/fetchRapMap.sh) - set(FETCHED_RAPMAP TRUE CACHE BOOL "Has RapMap been fetched?" FORCE) - endif() - -diff --git a/scripts/fetchRapMap.sh b/scripts/fetchRapMap.sh -deleted file mode 100755 -index cab05a1..0000000 ---- a/scripts/fetchRapMap.sh -+++ /dev/null -@@ -1,37 +0,0 @@ --#!/bin/bash -- --CURR_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd ) --EXTERNAL_DIR=${CURR_DIR}/../external --INSTALL_DIR=${CURR_DIR}/../external/install -- --if [ -d ${EXTERNAL_DIR}/RapMap ] ; then -- rm -fr ${EXTERNAL_DIR}/RapMap --fi -- --if [ -d ${INSTALL_DIR}/include/rapmap ] ; then -- rm -fr ${INSTALL_DIR}/include/rapmap --fi -- --if [ -d ${INSTALL_DIR}/src/rapmap ] ; then -- rm -fr ${INSTALL_DIR}/src/rapmap --fi -- --mkdir -p ${EXTERNAL_DIR} --curl -k -L https://github.com/COMBINE-lab/RapMap/archive/quasi-mph.zip -o ${EXTERNAL_DIR}/rapmap.zip --rm -fr ${EXTERNAL_DIR}/RapMap --unzip ${EXTERNAL_DIR}/rapmap.zip -d ${EXTERNAL_DIR} --mv ${EXTERNAL_DIR}/RapMap-quasi-mph ${EXTERNAL_DIR}/RapMap -- --mkdir -p ${INSTALL_DIR}/include/rapmap --mkdir -p ${INSTALL_DIR}/src/rapmap -- --rm ${EXTERNAL_DIR}/RapMap/src/xxhash.c --rm ${EXTERNAL_DIR}/RapMap/include/xxhash.h -- --cp -r ${EXTERNAL_DIR}/RapMap/external/libdivsufsort.zip ${EXTERNAL_DIR} --cp -r ${EXTERNAL_DIR}/RapMap/src/*.c ${INSTALL_DIR}/src/rapmap --cp -r ${EXTERNAL_DIR}/RapMap/src/*.cpp ${INSTALL_DIR}/src/rapmap --cp -r ${EXTERNAL_DIR}/RapMap/include/tclap ${INSTALL_DIR}/include/rapmap --cp -r ${EXTERNAL_DIR}/RapMap/include/*.h ${INSTALL_DIR}/include/rapmap --cp -r ${EXTERNAL_DIR}/RapMap/include/*.hpp ${INSTALL_DIR}/include/rapmap --cp -r ${EXTERNAL_DIR}/RapMap/include/emphf ${INSTALL_DIR}/include/rapmap diff --git a/sci-biology/sailfish/metadata.xml b/sci-biology/sailfish/metadata.xml deleted file mode 100644 index 530333987..000000000 --- a/sci-biology/sailfish/metadata.xml +++ /dev/null @@ -1,15 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <maintainer type="person"> - <email>mschu.dev@gmail.com</email> - <name>Michael Schubert</name> - </maintainer> - <upstream> - <remote-id type="github">kingsfordgroup/sailfish</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-biology/sailfish/sailfish-0.10.0.ebuild b/sci-biology/sailfish/sailfish-0.10.0.ebuild deleted file mode 100644 index 9fa4060ca..000000000 --- a/sci-biology/sailfish/sailfish-0.10.0.ebuild +++ /dev/null @@ -1,83 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit cmake - -DESCRIPTION="Rapid Mapping-based Isoform Quantification from RNA-Seq Reads" -HOMEPAGE="https://www.cs.cmu.edu/~ckingsf/software/sailfish/" -SRC_URI="https://github.com/kingsfordgroup/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz - https://github.com/COMBINE-lab/RapMap/archive/quasi-mph.zip - https://github.com/gmarcais/Jellyfish/releases/download/v2.2.5/jellyfish-2.2.5.tar.gz - https://github.com/COMBINE-lab/sparsehash/archive/sparsehash-2.0.2.tar.gz - https://github.com/Kingsford-Group/libgff/archive/v1.0.tar.gz -" - -LICENSE="GPL-3+" -SLOT="0" -KEYWORDS="" - -DEPEND=" - dev-libs/boost:0 - dev-libs/jemalloc - dev-libs/libdivsufsort - dev-cpp/tbb - dev-cpp/sparsehash - sci-biology/jellyfish:2 -" -RDEPEND="${DEPEND}" -BDEPEND="app-arch/unzip" -# a C++-11 compliant compiler is needs, aka >=gcc-4.7 - -# TODO: disable running wget/curl during src_compile -# https://github.com/kingsfordgroup/sailfish/issues/80 -# contains bundled RapMap https://github.com/COMBINE-lab/RapMap -# contains bundled libdivsufsort -# contains bundled libgff https://github.com/COMBINE-lab/libgff -# contains bundled jellyfish-2.2.5 -# contains bundled sparsehash-2.0.2 - -PATCHES=( - "${FILESDIR}/${PN}-0.9.2-no-boost-static.patch" - "${FILESDIR}/${PN}-no-curl.patch" - "${FILESDIR}/${PN}-allow-newer-boost.patch" -) - -src_unpack() { - default - mkdir -p "${S}/external" - cp "${DISTDIR}/quasi-mph.zip" "${S}/external/rapmap.zip" || die - mv "${WORKDIR}/RapMap-quasi-mph" "${S}/external/RapMap" || die - mv "${WORKDIR}/jellyfish-2.2.5" "${S}/external/jellyfish-2.2.5" || die - mv "${WORKDIR}/sparsehash-sparsehash-2.0.2" "${S}/external/sparsehash-sparsehash-2.0.2" || die - mv "${WORKDIR}/libgff-1.0" "${S}/external/libgff" || die - mkdir -p "${S}/external/install/lib" - cp "${EPREFIX}/usr/$(get_libdir)/libdivsufsort.so" "${S}/external/install/lib/" || die - cp "${EPREFIX}/usr/$(get_libdir)/libdivsufsort64.so" "${S}/external/install/lib/" || die - cp "${EPREFIX}/usr/$(get_libdir)/libjellyfish-2.0.so" "${S}/external/install/lib/" || die - mkdir -p "${S}/external/install/src/rapmap" - cp "${S}/external/RapMap/src/"* "${S}/external/install/src/rapmap" || die -} - -src_prepare() { - cmake_src_prepare - # use the dynamic library - sed -i -e 's/libdivsufsort.a/libdivsufsort.so/g' \ - -e 's/libdivsufsort64.a/libdivsufsort64.so/g' \ - -e 's/libjellyfish-2.0.a/libjellyfish-2.0.so/g' \ - src/CMakeLists.txt || die -} - -src_configure() { - JELLYFISH_INCLUDE_DIR="/usr/include/jellyfish2" cmake_src_configure - # jellyfish2 instead of jellyfish - find -type f -name "*.hpp" -exec sed -i -e 's/#include \"jellyfish\//#include \"jellyfish2\//g' {} + || die - find -type f -name "*.hpp" -exec sed -i -e 's/#include <jellyfish\//#include <jellyfish2\//g' {} + || die -} - -src_install() { - cmake_src_install - rm -r "${ED}"/usr/tests || die - rm -f "${ED}"/usr/bin/jellyfish "${ED}"/usr/$(get_libdir)/libjellyfish || die -} diff --git a/sci-biology/sailfish/sailfish-9999.ebuild b/sci-biology/sailfish/sailfish-9999.ebuild deleted file mode 100644 index a76e8ee89..000000000 --- a/sci-biology/sailfish/sailfish-9999.ebuild +++ /dev/null @@ -1,62 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit cmake git-r3 - -DESCRIPTION="Rapid Mapping-based Isoform Quantification from RNA-Seq Reads" -HOMEPAGE="https://www.cs.cmu.edu/~ckingsf/software/sailfish/" -EGIT_REPO_URI="https://github.com/kingsfordgroup/sailfish.git" - -LICENSE="GPL-3" -SLOT="0" - -PATCHES=( "${FILESDIR}/${PN}-0.9.2-no-boost-static.patch" ) - -DEPEND=" - dev-libs/boost:0 - dev-libs/jemalloc - dev-libs/libdivsufsort - dev-cpp/tbb - sci-biology/jellyfish:2 -" -RDEPEND="${DEPEND}" - -# TODO: disable running wget/curl during src_compile -# https://github.com/kingsfordgroup/sailfish/issues/80 -# contains bundled RapMap https://github.com/COMBINE-lab/RapMap -# contains bundled libdivsufsort -# contains bundled libgff https://github.com/COMBINE-lab/libgff -# contains bundled jellyfish-2.2.5 -# contains bundled sparsehash-2.0.2 - -src_unpack() { - default - mkdir -p "${S}/external" - cp "${DISTDIR}/quasi-mph.zip" "${S}/external/rapmap.zip" || die - mkdir -p "${S}/external/install/lib" - cp "${EPREFIX}/usr/$(get_libdir)/libdivsufsort.so" "${S}/external/install/lib/" || die - cp "${EPREFIX}/usr/$(get_libdir)/libdivsufsort64.so" "${S}/external/install/lib/" || die - cp "${EPREFIX}/usr/$(get_libdir)/libjellyfish-2.0.so" "${S}/external/install/lib/" || die -} - -src_prepare() { - cmake_src_prepare - # use the dynamic library - sed -i -e 's/libdivsufsort.a/libdivsufsort.so/g' \ - -e 's/libdivsufsort64.a/libdivsufsort64.so/g' \ - -e 's/libjellyfish-2.0.a/libjellyfish-2.0.so/g' \ - src/CMakeLists.txt || die - - # jellyfish2 instead of jellyfish - pushd external/install/include/rapmap - find -type f -name "*.hpp" -exec sed -i -e 's/jellyfish/jellyfish2/g' {} + || die - popd -} - -src_install() { - cmake_src_install - rm -r "${ED}"/usr/tests || die - rm -f "${ED}"/usr/bin/jellyfish "${ED}"/usr/$(get_libdir)/libjellyfish || die -} diff --git a/sci-biology/salmon/Manifest b/sci-biology/salmon/Manifest deleted file mode 100644 index cf8f50df3..000000000 --- a/sci-biology/salmon/Manifest +++ /dev/null @@ -1,8 +0,0 @@ -DIST bwa-0.7.12.5.tar.gz 224584 BLAKE2B af273aa6751d73e82ce1891acdd42c7cbb0f332312157e1bcaf3f6175417f7358f1d73fd900ede7bddc4071b62f68ea8c79d1e0eb04f02ee618130bd0c33579f SHA512 c56a08c115fd15ca017f5ca5a2e053aef4df9fdf7b3a8f575646b2443cb38853dcd17e72588750dc0c8acdd7accca173d84894220d6cd06959ba0d994851f6c9 -DIST cereal-1.2.2.tar.gz 335759 BLAKE2B 6804b9aabb235a546758c70554502208f1b7b6bcab9b602fa075123335331f0522191a83027fdbac4ee947881c6866f24f48223a00b9490fca5ca961f3e4b260 SHA512 9567b2e19add9446b24f8afd122eea09ba6ecd1a090335cf0ab31fdc8f64c6c97daa3d9eaf0801c36a770737488e0eebf81d96d7b7a65deed30da6130f2d47eb -DIST libgff-1.1.tgz 79006 BLAKE2B 626a62614c4c52d823104eae78e4f04e0976eb43cd2ea7b820ac6549535771fb2ecccbcf4476a22f53a66b5d8bea4fd260c6d3cee864a2c1b264c6f223744dac SHA512 af797fdc753c21a61a817f0b57da55c523220a9c831a71b73328a49ec66b667a503f1fcbddab714826f802a4e2becf310265535276973e2978d5ad73525fa0bb -DIST salmon-0.10.2.tar.gz 10766806 BLAKE2B f9ba6f208a72a11f37c44a056e9b464f4bf018db88c13e67ce84fcdecee98d878046b2018b144dd48a152300f1ba0a178cf03c5c541b16358e210a5013fdfdce SHA512 828c3d5f3f8f42181bf4b563a49f789bdb82843cbdc9aec4555e7623642e2c663a2552ea7bfd1967cc4f8033e6f0678f8f6f82ce776bc2312bc0b4b8ab7ed19f -DIST salmon-0.10.2_RapMap.zip 1141708 BLAKE2B 397341693e0388093af8ffe620fa91941c584de0887a648d219a3f5662ffd6f9af22179f205bfb83927bc8913756b4d68cbc9179cbfb11f9b329c6aed32220a1 SHA512 8aa593feb61a45d25cc757f39b907e6e0cc108831bad69857268f3ac19614d76cf88de6d8679e52d3eea43bcf5b603bfd55135ececf39acb1700a23408fca573 -DIST salmon-1.4.0.tar.gz 7061272 BLAKE2B d26685c0a1a888d1acc2d3b6789d572f5c3d811e20068fa923197b04c86ccdda3c9ddbe8cb6df99d6855dfdcdb90ac3b69371804c2fdc78b40469c205e1c96ed SHA512 9007899f91cef2589a965d2d039393e0a19b4fcea488b8f256431907323cadf2d182579ffc6203f19feafad4a72ddad1cbeee6a7acd81cd8d5a4fe890996c5ec -DIST spdlog-0.16.1.tar.gz 162408 BLAKE2B c90b94bac128f8b143d85522d224223b1361f7d552d9caa8b253e494dd72de56a2149cbd8d568eb4305224d7caf80d8067fbce606a1071bd94f74c43b3245782 SHA512 0ef741f2abcae7c925808b44bba7d2e55aa8bd3b07a77ab6e785068beb505cdbcd7835d7d103e8e96094235e262954969a176d9f4977e9d373f1bee8e2716ff2 -DIST staden-io_lib-1.14.8.tar.gz 2506985 BLAKE2B 0d64847d0958e0efc763e87bf0600e3af90d30b67c77908b2effa20b18ce43a0d5ad1b213747c46f9e9000a75c4f1260759b3c90cd632be821e039870a26eb4b SHA512 535c6701e61a1786ceb7b22905afe702d277e0383816fba82f69af553dd22ca497bf00766f9768fd9173621632483a02ea9919437e1786008b2236c1c2c8c69f diff --git a/sci-biology/salmon/files/salmon-0.10.2-no-boost-static.patch b/sci-biology/salmon/files/salmon-0.10.2-no-boost-static.patch deleted file mode 100644 index ac561d793..000000000 --- a/sci-biology/salmon/files/salmon-0.10.2-no-boost-static.patch +++ /dev/null @@ -1,18 +0,0 @@ ---- salmon-0.10.2/CMakeLists.txt 2018-06-25 10:51:47.179712781 +0200 -+++ salmon-0.10.2/CMakeLists.txt 2018-06-25 10:52:47.951289159 +0200 -@@ -213,15 +213,6 @@ - set (CMAKE_LIBRARY_PATH ${CUSTOM_BOOST_PATH}/lib ${CMAKE_LIBRARY_PATH}) - endif ( DEFINED CUSTOM_BOOST_PATH ) - --## --# We want static, multithreaded boost libraries --## --if(CONDA_BUILD) -- set (Boost_USE_STATIC_LIBS OFF) --else () -- set (Boost_USE_STATIC_LIBS ON) --endif(CONDA_BUILD) -- - set (Boost_USE_MULTITHREADED ON) - #set (Boost_USE_STATIC_RUNTIME OFF) - diff --git a/sci-biology/salmon/files/salmon-0.10.2_TestSalmonQuasi.cmake.patch b/sci-biology/salmon/files/salmon-0.10.2_TestSalmonQuasi.cmake.patch deleted file mode 100644 index 81edf96f5..000000000 --- a/sci-biology/salmon/files/salmon-0.10.2_TestSalmonQuasi.cmake.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- salmon-0.10.2/cmake/TestSalmonQuasi.cmake 2018-06-26 10:39:51.061971241 +0200 -+++ salmon-0.10.2/cmake/TestSalmonQuasi.cmake 2018-06-26 10:40:22.372822258 +0200 -@@ -5,7 +5,7 @@ - ) - - if (SALMON_QUASI_INDEX_RESULT) -- message(FATAL_ERROR "Error running ${SALMON_QUASI_INDEX_COMMAND}") -+ message(FATAL_ERROR "Error running ${SALMON_QUASI_INDEX_CMD}") - endif() - - set(SALMON_QUANT_COMMAND ${CMAKE_BINARY_DIR}/salmon quant -i sample_salmon_quasi_index -l IU -1 reads_1.fastq -2 reads_2.fastq -o sample_salmon_quasi_quant) diff --git a/sci-biology/salmon/files/salmon-0.10.2_fix_lib_dir.patch b/sci-biology/salmon/files/salmon-0.10.2_fix_lib_dir.patch deleted file mode 100644 index eb606c00c..000000000 --- a/sci-biology/salmon/files/salmon-0.10.2_fix_lib_dir.patch +++ /dev/null @@ -1,22 +0,0 @@ ---- salmon-0.10.2/src/CMakeLists.txt 2018-06-25 13:35:45.723519730 +0200 -+++ salmon-0.10.2/src/CMakeLists.txt 2018-06-25 13:44:01.326139539 +0200 -@@ -296,6 +296,8 @@ - ) - ENDIF(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT) - -+include(GNUInstallDirs) -+ - set(INSTALL_LIB_DIR lib ) - set(INSTALL_BIN_DIR bin ) - set(INSTALL_INCLUDE_DIR include ) -@@ -311,8 +313,8 @@ - - install(TARGETS salmon salmon_core - RUNTIME DESTINATION bin -- LIBRARY DESTINATION lib -- ARCHIVE DESTINATION lib -+ LIBRARY DESTINATION "${CMAKE_INSTALL_FULL_LIBDIR}" -+ ARCHIVE DESTINATION "${CMAKE_INSTALL_FULL_LIBDIR}" - ) - - add_custom_command(TARGET unitTests POST_BUILD diff --git a/sci-biology/salmon/files/salmon-0.10.2_fix_tests.patch b/sci-biology/salmon/files/salmon-0.10.2_fix_tests.patch deleted file mode 100644 index 0a95757a8..000000000 --- a/sci-biology/salmon/files/salmon-0.10.2_fix_tests.patch +++ /dev/null @@ -1,10 +0,0 @@ ---- salmon-0.10.2/src/CMakeLists.txt.ori 2018-06-26 10:34:29.293225671 +0200 -+++ salmon-0.10.2/src/CMakeLists.txt 2018-06-26 10:35:24.674730920 +0200 -@@ -335,6 +335,6 @@ - ) - - include(InstallRequiredSystemLibraries) --add_test( NAME unit_tests COMMAND ${CMAKE_COMMAND} -DTOPLEVEL_DIR=${CMAKE_INSTALL_PREFIX} -P ${GAT_SOURCE_DIR}/cmake/UnitTests.cmake ) -+add_test( NAME unit_tests COMMAND ${CMAKE_COMMAND} -DTOPLEVEL_DIR=${GAT_SOURCE_DIR} -P ${GAT_SOURCE_DIR}/cmake/UnitTests.cmake ) - add_test( NAME salmon_read_test_fmd COMMAND ${CMAKE_COMMAND} -DTOPLEVEL_DIR=${GAT_SOURCE_DIR} -P ${GAT_SOURCE_DIR}/cmake/TestSalmonFMD.cmake ) - add_test( NAME salmon_read_test_quasi COMMAND ${CMAKE_COMMAND} -DTOPLEVEL_DIR=${GAT_SOURCE_DIR} -P ${GAT_SOURCE_DIR}/cmake/TestSalmonQuasi.cmake ) diff --git a/sci-biology/salmon/files/salmon-0.10.2_remove_curl_call.patch b/sci-biology/salmon/files/salmon-0.10.2_remove_curl_call.patch deleted file mode 100644 index 8eddc6e3a..000000000 --- a/sci-biology/salmon/files/salmon-0.10.2_remove_curl_call.patch +++ /dev/null @@ -1,12 +0,0 @@ ---- salmon-9999/scripts/fetchRapMap.sh 2018-06-25 11:11:07.019798309 +0200 -+++ salmon-9999/scripts/fetchRapMap.sh 2018-06-25 11:12:25.131824486 +0200 -@@ -29,7 +29,8 @@ - EXPECTED_SHA256=c4ca27de299bee395b404d117d9d98ad9f0d6ee256ea1deb2890ea402893e688 - - mkdir -p ${EXTERNAL_DIR} --curl -k -L https://github.com/COMBINE-lab/RapMap/archive/${SVER}.zip -o ${EXTERNAL_DIR}/rapmap.zip -+# curl -k -L https://github.com/COMBINE-lab/RapMap/archive/${SVER}.zip -o ${EXTERNAL_DIR}/rapmap.zip -+cp ../../distdir/salmon-0.10.2_RapMap.zip ${EXTERNAL_DIR}/rapmap.zip - - hashcheck="" - if exists sha256sum; then diff --git a/sci-biology/salmon/files/salmon-0.10.2_remove_curl_calls.patch b/sci-biology/salmon/files/salmon-0.10.2_remove_curl_calls.patch deleted file mode 100644 index 438763960..000000000 --- a/sci-biology/salmon/files/salmon-0.10.2_remove_curl_calls.patch +++ /dev/null @@ -1,200 +0,0 @@ ---- salmon-0.10.2/CMakeLists.txt 2018-06-25 13:12:49.275828719 +0200 -+++ salmon-0.10.2/CMakeLists.txt 2018-06-25 13:12:38.945565690 +0200 -@@ -235,31 +235,7 @@ - - find_package (LibLZMA) - if (NOT LIBLZMA_FOUND) -- message ("Will attempt to fetch and build liblzma") -- message ("=======================================") --ExternalProject_Add(liblzma -- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external -- ## -- DOWNLOAD_COMMAND curl -k -L http://tukaani.org/xz/xz-5.2.2.tar.gz -o xz-5.2.2.tar.gz && -- ${SHASUM} 73df4d5d34f0468bd57d09f2d8af363e95ed6cc3a4a86129d2f2c366259902a2 xz-5.2.2.tar.gz && -- tar -xzvf xz-5.2.2.tar.gz -- #URL http://tukaani.org/xz/xz-5.2.2.tar.gz -- #URL_HASH SHA1=14663612422ab61386673be78fbb2556f50a1f08 -- ## -- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/xz-5.2.2 -- INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install -- BUILD_IN_SOURCE TRUE -- CONFIGURE_COMMAND ${CMAKE_CURRENT_SOURCE_DIR}/external/xz-5.2.2/configure --prefix=<INSTALL_DIR> CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} CFLAGS=${EXTRA_CMAKE_INCLUDE_FLAGS} CPPFLAGS=${EXTRA_CMAKE_INCLUDE_FLAGS} LDFLAGS=${EXTRA_CMAKE_LIBRARY_FLAGS} -- BUILD_COMMAND make ${QUIET_MAKE} -- INSTALL_COMMAND make ${QUIET_MAKE} install --) -- --# Tell cmake that the external project generated a library so we can --# add dependencies here instead of later --set (LIBLZMA_LIBRARIES ${GAT_SOURCE_DIR}/external/install/lib/liblzma.a) --set (LIBSTADEN_LDFLAGS "-L${GAT_SOURCE_DIR}/external/install/lib") --set (LIBSTADEN_CFLAGS "-I${GAT_SOURCE_DIR}/external/install/include") --set (FETCHED_LIBLZMA TRUE) -+ message (FATAL_ERROR "liblzma must be installed before configuration & building can proceed") - else() - message("Found liblzma library: ${LIBLZMA_LIBRARIES}") - message("===========================================") -@@ -267,28 +243,7 @@ - - find_package (BZip2) - if (NOT BZIP2_FOUND) -- message ("Will attempt to fetch and build libbz2") -- message ("=======================================") --ExternalProject_Add(libbz2 -- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external -- DOWNLOAD_COMMAND curl -k -L http://www.bzip.org/1.0.6/bzip2-1.0.6.tar.gz -o bzip2-1.0.6.tar.gz && -- ${SHASUM} a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd bzip2-1.0.6.tar.gz && -- tar -xzvf bzip2-1.0.6.tar.gz -- #URL http://www.bzip.org/1.0.6/bzip2-1.0.6.tar.gz -- #URL_HASH SHA1=3f89f861209ce81a6bab1fd1998c0ef311712002 -- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/bzip2-1.0.6 -- INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install -- BUILD_IN_SOURCE TRUE -- CONFIGURE_COMMAND "" -- BUILD_COMMAND make ${QUIET_MAKE} CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} -- INSTALL_COMMAND make ${QUIET_MAKE} install PREFIX=<INSTALL_DIR> --) --# Tell cmake that the external project generated a library so we can --# add dependencies here instead of later --set (BZIP2_LIBRARIES ${GAT_SOURCE_DIR}/external/install/lib/libbz2.a) --set (LIBSTADEN_LDFLAGS "-L${GAT_SOURCE_DIR}/external/install/lib -I${GAT_SOURCE_DIR}/external/install/include") --set (LIBSTADEN_CFLAGS "-I${GAT_SOURCE_DIR}/external/install/include") --set (FETCHED_LIBBZ2 TRUE) -+ message (FATAL_ERROR "libbz2 must be installed before configuration & building can proceed") - else() - message("Found libbz2 library: ${BZIP2_LIBRARIES}") - message("===========================================") -@@ -333,61 +288,15 @@ - # Either inform the user of how to obtain Boost, or, if they passed in the FETCH_BOOST - # option, go and grab it for them. - ## --if ((NOT Boost_FOUND) AND (NOT FETCH_BOOST)) -+if (NOT Boost_FOUND) - message(FATAL_ERROR - "Salmon cannot be compiled without Boost.\n" - "It is recommended to visit http://www.boost.org/ and install Boost according to those instructions.\n" - "This build system can also download and install a local version of boost for you (this takes a lot of time).\n" - "To fetch and build boost locally, call cmake with -DFETCH_BOOST=TRUE" - ) --elseif(FETCH_BOOST) -- ## Let the rest of the build process know we're going to be fetching boost -- set (BOOST_LIB_SUBSET --with-iostreams --with-atomic --with-chrono --with-container --with-date_time --with-exception -- --with-filesystem --with-graph --with-graph_parallel --with-math -- --with-program_options --with-system --with-thread -- --with-timer) -- set (BOOST_WILL_RECONFIGURE TRUE) -- set (FETCH_BOOST FALSE) -- message("Build system will fetch and build Boost") -- message("==================================================================") -- ExternalProject_Add(libboost -- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external -- DOWNLOAD_COMMAND curl -k -L http://downloads.sourceforge.net/project/boost/boost/1.66.0/boost_1_66_0.tar.gz -o boost_1_66_0.tar.gz && -- ${SHASUM} bd0df411efd9a585e5a2212275f8762079fed8842264954675a4fddc46cfcf60 boost_1_66_0.tar.gz && -- tar xzf boost_1_66_0.tar.gz -- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/boost_1_66_0 -- INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install -- #PATCH_COMMAND patch -p2 < ${CMAKE_CURRENT_SOURCE_DIR}/external/boost156.patch -- CONFIGURE_COMMAND CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} ${CMAKE_CURRENT_SOURCE_DIR}/external/boost_1_66_0/bootstrap.sh ${BOOST_CONFIGURE_TOOLSET} ${BOOST_BUILD_LIBS} --prefix=<INSTALL_DIR> -- BUILD_COMMAND CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} ${CMAKE_CURRENT_SOURCE_DIR}/external/boost_1_66_0/b2 -d0 -j2 ${BOOST_LIB_SUBSET} toolset=${BOOST_TOOLSET} ${BOOST_EXTRA_FLAGS} cxxflags=${BOOST_CXX_FLAGS} link=static install -- BUILD_IN_SOURCE 1 -- INSTALL_COMMAND "" -- ) -- -- ## -- # After we've installed boost, -- ## -- SET( RECONFIG_FLAGS ${RECONFIG_FLAGS} -DBOOST_WILL_RECONFIGURE=FALSE -DBOOST_RECONFIGURE=TRUE -DFETCH_BOOST=FALSE) -- ExternalProject_Add_Step(libboost reconfigure -- COMMAND ${CMAKE_COMMAND} ${CMAKE_CURRENT_SOURCE_DIR} ${RECONFIG_FLAGS} -- DEPENDEES install -- ) -- set (FETCHED_BOOST TRUE) - endif() - --## --# If we're fetching boost and we need to have dummy paths for these variables --# so that CMake won't complain --## --if (BOOST_WILL_RECONFIGURE) -- message("Setting Temporary Boost paths") -- set(Boost_INCLUDE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install/include) -- set(Boost_INCLUDE_DIRS ${CMAKE_CURRENT_SOURCE_DIR}/external/install/include) -- set(Boost_LIBRARY_DIRS ${CMAKE_CURRENT_SOURCE_DIR}/external/install/lib) -- set(Boost_FOUND TRUE) --endif() -- -- - message("BOOST INCLUDE DIR = ${Boost_INCLUDE_DIR}") - message("BOOST INCLUDE DIRS = ${Boost_INCLUDE_DIRS}") - message("BOOST LIB DIR = ${Boost_LIBRARY_DIRS}") -@@ -422,9 +331,9 @@ - include(ExternalProject) - ExternalProject_Add(libcereal - DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external -- DOWNLOAD_COMMAND curl -k -L https://github.com/USCiLab/cereal/archive/v1.2.2.tar.gz -o cereal-v1.2.2.tar.gz && -- ${SHASUM} 1921f26d2e1daf9132da3c432e2fd02093ecaedf846e65d7679ddf868c7289c4 cereal-v1.2.2.tar.gz && -- tar -xzvf cereal-v1.2.2.tar.gz -+ DOWNLOAD_COMMAND cp ../../../distdir/cereal-1.2.2.tar.gz . && -+ ${SHASUM} 1921f26d2e1daf9132da3c432e2fd02093ecaedf846e65d7679ddf868c7289c4 cereal-1.2.2.tar.gz && -+ tar -xzvf cereal-1.2.2.tar.gz - - ## - #URL https://github.com/USCiLab/cereal/archive/v1.2.2.tar.gz -@@ -455,12 +364,12 @@ - ExternalProject_Add(libbwa - DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external - #URL https://github.com/COMBINE-lab/bwa/archive/0.7.12.3.tar.gz -- #DOWNLOAD_NAME bwa-master.tar.gz -- DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/bwa/archive/v0.7.12.5.tar.gz -o bwa-master.tar.gz && -- ${SHASUM} 1ac5661d9e12e9017a47f0264201a75d9128f28dbd9a26952925f7745ddf6036 bwa-master.tar.gz && -- mkdir -p bwa-master && -- tar -xzvf bwa-master.tar.gz --strip-components=1 -C bwa-master -- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/bwa-master -+ #DOWNLOAD_NAME bwa-0.7.12.5.tar.gz -+ DOWNLOAD_COMMAND cp ../../../distdir/bwa-0.7.12.5.tar.gz . && -+ ${SHASUM} 1ac5661d9e12e9017a47f0264201a75d9128f28dbd9a26952925f7745ddf6036 bwa-0.7.12.5.tar.gz && -+ mkdir -p bwa-0.7.12.5 && -+ tar -xzvf bwa-0.7.12.5.tar.gz --strip-components=1 -C bwa-0.7.12.5 -+ SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/bwa-0.7.12.5 - INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install - CONFIGURE_COMMAND "" - BUILD_COMMAND sh -c "make ${QUIET_MAKE} CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER}" -@@ -562,9 +471,9 @@ - message("==================================================================") - ExternalProject_Add(libgff - DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external -- DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/libgff/archive/v1.1.tar.gz -o libgff.tgz && -- ${SHASUM} 34597ecd3718e6d6e7a1dd4350220664be2c1cd992070d1218564a20d7aa5697 libgff.tgz && -- tar -xzvf libgff.tgz -+ DOWNLOAD_COMMAND cp ../../../distdir/libgff-1.1.tgz . && -+ ${SHASUM} 34597ecd3718e6d6e7a1dd4350220664be2c1cd992070d1218564a20d7aa5697 libgff-1.1.tgz && -+ tar -xzvf libgff-1.1.tgz - ## - #URL https://github.com/COMBINE-lab/libgff/archive/v1.1.tar.gz - #DOWNLOAD_NAME libff.tgz -@@ -600,10 +509,10 @@ - message("==================================================================") - ExternalProject_Add(libstadenio - DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external -- DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/staden-io_lib/archive/v1.14.8.1.tar.gz -o staden-io_lib-v1.14.8.tar.gz && -- ${SHASUM} f6f30eefa478cfb708f3109a35fb6ffa0e24951d9d971985df2cef5919dd0bc3 staden-io_lib-v1.14.8.tar.gz && -+ DOWNLOAD_COMMAND cp ../../../distdir/staden-io_lib-1.14.8.tar.gz . && -+ ${SHASUM} f6f30eefa478cfb708f3109a35fb6ffa0e24951d9d971985df2cef5919dd0bc3 staden-io_lib-1.14.8.tar.gz && - mkdir -p staden-io_lib-1.14.8 && -- tar -xzf staden-io_lib-v1.14.8.tar.gz --strip-components=1 -C staden-io_lib-1.14.8 && -+ tar -xzf staden-io_lib-1.14.8.tar.gz --strip-components=1 -C staden-io_lib-1.14.8 && - rm -fr staden-io_lib && - mv -f staden-io_lib-1.14.8 staden-io_lib - SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/staden-io_lib -@@ -620,9 +529,9 @@ - message("==================================================================") - ExternalProject_Add(libspdlog - DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external -- DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/spdlog/archive/v0.16.1.tar.gz -o spdlog-v0.16.1.tar.gz && -- ${SHASUM} 733260e1fbdcf1b3dc307fc585e4476240026de8be28eb905731d2ab0942deae spdlog-v0.16.1.tar.gz && -- tar -xzf spdlog-v0.16.1.tar.gz -+ DOWNLOAD_COMMAND cp ../../../distdir/spdlog-0.16.1.tar.gz . && -+ ${SHASUM} 733260e1fbdcf1b3dc307fc585e4476240026de8be28eb905731d2ab0942deae spdlog-0.16.1.tar.gz && -+ tar -xzf spdlog-0.16.1.tar.gz - ## - #URL https://github.com/COMBINE-lab/spdlog/archive/v0.12.0.tar.gz - #DOWNLOAD_NAME spdlog-v0.12.0.tar.gz diff --git a/sci-biology/salmon/salmon-0.10.2.ebuild b/sci-biology/salmon/salmon-0.10.2.ebuild deleted file mode 100644 index c3ef9e50a..000000000 --- a/sci-biology/salmon/salmon-0.10.2.ebuild +++ /dev/null @@ -1,73 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit cmake - -DESCRIPTION="Transcript-level quantification from RNA-seq reads using lightweight alignments" -HOMEPAGE="https://github.com/COMBINE-lab/salmon" -SRC_URI="https://github.com/COMBINE-lab/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz - https://github.com/COMBINE-lab/RapMap/archive/salmon-v0.10.2.zip -> ${P}_RapMap.zip - https://github.com/USCiLab/cereal/archive/v1.2.2.tar.gz -> cereal-1.2.2.tar.gz - https://github.com/COMBINE-lab/bwa/archive/v0.7.12.5.tar.gz -> bwa-0.7.12.5.tar.gz - https://github.com/COMBINE-lab/libgff/archive/v1.1.tar.gz -> libgff-1.1.tgz - https://github.com/COMBINE-lab/staden-io_lib/archive/v1.14.8.1.tar.gz -> staden-io_lib-1.14.8.tar.gz - https://github.com/COMBINE-lab/spdlog/archive/v0.16.1.tar.gz -> spdlog-0.16.1.tar.gz" - -LICENSE="GPL-3" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -PATCHES=( "${FILESDIR}"/${P}-no-boost-static.patch - "${FILESDIR}"/salmon-0.10.2_remove_curl_call.patch - "${FILESDIR}"/salmon-0.10.2_remove_curl_calls.patch - "${FILESDIR}"/salmon-0.10.2_fix_lib_dir.patch - "${FILESDIR}"/salmon-0.10.2_fix_tests.patch - "${FILESDIR}"/salmon-0.10.2_TestSalmonQuasi.cmake.patch ) - -RDEPEND="${DEPEND}" -# budled copies of: -# sci-biology/bwa-0.7.12.5 -# sci-biology/jellyfish -# sci-biology/staden-1.14.8.1 -# sci-biology/gfftools -# -# libgff-1.1 from https://github.com/Kingsford-Group/libgff -# actually unreleased version from https://github.com/COMBINE-lab/libgff/archive/v1.1.tar.gz -# https://github.com/Kingsford-Group/libgff/issues/1 -# -# dev-libs/spdlog-0.16.1 -# cereal-1.2.2 - -# see the many curl executions: -# salmon-0.10.2$ find . -type f | xargs grep curl 2>/dev/null -# -DEPEND=" - sys-libs/zlib - app-arch/bzip2 - app-arch/xz-utils - dev-libs/boost:0= - dev-libs/libdivsufsort - sci-biology/bwa - >=dev-libs/jemalloc-5.0.1 - >=dev-cpp/tbb-2018.20180312 -" -RDEPEND="${DEPEND}" -BDEPEND=" - net-misc/curl - app-arch/unzip -" - -src_prepare() { - # use system libs - sed -i \ - -e "s%\${GAT_SOURCE_DIR}/external/install/lib/libstaden-read.a%/usr/$(get_libdir)/libstaden-read.so%g" \ - -e "s%\${GAT_SOURCE_DIR}/external/install/lib/libdivsufsort.a%/usr/$(get_libdir)/libdivsufsort.so%g" \ - -e "s%\${GAT_SOURCE_DIR}/external/install/lib/libdivsufsort64.a%/usr/$(get_libdir)/libdivsufsort64.so%g" \ - -e "s%\${GAT_SOURCE_DIR}/external/install/lib/libbwa.a%/usr/$(get_libdir)/libbwa.so%g" \ - src/CMakeLists.txt || die - - cmake_src_prepare -} diff --git a/sci-biology/salmon/salmon-1.4.0.ebuild b/sci-biology/salmon/salmon-1.4.0.ebuild deleted file mode 100644 index 420cb2ae2..000000000 --- a/sci-biology/salmon/salmon-1.4.0.ebuild +++ /dev/null @@ -1,38 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit cmake - -DESCRIPTION="Transcript-level quantification from RNA-seq reads using lightweight alignments" -HOMEPAGE="https://github.com/COMBINE-lab/salmon" -SRC_URI="https://github.com/COMBINE-lab/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="GPL-3" -SLOT="0" -KEYWORDS="" - -RDEPEND=" - dev-libs/boost:=[threads(-)] - sys-libs/zlib -" - -DEPEND="${RDEPEND} - app-arch/bzip2 - app-arch/xz-utils - >=dev-libs/jemalloc-5.0.1 - >=dev-cpp/tbb-2018.20180312 - sci-biology/pufferfish - dev-libs/cereal -" - -BDEPEND=" - app-arch/unzip - net-misc/curl -" - -PATCHES=( - "${FILESDIR}/${P}-do-not-fetch-pufferfish.patch" - "${FILESDIR}/${P}-allow-newer-boost.patch" -) diff --git a/sci-biology/sambamba/Manifest b/sci-biology/sambamba/Manifest deleted file mode 100644 index 0c4fb09d1..000000000 --- a/sci-biology/sambamba/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -DIST lz4-sambamba-0.8.0.tar.gz 320972 BLAKE2B e9af776d3a867f551e20c2a3c234f2c9a27e729b972a0b40e25eee830f1c2a2975fe939de68459fda6d56a1b3a63e26937cfbf77fcbb2b711ecdbc9385069d91 SHA512 f51c5332fdc5a74bcd4f9597b187721cc2f33bc535c374c0ff47f438f79f6bec382e20462bb90d8be5f6bdf02ff5d7b4f5bf358bba55e03211ee566035ef3fbd -DIST sambamba-0.8.0.tar.gz 630637 BLAKE2B ea51a86bb546de3792e6d8bc0494aa2afe525d3914d1cc15ad8d52ca1acd2d109f726154273e98ef0e6144266fc34048f8c5008fe5c50be093b4082fb3fac1b5 SHA512 2d74c5ca3188fe0628b4873891eebecb1f514474bb1a2a8aca4ca3f40275acfb0fda0de5e11097754d317cac39b982b6ae45c5dde457cd83d6f684596ca5a5ac diff --git a/sci-biology/sambamba/metadata.xml b/sci-biology/sambamba/metadata.xml deleted file mode 100644 index 3c6df6245..000000000 --- a/sci-biology/sambamba/metadata.xml +++ /dev/null @@ -1,15 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="github">lomereiter/sambamba</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-biology/sambamba/sambamba-0.8.0.ebuild b/sci-biology/sambamba/sambamba-0.8.0.ebuild deleted file mode 100644 index d5f7c1359..000000000 --- a/sci-biology/sambamba/sambamba-0.8.0.ebuild +++ /dev/null @@ -1,36 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -LZ4_COMMIT="b3692db46d2b23a7c0af2d5e69988c94f126e10a" - -DESCRIPTION="Parallell process SAM/BAM/CRAM files faster than samtools" -HOMEPAGE="https://lomereiter.github.io/sambamba/" -SRC_URI="https://github.com/lomereiter/sambamba/archive/v${PV}.tar.gz -> ${P}.tar.gz - https://github.com/lz4/lz4/archive/${LZ4_COMMIT}.tar.gz -> lz4-${P}.tar.gz" - -LICENSE="GPL-2+" -SLOT="0" -KEYWORDS="" -IUSE="debug" - -# https://github.com/ldc-developers/gentoo-overlay/tree/master/dev-lang/ldc2 -# -# contains bundled htslib -DEPEND="" -RDEPEND="${DEPEND}" - -src_unpack() { - default - rm -r "${S}/lz4" || die - mv "${WORKDIR}/lz4-${LZ4_COMMIT}" "${S}/lz4" || die -} - -src_compile(){ - if use debug ; then - emake debug all - else - emake all - fi -} diff --git a/sci-biology/sambamba/sambamba-9999.ebuild b/sci-biology/sambamba/sambamba-9999.ebuild deleted file mode 100644 index e655b10b0..000000000 --- a/sci-biology/sambamba/sambamba-9999.ebuild +++ /dev/null @@ -1,28 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit git-r3 - -DESCRIPTION="Parallell process SAM/BAM/CRAM files faster than samtools" -HOMEPAGE="https://lomereiter.github.io/sambamba/" -EGIT_REPO_URI="https://github.com/lomereiter/sambamba.git" - -LICENSE="GPL-2+" -SLOT="0" -KEYWORDS="" -IUSE="debug" - -DEPEND="" -RDEPEND="${DEPEND}" - -# https://github.com/ldc-developers/gentoo-overlay/tree/master/dev-lang/ldc2 - -src_compile(){ - if use debug ; then - emake debug all - else - emake all - fi -} diff --git a/sci-biology/samri/Manifest b/sci-biology/samri/Manifest index d8c689507..26d7dd5ed 100644 --- a/sci-biology/samri/Manifest +++ b/sci-biology/samri/Manifest @@ -1,2 +1,2 @@ -DIST samri-0.4.1.tar.gz 4115417 BLAKE2B 882b1fbf213f85919a790d669365498c06269a2cb37ba859606e0e4bd696116e954b6683dd636ff34406b2394b4ae3d743c1840a789a828ca3d535b27c0a80da SHA512 c2eef33e725d0d5b87f30ce8da51d9c46ce735a8d82e41f93eba8d225b58eead4777441db4be9078e7f29b3f92d12525d729dddea888fd7e9a66ba5e607d8caf -DIST samri-0.5.tar.gz 4117149 BLAKE2B 1767d6d07726431e43dad5f843eee04bd5111dde3174905b79b938aa94dbb340ca3f3d6316c6720bf01212b87c895df47c965738dff70ec1debbbd542bb77043 SHA512 94fb981adf78b2062e1beac8433bca34e3db90964f720918603e2b89d617b4dfe9f4bc1591b6953e060553ea0014ebca4db62aa0f5b264feb084bc785a48c367 +DIST samri-0.5.3.tar.gz 4122035 BLAKE2B 343dc6de7acf74b5fc169c1f07a4a7209483bee1d050021045a9582d13ea9ae2b8bd4dba0f7f876548e218863cd01bf6d12e571e2d83860366e88ceec7f8441c SHA512 fb9c98843477a35ec313d9284c1c23777af7c6c29fbaa3672b6aa7f7357a81ef874883e0f09f97f52a75febed11deb714343bdadc06708f3a5dcb12fea121a06 +DIST samri-0.5.4.tar.gz 4122057 BLAKE2B 3afdfe6198bc61697cac9ab80560d438d3c488b182d0da9b4a8321efca99d733c964bde000ef8a6a8b849df753f3369d8ea3ba984c8a9736fef466fe196dc003 SHA512 c783156b4eb66b146d039338381867d5683c2f90214d4451448da631609e1e0113f803851a04965b9e400ca5bc69910ec8cbaa1af4b023a89ded0ba6b38901b8 diff --git a/sci-biology/samri/samri-0.5.ebuild b/sci-biology/samri/samri-0.5.3.ebuild index 84161f65f..f632f83a8 100644 --- a/sci-biology/samri/samri-0.5.ebuild +++ b/sci-biology/samri/samri-0.5.3.ebuild @@ -1,25 +1,31 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 -PYTHON_COMPAT=( python3_{7..8} ) +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools inherit distutils-r1 prefix DESCRIPTION="Small Animal Magnetic Resonance Imaging" HOMEPAGE="https://github.com/IBT-FMI/SAMRI" -SRC_URI="https://github.com/IBT-FMI/SAMRI/archive/${PV}.tar.gz -> ${P}.tar.gz" +if [ "$PV" == "9999" ]; then + inherit git-r3 + EGIT_REPO_URI="https://github.com/IBT-FMI/SAMRI.git" +else + SRC_URI="https://github.com/IBT-FMI/SAMRI/archive/${PV}.tar.gz -> ${P}.tar.gz" + KEYWORDS="~amd64" + S="${WORKDIR}/SAMRI-${PV}" +fi LICENSE="GPL-3" SLOT="0" -IUSE="+atlases labbookdb test" -KEYWORDS="~amd64" -RESTRICT="!test? ( test )" +IUSE="+atlases labbookdb" +REQUIRED_USE="test? ( atlases )" DEPEND=" test? ( - dev-python/pytest[${PYTHON_USEDEP}] sci-biology/samri_bidsdata sci-biology/samri_bindata ) @@ -36,26 +42,25 @@ RDEPEND=" >=media-gfx/blender-2.83.4 >=sci-biology/fsl-5.0.9 sci-biology/bru2nii - atlases? ( sci-biology/mouse-brain-atlases ) + atlases? ( sci-biology/mouse-brain-templates ) labbookdb? ( sci-libs/labbookdb[${PYTHON_USEDEP}] ) sci-libs/nibabel[${PYTHON_USEDEP}] >=sci-libs/nipy-0.4.1[${PYTHON_USEDEP}] >=sci-libs/nipype-1.0.0[${PYTHON_USEDEP}] - sci-libs/pybids[${PYTHON_USEDEP}] - sci-libs/scikit-image[${PYTHON_USEDEP}] + <sci-libs/pybids-0.10.2[${PYTHON_USEDEP}] + dev-python/scikit-image[${PYTHON_USEDEP}] sci-biology/ants sci-biology/afni sci-biology/nilearn[${PYTHON_USEDEP}] " -REQUIRED_USE="test? ( atlases )" - -S="${WORKDIR}/SAMRI-${PV}" +distutils_enable_tests pytest +distutils_enable_sphinx doc/source dev-python/sphinxcontrib-napoleon src_prepare() { distutils-r1_src_prepare - sed -i -e "s:/usr:@GENTOO_PORTAGE_EPREFIX@/usr:g" `grep -rlI \'/usr/ samri` - sed -i -e "s:/usr:@GENTOO_PORTAGE_EPREFIX@/usr:g" `grep -rlI /usr/ test_scripts.sh` + sed -i -e "s:/usr:@GENTOO_PORTAGE_EPREFIX@/usr:g" `grep -rlI \'/usr/ samri` || die + sed -i -e "s:/usr:@GENTOO_PORTAGE_EPREFIX@/usr:g" `grep -rlI /usr/ test_scripts.sh` || die eprefixify $(grep -rl GENTOO_PORTAGE_EPREFIX samri/* test_scripts.sh) } @@ -68,5 +73,5 @@ python_test() { sed -i -e \ "/def test_bru2bids():/i@pytest.mark.skip('Removed in full test suite, as this is already tested in `test_scripts.sh`')" \ samri/pipelines/tests/test_repos.py || die - pytest -vv -k "not longtime" || die + epytest -k "not longtime" } diff --git a/sci-biology/samri/samri-0.4.1.ebuild b/sci-biology/samri/samri-0.5.4.ebuild index f94119541..f632f83a8 100644 --- a/sci-biology/samri/samri-0.4.1.ebuild +++ b/sci-biology/samri/samri-0.5.4.ebuild @@ -1,58 +1,77 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 -PYTHON_COMPAT=( python3_{7..8} ) +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools inherit distutils-r1 prefix DESCRIPTION="Small Animal Magnetic Resonance Imaging" HOMEPAGE="https://github.com/IBT-FMI/SAMRI" -SRC_URI="https://github.com/IBT-FMI/SAMRI/archive/${PV}.tar.gz -> ${P}.tar.gz" +if [ "$PV" == "9999" ]; then + inherit git-r3 + EGIT_REPO_URI="https://github.com/IBT-FMI/SAMRI.git" +else + SRC_URI="https://github.com/IBT-FMI/SAMRI/archive/${PV}.tar.gz -> ${P}.tar.gz" + KEYWORDS="~amd64" + S="${WORKDIR}/SAMRI-${PV}" +fi LICENSE="GPL-3" SLOT="0" -IUSE="labbookdb test" -KEYWORDS="~amd64" -RESTRICT="!test? ( test )" +IUSE="+atlases labbookdb" +REQUIRED_USE="test? ( atlases )" DEPEND=" test? ( - dev-python/pytest[${PYTHON_USEDEP}] sci-biology/samri_bidsdata sci-biology/samri_bindata - ) -" + ) + " RDEPEND=" dev-python/argh[${PYTHON_USEDEP}] dev-python/joblib[${PYTHON_USEDEP}] >=dev-python/matplotlib-2.0.2[${PYTHON_USEDEP}] >=dev-python/numpy-1.13.3[${PYTHON_USEDEP}] dev-python/pandas[${PYTHON_USEDEP}] + dev-python/scipy[${PYTHON_USEDEP}] dev-python/seaborn[${PYTHON_USEDEP}] dev-python/statsmodels[${PYTHON_USEDEP}] - media-gfx/blender + >=media-gfx/blender-2.83.4 >=sci-biology/fsl-5.0.9 sci-biology/bru2nii - sci-biology/mouse-brain-atlases + atlases? ( sci-biology/mouse-brain-templates ) labbookdb? ( sci-libs/labbookdb[${PYTHON_USEDEP}] ) sci-libs/nibabel[${PYTHON_USEDEP}] >=sci-libs/nipy-0.4.1[${PYTHON_USEDEP}] >=sci-libs/nipype-1.0.0[${PYTHON_USEDEP}] - <=sci-libs/pybids-0.6.5[${PYTHON_USEDEP}] - sci-libs/scikit-image[${PYTHON_USEDEP}] - dev-python/scipy[${PYTHON_USEDEP}] + <sci-libs/pybids-0.10.2[${PYTHON_USEDEP}] + dev-python/scikit-image[${PYTHON_USEDEP}] sci-biology/ants sci-biology/afni sci-biology/nilearn[${PYTHON_USEDEP}] " -S="${WORKDIR}/SAMRI-${PV}" +distutils_enable_tests pytest +distutils_enable_sphinx doc/source dev-python/sphinxcontrib-napoleon src_prepare() { distutils-r1_src_prepare - sed -i -e "s:/usr:@GENTOO_PORTAGE_EPREFIX@/usr:g" `grep -rlI \'/usr/ samri` - sed -i -e "s:/usr:@GENTOO_PORTAGE_EPREFIX@/usr:g" `grep -rlI /usr/ test_scripts.sh` + sed -i -e "s:/usr:@GENTOO_PORTAGE_EPREFIX@/usr:g" `grep -rlI \'/usr/ samri` || die + sed -i -e "s:/usr:@GENTOO_PORTAGE_EPREFIX@/usr:g" `grep -rlI /usr/ test_scripts.sh` || die eprefixify $(grep -rl GENTOO_PORTAGE_EPREFIX samri/* test_scripts.sh) } + +python_test() { + distutils_install_for_testing + export MPLBACKEND="agg" + export PATH=${TEST_DIR}/scripts:$PATH + export PYTHONIOENCODING=utf-8 + ./test_scripts.sh || die "Test scripts failed." + sed -i -e \ + "/def test_bru2bids():/i@pytest.mark.skip('Removed in full test suite, as this is already tested in `test_scripts.sh`')" \ + samri/pipelines/tests/test_repos.py || die + epytest -k "not longtime" +} diff --git a/sci-biology/samri/samri-9999.ebuild b/sci-biology/samri/samri-9999.ebuild index 8dba8864c..f632f83a8 100644 --- a/sci-biology/samri/samri-9999.ebuild +++ b/sci-biology/samri/samri-9999.ebuild @@ -1,26 +1,31 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 -PYTHON_COMPAT=( python3_{7..8} ) +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools -inherit distutils-r1 prefix git-r3 +inherit distutils-r1 prefix DESCRIPTION="Small Animal Magnetic Resonance Imaging" HOMEPAGE="https://github.com/IBT-FMI/SAMRI" -SRC_URI="" -EGIT_REPO_URI="https://github.com/IBT-FMI/SAMRI" +if [ "$PV" == "9999" ]; then + inherit git-r3 + EGIT_REPO_URI="https://github.com/IBT-FMI/SAMRI.git" +else + SRC_URI="https://github.com/IBT-FMI/SAMRI/archive/${PV}.tar.gz -> ${P}.tar.gz" + KEYWORDS="~amd64" + S="${WORKDIR}/SAMRI-${PV}" +fi LICENSE="GPL-3" SLOT="0" -IUSE="+atlases labbookdb test" -KEYWORDS="" -RESTRICT="!test? ( test )" +IUSE="+atlases labbookdb" +REQUIRED_USE="test? ( atlases )" DEPEND=" test? ( - dev-python/pytest[${PYTHON_USEDEP}] sci-biology/samri_bidsdata sci-biology/samri_bindata ) @@ -37,24 +42,25 @@ RDEPEND=" >=media-gfx/blender-2.83.4 >=sci-biology/fsl-5.0.9 sci-biology/bru2nii - atlases? ( sci-biology/mouse-brain-atlases ) + atlases? ( sci-biology/mouse-brain-templates ) labbookdb? ( sci-libs/labbookdb[${PYTHON_USEDEP}] ) sci-libs/nibabel[${PYTHON_USEDEP}] >=sci-libs/nipy-0.4.1[${PYTHON_USEDEP}] >=sci-libs/nipype-1.0.0[${PYTHON_USEDEP}] - sci-libs/pybids[${PYTHON_USEDEP}] - sci-libs/scikit-image[${PYTHON_USEDEP}] + <sci-libs/pybids-0.10.2[${PYTHON_USEDEP}] + dev-python/scikit-image[${PYTHON_USEDEP}] sci-biology/ants sci-biology/afni sci-biology/nilearn[${PYTHON_USEDEP}] " -REQUIRED_USE="test? ( atlases )" +distutils_enable_tests pytest +distutils_enable_sphinx doc/source dev-python/sphinxcontrib-napoleon src_prepare() { distutils-r1_src_prepare - sed -i -e "s:/usr:@GENTOO_PORTAGE_EPREFIX@/usr:g" `grep -rlI \'/usr/ samri` - sed -i -e "s:/usr:@GENTOO_PORTAGE_EPREFIX@/usr:g" `grep -rlI /usr/ test_scripts.sh` + sed -i -e "s:/usr:@GENTOO_PORTAGE_EPREFIX@/usr:g" `grep -rlI \'/usr/ samri` || die + sed -i -e "s:/usr:@GENTOO_PORTAGE_EPREFIX@/usr:g" `grep -rlI /usr/ test_scripts.sh` || die eprefixify $(grep -rl GENTOO_PORTAGE_EPREFIX samri/* test_scripts.sh) } @@ -67,5 +73,5 @@ python_test() { sed -i -e \ "/def test_bru2bids():/i@pytest.mark.skip('Removed in full test suite, as this is already tested in `test_scripts.sh`')" \ samri/pipelines/tests/test_repos.py || die - pytest -vv -k "not longtime" || die + epytest -k "not longtime" } diff --git a/sci-biology/samri_bidsdata/samri_bidsdata-0.3.ebuild b/sci-biology/samri_bidsdata/samri_bidsdata-0.3.ebuild index 8216eada8..8e47fb775 100644 --- a/sci-biology/samri_bidsdata/samri_bidsdata-0.3.ebuild +++ b/sci-biology/samri_bidsdata/samri_bidsdata-0.3.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2020 Gentoo Authors +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=7 @@ -7,7 +7,6 @@ DESCRIPTION="BIDS-formatted example mouse brain data for SAMRI" HOMEPAGE="https://github.com/IBT-FMI/SAMRI" SRC_URI=" https://zenodo.org/record/3831124/files/${P}.tar.xz - http://chymera.eu/distfiles/${P}.tar.xz " LICENSE="GPL-3" diff --git a/sci-biology/samri_bindata/samri_bindata-0.4.ebuild b/sci-biology/samri_bindata/samri_bindata-0.4.ebuild index 17873ce56..9ab92211a 100644 --- a/sci-biology/samri_bindata/samri_bindata-0.4.ebuild +++ b/sci-biology/samri_bindata/samri_bindata-0.4.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2020 Gentoo Authors +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=7 @@ -7,7 +7,6 @@ DESCRIPTION="ParaVision Mouse, Rat, and Lemur Testing Data for SAMRI" HOMEPAGE="https://github.com/IBT-FMI/SAMRI" SRC_URI=" https://zenodo.org/record/3823441/files/${P}.tar.xz - http://chymera.eu/distfiles/${P}.tar.xz " LICENSE="GPL-3" diff --git a/sci-biology/screed/Manifest b/sci-biology/screed/Manifest deleted file mode 100644 index ff390a90d..000000000 --- a/sci-biology/screed/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST screed-1.0.4.tar.gz 121589 BLAKE2B 0d234e1b03247dca1515c7a6e03d297b75d708dfc6303124c28a0cd936704eb921d76560fd06956d190b8f8277ed301f27e776b6a3642209655d9218e32a3fe3 SHA512 6176029f7efa0319e4a7bf03727aad1729733859445fd0df51f39edfa660f44057e1849d487fe37c34289b023f1e85bc6f29b5f7ece189aea861637afd5fa516 diff --git a/sci-biology/screed/metadata.xml b/sci-biology/screed/metadata.xml deleted file mode 100644 index 297401f3d..000000000 --- a/sci-biology/screed/metadata.xml +++ /dev/null @@ -1,12 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="github">ged-lab/screed</remote-id> - <remote-id type="pypi">screed</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-biology/screed/screed-1.0.4.ebuild b/sci-biology/screed/screed-1.0.4.ebuild deleted file mode 100644 index eab1748f4..000000000 --- a/sci-biology/screed/screed-1.0.4.ebuild +++ /dev/null @@ -1,26 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7,8,9} ) - -inherit distutils-r1 - -DESCRIPTION="Short read sequence utilities" -HOMEPAGE="https://pypi.python.org/pypi/screed https://github.com/ged-lab/screed/" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -SLOT="0" -LICENSE="BSD" -KEYWORDS="~amd64 ~x86" - -distutils_enable_tests --install pytest - -RDEPEND="dev-python/bz2file[${PYTHON_USEDEP}]" - -python_prepare_all() { - # do not depend on pytest-runner - sed -i "/pytest-runner/d" setup.py || die - distutils-r1_python_prepare_all -} diff --git a/sci-biology/seqtk/metadata.xml b/sci-biology/seqtk/metadata.xml index 138cb7705..a2d91d1c4 100644 --- a/sci-biology/seqtk/metadata.xml +++ b/sci-biology/seqtk/metadata.xml @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">lh3/seqtk</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/signalp/Manifest b/sci-biology/signalp/Manifest deleted file mode 100644 index 4f4d96631..000000000 --- a/sci-biology/signalp/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST signalp-3.0.Linux.tar.Z 1216617 SHA256 260c2e5bd945b386e833a7b7326cff6d7332302868e99c0aeae306212047c0c2 diff --git a/sci-biology/signalp/metadata.xml b/sci-biology/signalp/metadata.xml deleted file mode 100644 index 8417d1580..000000000 --- a/sci-biology/signalp/metadata.xml +++ /dev/null @@ -1,8 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-biology/signalp/signalp-3.0.ebuild b/sci-biology/signalp/signalp-3.0.ebuild deleted file mode 100644 index dcd83d920..000000000 --- a/sci-biology/signalp/signalp-3.0.ebuild +++ /dev/null @@ -1,46 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -DESCRIPTION="Prediction of signal peptide cleavage sites in amino acid sequences" -HOMEPAGE="http://www.cbs.dtu.dk/services/SignalP/" -SRC_URI="${P}.Linux.tar.Z" - -LICENSE="signalp" -SLOT="0" -IUSE="gnuplot" -KEYWORDS="~amd64 ~x86" - -DEPEND="" -RDEPEND="gnuplot? ( - sci-visualization/gnuplot - media-libs/netpbm )" - -RESTRICT="fetch strip" - -pkg_nofetch() { - einfo "Please visit ${HOMEPAGE} and obtain the file" - einfo "\"${SRC_URI}\", then place it into your DISTDIR folder" -} - -src_prepare() { - default - sed -i -e '/SIGNALP=/ s/\/usr//' \ - -e '/TMPDIR=/ s/$SIGNALP//' "${S}/signalp" || die - sed -i 's/nawk/gawk/' "${S}"/bin/* || die -} - -src_install() { - dobin signalp - insinto /opt/${P} - doins -r bin hmm how mod syn* test - exeinto /opt/${P}/bin - doexe bin/* - exeinto /opt/${P}/hmm - doexe hmm/* - exeinto /opt/${P}/how - doexe how/* - doman signalp.1 - dodoc *readme -} diff --git a/sci-biology/snapgene-viewer/Manifest b/sci-biology/snapgene-viewer/Manifest new file mode 100644 index 000000000..2e6582002 --- /dev/null +++ b/sci-biology/snapgene-viewer/Manifest @@ -0,0 +1 @@ +DIST snapgene_7.0.3_linux.deb 129706720 BLAKE2B 539257921cc36c8770f5786e3af37502a6e958636ed32f861dcb2fd4621dfbac19d39c9a0772e0d08a532226f9b1875964bf657638917b52c606ff448a03b6f3 SHA512 b902d2bc229e697c4409b09b4f8e2a0ef6583a1958e7a38ef8321b453cdda687e33bc42adb14133d7320cc18791ec1b79409701efbfc5f6be0bbcce2f4e6e87f diff --git a/sci-biology/canu/metadata.xml b/sci-biology/snapgene-viewer/metadata.xml index 138cb7705..5c83ce208 100644 --- a/sci-biology/canu/metadata.xml +++ b/sci-biology/snapgene-viewer/metadata.xml @@ -2,11 +2,11 @@ <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> + <email>pacho@gentoo.org</email> + <name>Pacho Ramos</name> </maintainer> <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> </maintainer> </pkgmetadata> diff --git a/sci-biology/snapgene-viewer/snapgene-viewer-7.0.3.ebuild b/sci-biology/snapgene-viewer/snapgene-viewer-7.0.3.ebuild new file mode 100644 index 000000000..d117fbc14 --- /dev/null +++ b/sci-biology/snapgene-viewer/snapgene-viewer-7.0.3.ebuild @@ -0,0 +1,65 @@ +# Copyright 2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 +inherit unpacker wrapper xdg + +DESCRIPTION="Software for plasmid mapping, primer design, and restriction site analysis" +HOMEPAGE="https://www.snapgene.com/features" +SRC_URI="snapgene_${PV}_linux.deb" +SNAPGENE_DOWNLOAD="https://www.snapgene.com/local/targets/download.php?os=linux_deb&variant=paid&release=${PV}" +RESTRICT="fetch" + +LICENSE="GSL" +SLOT="0" +KEYWORDS="~amd64" + +DEPEND="" +# ldd /opt/gslbiotech/snapgene/snapgene +RDEPEND="${DEPEND} + app-arch/bzip2 + app-arch/xz-utils + app-crypt/qca[qt6] + dev-libs/openssl-compat:1.1.1 + dev-qt/qt5compat:6 + dev-qt/qtbase:6[concurrent,gui,network,opengl,sql,widgets,xml] + dev-qt/qtdeclarative:6 + dev-qt/qtpositioning:6 + dev-qt/qtwebchannel:6 + dev-qt/qtwebengine:6 + media-libs/libglvnd + media-libs/tiff-compat:4 + sci-libs/htslib:0/3 + sys-devel/gcc + sys-libs/glibc + sys-libs/libcxx[libcxxabi] + sys-libs/libunwind:0/8 + x11-libs/libX11 + x11-libs/libXau + x11-libs/libXdmcp + x11-libs/libxcb +" +BDEPEND=">=dev-util/patchelf-0.10" + +S="${WORKDIR}" +QA_PREBUILT="*" + +pkg_nofetch() { + elog "Please download ${SRC_URI} from" + elog "${SNAPGENE_DOWNLOAD}" + elog "and place it into your DISTDIR directory." +} + +src_install() { + patchelf --replace-needed libunwind.so.1 libunwind.so.8 \ + opt/gslbiotech/snapgene/snapgene || die + + mv usr/share/doc/snapgene usr/share/doc/${PF} || die + gzip -d usr/share/doc/${PF}/changelog.Debian.gz || die + + insinto / + doins -r * + + fperms +x /opt/gslbiotech/snapgene/snapgene{,.sh} + make_wrapper ${PN} ./snapgene.sh /opt/gslbiotech/snapgene/ +} diff --git a/sci-biology/spm/metadata.xml b/sci-biology/spm/metadata.xml index ae9640ffb..d888971d1 100644 --- a/sci-biology/spm/metadata.xml +++ b/sci-biology/spm/metadata.xml @@ -5,4 +5,7 @@ <email>sci@gentoo.org</email> <name>Gentoo Science Project</name> </maintainer> + <upstream> + <remote-id type="github">spm/spm12</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/sra-tools/files/libs_sra_Makefile.patch b/sci-biology/sra-tools/files/libs_sra_Makefile.patch deleted file mode 100644 index 44acc42b0..000000000 --- a/sci-biology/sra-tools/files/libs_sra_Makefile.patch +++ /dev/null @@ -1,77 +0,0 @@ -diff -u -w sra_sdk-2.1.9/work/sra_sdk-2.1.9/libs/sra/Makefile sra_sdk-2.1.9/work/sra_sdk-2.1.9/libs/sra/Makefile ---- sra_sdk-2.1.9/work/sra_sdk-2.1.9/libs/sra/Makefile 2011-12-02 21:30:12.000000000 +0100 -+++ sra_sdk-2.1.9/work/sra_sdk-2.1.9/libs/sra/Makefile 2012-02-06 18:38:45.000000000 +0100 -@@ -100,7 +100,7 @@ - $(addsuffix .$(LOBX),$(SRAPATH_SRC)) - - $(LIBDIR)/libsrapath.$(LIBX): $(SRAPATH_OBJ) -- $(LD) --slib -o $@ $^ -+ $(LD) --slib -o $(DESTDIR)$@ $^ - - libsrapath.vers.h: - @ true -@@ -138,10 +138,10 @@ - -dklib - - $(LIBDIR)/libsra-schema.$(SHLX): $(SRA_SCHEMA_OBJ) -- $(LD) --dlib --vers $(SRCDIR) -o $@ $^ $(SRA_SCHEMA_LIB) -+ $(LD) --dlib --vers $(SRCDIR) -o $(DESTDIR)$@ $^ $(SRA_SCHEMA_LIB) - - $(LIBDIR)/libwsra-schema.$(SHLX): $(WSRA_SCHEMA_OBJ) -- $(LD) --dlib --vers $(SRCDIR) -o $@ $^ $(WSRA_SCHEMA_LIB) -+ $(LD) --dlib --vers $(SRCDIR) -o $(DESTDIR)$@ $^ $(WSRA_SCHEMA_LIB) - - SRASCHEMA_SRC = \ - sraschema-stub -@@ -168,10 +168,10 @@ - $(addsuffix .$(LOBX),$(WSRASCHEMA_SRC)) - - $(LIBDIR)/libsraschema.$(LIBX): $(SRASCHEMA_OBJ) $(SRASCHEMA_DEPS) -- $(LD) --slib -o $@ $(SRASCHEMA_OBJ) $(SRA_SCHEMA_LIB) -+ $(LD) --slib -o $(DESTDIR)$@ $(SRASCHEMA_OBJ) $(SRA_SCHEMA_LIB) - - $(LIBDIR)/libwsraschema.$(LIBX): $(WSRASCHEMA_OBJ) $(WSRASCHEMA_DEPS) -- $(LD) --slib -o $@ $(WSRASCHEMA_OBJ) $(WSRA_SCHEMA_LIB) -+ $(LD) --slib -o $(DESTDIR)$@ $(WSRASCHEMA_OBJ) $(WSRA_SCHEMA_LIB) - - libsraschema_tag: - @ $(TOP)/build/tag-module.sh $(MODULE) libsraschema $(SRASCHEMA_OBJ) -@@ -205,10 +205,10 @@ - -dklib - - $(LIBDIR)/libsradb.$(SHLX): $(SRADB_OBJ) -- $(LD) --dlib --vers $(SRCDIR) -o $@ $^ $(SRADB_LIB) -+ $(LD) --dlib --vers $(SRCDIR) -o $(DESTDIR)$@ $^ $(SRADB_LIB) - - $(LIBDIR)/libsradb.$(LIBX): $(SRADB_OBJ) -- $(LD) --slib --vers $(SRCDIR) -o $@ $^ $(SRADB_LIB) -+ $(LD) --slib --vers $(SRCDIR) -o $(DESTDIR)$@ $^ $(SRADB_LIB) - - libsradb_tag: $(SRADB_TAGS) - @ $(TOP)/build/tag-module.sh $(MODULE) libsradb $(SRADB_OBJ) -@@ -236,10 +236,10 @@ - -dklib - - $(LIBDIR)/libwsradb.$(SHLX): $(WSRADB_OBJ) -- $(LD) --dlib --vers $(SRCDIR) -o $@ $^ $(WSRADB_LIB) -+ $(LD) --dlib --vers $(SRCDIR) -o $(DESTDIR)$@ $^ $(WSRADB_LIB) - - $(LIBDIR)/libwsradb.$(LIBX): $(WSRADB_OBJ) -- $(LD) --slib --vers $(SRCDIR) -o $@ $^ $(WSRADB_LIB) -+ $(LD) --slib --vers $(SRCDIR) -o $(DESTDIR)$@ $^ $(WSRADB_LIB) - - libwsradb_tag: $(WSRADB_TAGS) - @ $(TOP)/build/tag-module.sh $(MODULE) libwsradb $(WSRADB_OBJ) -@@ -266,10 +266,10 @@ - -dklib - - $(LIBDIR)/libsrareader.$(SHLX): $(SRAREADER_OBJ) -- $(LD) --dlib --vers $(SRCDIR) -o $@ $^ $(SRAREADER_LIB) -+ $(LD) --dlib --vers $(SRCDIR) -o $(DESTDIR)$@ $^ $(SRAREADER_LIB) - - $(LIBDIR)/libsrareader.$(LIBX): $(SRAREADER_OBJ) -- $(LD) --slib --vers $(SRCDIR) -o $@ $^ $(SRAREADER_LIB) -+ $(LD) --slib --vers $(SRCDIR) -o $(DESTDIR)$@ $^ $(SRAREADER_LIB) - - libsrareader_tag: - @ $(TOP)/build/tag-module.sh $(MODULE) libsrareader $(SRAREADER_OBJ) diff --git a/sci-biology/sra-tools/files/sra_sdk-destdir.patch b/sci-biology/sra-tools/files/sra_sdk-destdir.patch deleted file mode 100644 index bf66c6e46..000000000 --- a/sci-biology/sra-tools/files/sra_sdk-destdir.patch +++ /dev/null @@ -1,76 +0,0 @@ -diff -r -u -w sra_sdk-2.1.9/work/sra_sdk-2.1.9/build/Makefile.env sra_sdk-2.1.9-/work/sra_sdk-2.1.9/build/Makefile.env ---- sra_sdk-2.1.9/work/sra_sdk-2.1.9/build/Makefile.env 2011-08-31 21:46:21.000000000 +0200 -+++ sra_sdk-2.1.9-/work/sra_sdk-2.1.9/build/Makefile.env 2012-02-06 02:02:38.000000000 +0100 -@@ -141,7 +141,7 @@ - - # create all required output directories - makedirs: -- @ mkdir -p $(addprefix $(TARGDIR)/,$(SUBDIRS) obj/$(MODULE)) $(NCBIDIR) -+ @ mkdir -p $(addprefix $(TARGDIR)/,$(SUBDIRS) obj/$(MODULE)) $(DESTDIR)/$(NCBIDIR) - - ifeq (win,$(OS)) - -diff -r -u -w sra_sdk-2.1.9/work/sra_sdk-2.1.9/build/ld.linux.gcc.sh sra_sdk-2.1.9-/work/sra_sdk-2.1.9/build/ld.linux.gcc.sh ---- sra_sdk-2.1.9/work/sra_sdk-2.1.9/build/ld.linux.gcc.sh 2010-12-28 22:46:39.000000000 +0100 -+++ sra_sdk-2.1.9-/work/sra_sdk-2.1.9/build/ld.linux.gcc.sh 2012-02-06 02:23:07.000000000 +0100 -@@ -38,10 +38,10 @@ - # versioned output - if [ "$VERS" = "" ] - then -- DLIB_CMD="$DLIB_CMD -o $TARG" -- EXE_CMD="$EXE_CMD -o $TARG" -+ DLIB_CMD="$DLIB_CMD -o $DESTDIR$TARG" -+ EXE_CMD="$EXE_CMD -o $TARG" - else - set-vers $(echo $VERS | tr '.' ' ') -- DLIB_CMD="$DLIB_CMD -o $OUTDIR/$NAME$DBGAP.so.$VERS -Wl,-soname,$NAME.so.$MAJ" -- EXE_CMD="$EXE_CMD -o $OUTDIR/$NAME$DBGAP.$VERS" -+ DLIB_CMD="$DLIB_CMD -o $DESTDIR$OUTDIR/$NAME$DBGAP.so.$VERS -Wl,-soname,$NAME.so.$MAJ" -+ EXE_CMD="$EXE_CMD -o $DESTDIR$OUTDIR/$NAME$DBGAP.$VERS" - fi -diff -r -u -w sra_sdk-2.1.9/work/sra_sdk-2.1.9/build/ld.linux.ln.sh sra_sdk-2.1.9-/work/sra_sdk-2.1.9/build/ld.linux.ln.sh ---- sra_sdk-2.1.9/work/sra_sdk-2.1.9/build/ld.linux.ln.sh 2010-12-28 22:46:39.000000000 +0100 -+++ sra_sdk-2.1.9-/work/sra_sdk-2.1.9/build/ld.linux.ln.sh 2012-02-06 02:34:46.000000000 +0100 -@@ -52,12 +52,12 @@ - - set-vers $(echo $VERS | tr '.' ' ') - --cd "$OUTDIR" || exit 5 -+cd $DESTDIR$OUTDIR || exit 5 - - # create link - create-link () - { -- rm -f "$2" -+ rm -f $DESTDIR"$2" - local CMD="ln -s $1 $2" - echo $CMD - $CMD ---- sra_sdk-2.1.9/work/sra_sdk-2.1.9/build/ld.linux.slib.sh 2012-02-06 04:05:16.000000000 +0100 -+++ sra_sdk-2.1.9-/work/sra_sdk-2.1.9/build/ld.linux.slib.sh 2012-02-06 04:05:29.000000000 +0100 -@@ -77,7 +77,7 @@ - CMD="$CMD $TARG" - else - set-vers $(echo $VERS | tr '.' ' ') -- CMD="$CMD $OUTDIR/$NAME$DBGAP.a.$VERS" -+ CMD="$CMD $DESTDIR/$OUTDIR/$NAME$DBGAP.a.$VERS" - fi - - # tack on object files ---- sra_sdk-2.1.9/work/sra_sdk-2.1.9/build/Makefile.gcc.ori 2012-02-06 04:24:39.000000000 +0100 -+++ sra_sdk-2.1.9/work/sra_sdk-2.1.9/build/Makefile.gcc 2012-02-06 04:22:57.000000000 +0100 -@@ -36,12 +36,12 @@ - LD = @ $(TOP)/build/ld.sh $(OS) $(ARCH) gcc \ - --build $(BUILD) --ldflags "$(LDFLAGS)" $(STATIC) \ - $(STATICSYSLIBS) $(CHECKSUM) --objx $(OBJX) --shlx $(SHLX) --libx $(LIBX) \ -- -MD --srcdir $(SRCDIR) --bindir $(BINDIR) -L$(LIBDIR):$(ILIBDIR) -+ -MD --srcdir $(SRCDIR) --bindir $(BINDIR) -L$(DESTDIR)$(LIBDIR):$(ILIBDIR) - - LP = @ $(TOP)/build/ld.sh $(OS) $(ARCH) g++ \ - --build $(BUILD) --ldflags "$(LDFLAGS)" $(STATIC) \ - $(STATICSYSLIBS) $(CHECKSUM) --objx $(OBJX) --shlx $(SHLX) --libx $(LIBX) \ -- -MD --srcdir $(SRCDIR) --bindir $(BINDIR) -L$(LIBDIR):$(ILIBDIR) -+ -MD --srcdir $(SRCDIR) --bindir $(BINDIR) -L$(DESTDIR)$(LIBDIR):$(ILIBDIR) - - # tool options - WARN = -Wall -Wno-variadic-macros # -Wconversion diff --git a/sci-biology/sra-tools/files/tools_vdb-vcopy_Makefile.patch b/sci-biology/sra-tools/files/tools_vdb-vcopy_Makefile.patch deleted file mode 100644 index 738d67cbd..000000000 --- a/sci-biology/sra-tools/files/tools_vdb-vcopy_Makefile.patch +++ /dev/null @@ -1,12 +0,0 @@ -diff -u -w sra_sdk-2.1.9/work/sra_sdk-2.1.9/tools/vdb-copy/Makefile sra_sdk-2.1.9/work/sra_sdk-2.1.9/tools/vdb-copy/Makefile ---- sra_sdk-2.1.9/work/sra_sdk-2.1.9/tools/vdb-copy/Makefile 2011-12-02 22:00:36.000000000 +0100 -+++ sra_sdk-2.1.9/work/sra_sdk-2.1.9/tools/vdb-copy/Makefile 2012-02-06 18:39:05.000000000 +0100 -@@ -89,7 +89,7 @@ - $(BINDIR)/vdb-copy: $(NCBIDIR)/vdb-copy.kfg - - $(NCBIDIR)/vdb-copy.kfg: $(SRCDIR)/vdb-copy.kfg -- cp $^ $@ -+ cp $^ $(DESTDIR)$@ - - VDB_COPY_SRC = \ - num-gen \ diff --git a/sci-biology/ssaha2-bin/ssaha2-bin-2.5.5.ebuild b/sci-biology/ssaha2-bin/ssaha2-bin-2.5.5-r1.ebuild index 3122e2188..2c0d5f63d 100644 --- a/sci-biology/ssaha2-bin/ssaha2-bin-2.5.5.ebuild +++ b/sci-biology/ssaha2-bin/ssaha2-bin-2.5.5-r1.ebuild @@ -1,7 +1,7 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 inherit toolchain-funcs @@ -20,9 +20,10 @@ LICENSE="all-rights-reserved" SLOT="0" KEYWORDS="~amd64 ~x86" -QA_PREBUILT="/opt/.*" +QA_PREBUILT="*" -pkg_setup() { +src_unpack() { + default use x86 && export S="${WORKDIR}"/${MY_P}_i686 use amd64 && export S="${WORKDIR}"/${MY_P}_x86_64 } @@ -31,8 +32,7 @@ src_compile() { } src_install() { - dobin samflag - exeinto /opt/bin - doexe ssaha2 ssaha2Build ssahaSNP + dobin samflag ssaha2 ssaha2Build ssahaSNP dodoc README "${DISTDIR}"/ssaha2-manual.pdf + einstalldocs } diff --git a/sci-biology/stacks/Manifest b/sci-biology/stacks/Manifest index 51adfa214..06b5c03ad 100644 --- a/sci-biology/stacks/Manifest +++ b/sci-biology/stacks/Manifest @@ -1 +1 @@ -DIST stacks-2.55.tar.gz 11716625 BLAKE2B ab359095a546a6ae946fd4196f7955b1e6f294c5ade94e1474984c435c3f2dd468fe8665afbcf201b567d2dd84b999bfc8f9ff7a6dd2712e6be0d4b0d609f0f6 SHA512 eb517f5d9a677095efe3000d0e88ee3be3a6abb725290a0fb1cdb9113a4f19d929dd8eb0d8ce3fd3f9d8234fc0b936523f06d754d5c428381fd97fcebbe89a0b +DIST stacks-2.60.tar.gz 12135281 BLAKE2B 8d529ba75af4c78710bc36230ef7c564551cd2f2cb9c2ff2cfdc9372f5721bcb463b959b67b7082cdc95f88c772b4e6146cd0c48c25a7b4a6f21d8cdb3045b8e SHA512 9bb2bf730ab5a35cb732107b989ca5068c1e2a8d7a647423d62195ab2049f61409e5ad5b9f16444c10791196f322d677aa7f0e0e73bcfccb9b7c4c00ec40ad32 diff --git a/sci-biology/stacks/stacks-2.55.ebuild b/sci-biology/stacks/stacks-2.60.ebuild index becd91a5d..4de3f8da8 100644 --- a/sci-biology/stacks/stacks-2.55.ebuild +++ b/sci-biology/stacks/stacks-2.60.ebuild @@ -1,7 +1,7 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 inherit perl-module webapp autotools @@ -10,10 +10,8 @@ HOMEPAGE="http://creskolab.uoregon.edu/stacks" SRC_URI="http://creskolab.uoregon.edu/stacks/source/${P}.tar.gz" LICENSE="GPL-3" -# SLOT="0" # webapp ebuilds do not set SLOT -KEYWORDS="" +KEYWORDS="~amd64" -# No rule to make target test RESTRICT="test" DEPEND=" @@ -21,11 +19,14 @@ DEPEND=" dev-cpp/sparsehash sci-biology/samtools:* sci-biology/bamtools - sci-biology/gmap" # Source code for both GMAP and GSNAP + sci-biology/gmap +" + RDEPEND="${DEPEND} dev-lang/perl - >=dev-lang/php-5 - dev-perl/DBD-mysql" + >=dev-lang/php-5:* + dev-perl/DBD-mysql +" PATCHES=( "${FILESDIR}/${PN}-make-install.patch" @@ -41,17 +42,13 @@ src_prepare(){ src_configure() { econf - webapp_src_preinst sed -e 's#/usr/lib/libbam.a#-lbam#;#./htslib/libhts.a#-lhts#' -i Makefile || die } src_install() { - emake install DESTDIR="${ED}" - mydoc="Changes README TODO INSTALL" - perl-module_src_install DESTDIR="${ED}" - webapp_src_install || die "Failed running webapp_src_install" -} - -pkg_postinst() { - webapp_pkg_postinst || die "webapp_pkg_postinst failed" + webapp_src_preinst + DESTDIR="${ED}" default + DESTDIR="${ED}" perl-module_src_install + dodir /usr/share/webapps/${PN}/${PV} + webapp_src_install } diff --git a/sci-biology/staden/Manifest b/sci-biology/staden/Manifest deleted file mode 100644 index 13f7d3536..000000000 --- a/sci-biology/staden/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST staden-2.0.0_beta11-src.tar.gz 4754651 BLAKE2B d55dcff2192a5f6c505d141960f624ad30afb358e481c438d285a267bb116f8e26e1b7d6562c222b4c7392729bacd14524ee9275ada5201b7d8bcefbd244112f SHA512 6f85cc3aa3b909431333a4998566b267f1d344b3160603604306caf41504cc36c05980790bf5a8f2b4a53f7aea2a369ffafbce163b41c3ea94605f7fee07a26a diff --git a/sci-biology/staden/files/staden-2.0.0_beta10-ldflags.patch b/sci-biology/staden/files/staden-2.0.0_beta10-ldflags.patch deleted file mode 100644 index 735feb315..000000000 --- a/sci-biology/staden/files/staden-2.0.0_beta10-ldflags.patch +++ /dev/null @@ -1,30 +0,0 @@ - abi/Makefile | 2 +- - alf/Makefile | 2 +- - 2 files changed, 2 insertions(+), 2 deletions(-) - -diff --git a/abi/Makefile b/abi/Makefile -index 3c1f8fb..58b4353 100644 ---- a/abi/Makefile -+++ b/abi/Makefile -@@ -23,7 +23,7 @@ getABISampleName: $(OBJSSN) - $(CLD) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(OBJSSN) $(LIBS) $(LIBSC) - - getABIdate: $(OBJSD) -- $(CLD) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(OBJSD) $(IOUTILS_LIB) $(MISC_LIB) $(LIBSC) -+ $(CLD) $(LDFLAGS) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(OBJSD) $(IOUTILS_LIB) $(MISC_LIB) $(LIBSC) - - getABIcomment: $(OBJSC) - $(CLD) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(OBJSC) $(LIBS) $(LIBSC) -diff --git a/alf/Makefile b/alf/Makefile -index 94b7480..ef41a26 100644 ---- a/alf/Makefile -+++ b/alf/Makefile -@@ -16,7 +16,7 @@ INCLUDES_E += $(MISC_INC) - ALFOBJ = alfsplit.o - - alfsplit: $(ALFOBJ) -- $(CLD) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(ALFOBJ) $(LIBSC) -+ $(CLD) $(LDFLAGS) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(ALFOBJ) $(LIBSC) - - RSOBJ = $(ALFBIN)/2rs.o - diff --git a/sci-biology/staden/files/staden-2.0.0_beta10-zlib.patch b/sci-biology/staden/files/staden-2.0.0_beta10-zlib.patch deleted file mode 100644 index 39537604e..000000000 --- a/sci-biology/staden/files/staden-2.0.0_beta10-zlib.patch +++ /dev/null @@ -1,16 +0,0 @@ - gap5/zfio.c | 2 +- - 1 file changed, 1 insertion(+), 1 deletion(-) - -diff --git a/gap5/zfio.c b/gap5/zfio.c -index 35da12a..1b628e4 100644 ---- a/gap5/zfio.c -+++ b/gap5/zfio.c -@@ -51,7 +51,7 @@ int zfpeek(zfp *zf) { - if (c != EOF) - ungetc(c, zf->fp); - } else { -- c = gzgetc(zf->gz); -+ c = gzgetc((gzFile)zf->gz); - if (c != EOF) - gzungetc(c, zf->gz); - } diff --git a/sci-biology/staden/files/staden-2.0.0_beta11-ldflags.patch b/sci-biology/staden/files/staden-2.0.0_beta11-ldflags.patch deleted file mode 100644 index 735feb315..000000000 --- a/sci-biology/staden/files/staden-2.0.0_beta11-ldflags.patch +++ /dev/null @@ -1,30 +0,0 @@ - abi/Makefile | 2 +- - alf/Makefile | 2 +- - 2 files changed, 2 insertions(+), 2 deletions(-) - -diff --git a/abi/Makefile b/abi/Makefile -index 3c1f8fb..58b4353 100644 ---- a/abi/Makefile -+++ b/abi/Makefile -@@ -23,7 +23,7 @@ getABISampleName: $(OBJSSN) - $(CLD) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(OBJSSN) $(LIBS) $(LIBSC) - - getABIdate: $(OBJSD) -- $(CLD) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(OBJSD) $(IOUTILS_LIB) $(MISC_LIB) $(LIBSC) -+ $(CLD) $(LDFLAGS) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(OBJSD) $(IOUTILS_LIB) $(MISC_LIB) $(LIBSC) - - getABIcomment: $(OBJSC) - $(CLD) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(OBJSC) $(LIBS) $(LIBSC) -diff --git a/alf/Makefile b/alf/Makefile -index 94b7480..ef41a26 100644 ---- a/alf/Makefile -+++ b/alf/Makefile -@@ -16,7 +16,7 @@ INCLUDES_E += $(MISC_INC) - ALFOBJ = alfsplit.o - - alfsplit: $(ALFOBJ) -- $(CLD) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(ALFOBJ) $(LIBSC) -+ $(CLD) $(LDFLAGS) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(ALFOBJ) $(LIBSC) - - RSOBJ = $(ALFBIN)/2rs.o - diff --git a/sci-biology/staden/metadata.xml b/sci-biology/staden/metadata.xml deleted file mode 100644 index 1ed1820a4..000000000 --- a/sci-biology/staden/metadata.xml +++ /dev/null @@ -1,15 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="sourceforge">staden</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-biology/staden/staden-2.0.0_beta11.ebuild b/sci-biology/staden/staden-2.0.0_beta11.ebuild deleted file mode 100644 index a0f91720b..000000000 --- a/sci-biology/staden/staden-2.0.0_beta11.ebuild +++ /dev/null @@ -1,76 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit flag-o-matic fortran-2 - -DESCRIPTION="DNA sequence assembly (gap4, gap5), editing and analysis tools (Spin)" -HOMEPAGE="https://sourceforge.net/projects/staden" -SRC_URI="https://downloads.sourceforge.net/staden/staden-${PV/_beta/b}-2016-src.tar.gz -> ${P}-src.tar.gz" - -LICENSE="staden" -SLOT="0" -KEYWORDS="~amd64" -IUSE="debug doc fortran png tcl tk X zlib" - -# either g77 or gfortran must be available -# edit src/mk/linux.mk accordingly -# -# this is a glibc-2.9 issue, see https://sourceforge.net/tracker/index.php?func=detail&aid=2629155&group_id=100316&atid=627058 -# -# -# - -DEPEND=" - app-arch/xz-utils - dev-lang/tk:0= - dev-tcltk/tklib - media-libs/libpng:0 - sci-biology/samtools:0 - >=sci-libs/io_lib-1.13.8 - sys-libs/zlib" -RDEPEND="${DEPEND} - >=dev-tcltk/iwidgets-4.0 - tcl? ( >=dev-tcltk/itcl-3.2 ) - tk? ( >=dev-tcltk/itk-3.2 ) - net-misc/curl - doc? ( sci-biology/staden_doc )" - -S="${WORKDIR}"/staden-${PV/_beta/b}-2016-src - -PATCHES=( - "${FILESDIR}/${P}-ldflags.patch" -) - -src_prepare() { - default - sed \ - -e 's:svnversion:false:' \ - -i configure.in || die -} - -src_configure(){ - use debug && append-cflags "-DCACHE_REF_DEBUG" - econf \ - $(use_enable X x) \ - $(use_enable amd64 64bit) \ - --with-tklib="/usr/$(get_libdir)/tklib" -} - -src_install() { - default - # install the LDPATH so that it appears in /etc/ld.so.conf after env-update - # subsequently, apps linked against /usr/lib/staden can be run because - # loader can find the library (I failed to use '-Wl,-rpath,/usr/lib/staden' - # somehow for gap2caf, for example - cat >> "${T}"/99staden <<- EOF - STADENROOT="${EPREFIX}"/usr/share/staden - LDPATH="${EPREFIX}/usr/$(get_libdir)/staden" - EOF - doenvd "${T}"/99staden -} - -pkg_postinst(){ - einfo "There is a tutorial at https://sourceforge.net/projects/staden/files/tutorials/1.1/course-1.1.tar.gz" -} diff --git a/sci-biology/staden/staden-9999.ebuild b/sci-biology/staden/staden-9999.ebuild deleted file mode 100644 index b2ed35724..000000000 --- a/sci-biology/staden/staden-9999.ebuild +++ /dev/null @@ -1,69 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit flag-o-matic fortran-2 subversion - -DESCRIPTION="DNA sequence assembly (gap4, gap5), editing and analysis tools (Spin)" -HOMEPAGE="https://sourceforge.net/projects/staden/" -ESVN_REPO_URI="https://svn.code.sf.net/p/${PN}/code/${PN}/trunk" - -LICENSE="staden" -SLOT="0" -KEYWORDS="" -IUSE="debug doc fortran png tcl tk X zlib" - -# either g77 or gfortran must be available -# edit src/mk/linux.mk accordingly -# -# this is a glibc-2.9 issue, see https://sourceforge.net/tracker/index.php?func=detail&aid=2629155&group_id=100316&atid=627058 -# -# -# -DEPEND=" - app-arch/xz-utils - dev-lang/tk:0= - dev-tcltk/tklib - media-libs/libpng:0 - sci-biology/samtools:0 - >=sci-libs/io_lib-1.13.8 - sys-libs/zlib" -RDEPEND="${DEPEND} - >=dev-tcltk/iwidgets-4.0 - tcl? ( >=dev-tcltk/itcl-3.2 ) - tk? ( >=dev-tcltk/itk-3.2 ) - net-misc/curl - doc? ( sci-biology/staden_doc )" - -src_prepare() { - default - sed \ - -e 's:svnversion:false:' \ - -i configure.in || die -} - -src_configure(){ - use debug && append-cflags "-DCACHE_REF_DEBUG" - econf \ - $(use_enable X x) \ - $(use_enable amd64 64bit) \ - --with-tklib="/usr/$(get_libdir)/tklib" -} - -src_install() { - default - # install the LDPATH so that it appears in /etc/ld.so.conf after env-update - # subsequently, apps linked against /usr/lib/staden can be run because - # loader can find the library (I failed to use '-Wl,-rpath,/usr/lib/staden' - # somehow for gap2caf, for example - cat >> "${T}"/99staden <<- EOF - STADENROOT="${EPREFIX}"/usr/share/staden - LDPATH="${EPREFIX}/usr/$(get_libdir)/staden" - EOF - doenvd "${T}"/99staden -} - -pkg_postinst(){ - einfo "There is a tutorial at https://sourceforge.net/projects/staden/files/tutorials/1.1/course-1.1.tar.gz" -} diff --git a/sci-biology/staden_doc/Manifest b/sci-biology/staden_doc/Manifest deleted file mode 100644 index 108aad2fe..000000000 --- a/sci-biology/staden_doc/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST staden_doc-2.0.0b11-src.tar.gz 3184526 BLAKE2B cf67f702efd0743899b0f955434b815bdb695d28641069a4da981e5fe5de9091980b997e55d10897ff21fca1928f1afb787aa9a89d66ab658b14f8db9b35d110 SHA512 ca8aad2ab3ec660dbd8631bb65df95b10fa64e20d5d509925a03e277896ed8a2eebef89f6b170fe2acd0dd10e0075585620dd162b7b5c9153b248ee6dedd6ef1 diff --git a/sci-biology/staden_doc/metadata.xml b/sci-biology/staden_doc/metadata.xml deleted file mode 100644 index 1ed1820a4..000000000 --- a/sci-biology/staden_doc/metadata.xml +++ /dev/null @@ -1,15 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="sourceforge">staden</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-biology/staden_doc/staden_doc-2.0.0_beta11.ebuild b/sci-biology/staden_doc/staden_doc-2.0.0_beta11.ebuild deleted file mode 100644 index 5a70701b0..000000000 --- a/sci-biology/staden_doc/staden_doc-2.0.0_beta11.ebuild +++ /dev/null @@ -1,42 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -DESCRIPTION="Documentation files for the staden package" -HOMEPAGE="https://sourceforge.net/projects/staden" -SRC_URI="https://sourceforge.net/projects/staden/files/staden/${PV/_beta/b}/staden_doc-${PV/_beta/b}-src.tar.gz" - -LICENSE="staden" -SLOT="0" -KEYWORDS="~amd64" - -DEPEND=" - dev-lang/perl - app-text/texlive - app-text/texi2html" -BDEPEND="app-editors/emacs" -RDEPEND="${DEPEND} ${BDEPEND}" - -S="${WORKDIR}"/staden_doc-${PV/_beta/b}-src - -# do not use texi2html-5 because it fails with: -# texi2html -menu -verbose -split_chapter -index_chars interface.htmlinfo -# Unknown option: index_char -# src_prepare(){ -# default -# # avoid running bundled texi2html code -# sed -e "s#./tools/texi2html#texi2html#" -i manual/Makefile || die -# } - -src_compile(){ - cd manual || die - emake -j1 spotless || die - cd .. || die - emake -j1 unix PAPER=A4 -} - -src_install(){ - emake -j1 install prefix="${D}"/usr - dodoc gkb547_gml.pdf -} diff --git a/sci-biology/subread/Manifest b/sci-biology/subread/Manifest index 48a9f7ca3..8b4dcee7c 100644 --- a/sci-biology/subread/Manifest +++ b/sci-biology/subread/Manifest @@ -1 +1 @@ -DIST subread-2.0.1-source.tar.gz 23260381 BLAKE2B 498f898c9b5f5e0819fb7ae0a1407805fb3dc34cf5a07b4354d1493315a9e9190735916fb5c5587f972a67a7d47880e31dc3cc627e271dd2e452e856f5fd79c1 SHA512 e7548c426f75a5705a7c0538787007c5d3f23e4a4561022f192b3219f333483a02312986936cbbfcc8f9afa24cb4d91a1cc62fbebb6c6aef957568d5d8fa3505 +DIST subread-2.0.3-source.tar.gz 23304665 BLAKE2B 715907360f477a8ef69ba0465d6de1f23224da0c2095a21141f597a9cfe5c787cbafaa5d3c9cb04175f4d73cc4d184e13628541072d164596ee0b9b24175b501 SHA512 085d436d933c317555f36cbfb8e8c200ca15f20e56e48ae5427a673a74017dca7818320143a4841b78946685839931d48ae563b8b8e3ee6074581536cd0ff13b diff --git a/sci-biology/subread/files/subread-2.0.1-fno-common.patch b/sci-biology/subread/files/subread-2.0.1-fno-common.patch deleted file mode 100644 index 8f86840c5..000000000 --- a/sci-biology/subread/files/subread-2.0.1-fno-common.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- a/src/gene-algorithms.h -+++ b/src/gene-algorithms.h -@@ -60,7 +60,7 @@ void add_allvote_q(gene_allvote_t* allvote,int qid , int pos, gene_vote_number_t - - unsigned char get_next_char(FILE * fp); - --unsigned char * replica_index; -+extern unsigned char * replica_index; - - extern double begin_ftime; - diff --git a/sci-biology/subread/subread-2.0.1.ebuild b/sci-biology/subread/subread-2.0.3.ebuild index a16d0af5f..624509aa5 100644 --- a/sci-biology/subread/subread-2.0.1.ebuild +++ b/sci-biology/subread/subread-2.0.3.ebuild @@ -1,22 +1,20 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 DESCRIPTION="NGS suite for analysis of mapped reads, summary of exon/intron/gene counts" HOMEPAGE="http://bioinf.wehi.edu.au/featureCounts/" # no https SRC_URI="https://sourceforge.net/projects/subread/files/${P}/${P}-source.tar.gz" +S="${S}-source" LICENSE="GPL-3" SLOT="0" +KEYWORDS="~amd64" DEPEND="sys-libs/zlib" RDEPEND="${DEPEND}" -S="${S}-source" - -PATCHES=( "${FILESDIR}"/${P}-fno-common.patch ) - src_prepare(){ default sed -e "s/-mtune=core2//g" -e "s/-O9//g" -i src/Makefile.Linux || die diff --git a/sci-biology/symap/Manifest b/sci-biology/symap/Manifest deleted file mode 100644 index 4e5ac6ea6..000000000 --- a/sci-biology/symap/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST symap-5.0.6.tar.gz 39447370 BLAKE2B 749769c36d7a46c11ab8bc874915b1dc2e4402b881c7f1fbd56353b4c0dc10cb20864c426c8bdb3ab28aa34d5f7d9bfbf8df66a99de34eebc13f3aa66b4a8d27 SHA512 356bebd7e1afeb78d00e748e1ec4488f180f1225aa3ca117b58cc381dc1d910241d54bc84d932ff6de955b6f4150043508fae6bc0f33c4486025aeb7deb010a8 diff --git a/sci-biology/symap/symap-5.0.6.ebuild b/sci-biology/symap/symap-5.0.6.ebuild deleted file mode 100644 index 58b444b3d..000000000 --- a/sci-biology/symap/symap-5.0.6.ebuild +++ /dev/null @@ -1,40 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -DESCRIPTION="Synteny Mapping and Analysis Program" -HOMEPAGE="http://www.agcol.arizona.edu/software/symap/ https://github.com/csoderlund/SyMAP" -SRC_URI="https://github.com/csoderlund/SyMAP/archive/v${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="GPL-2" -SLOT="0" -# error: package netscape.javascript does not exist -KEYWORDS="" - -DEPEND=" - sci-biology/blat - sci-biology/mummer - sci-biology/muscle" -RDEPEND="${DEPEND} - >=virtual/jre-1.7:*" - -S="${WORKDIR}/SyMAP-${PV}/java" - -src_unpack() { - default - cd "${S}" - tar xvf classes_ext.tar.gz - cd ../ - tar xvf ext.tar.gz -} - -src_prepare() { - default - sed -e 's/#JAVA_PATH=\/usr/JAVA_PATH=\/usr/g' -i Makefile || die -} - -src_compile() { - emake class_dirs - emake -} diff --git a/sci-biology/tigmint/tigmint-1.2.4-r1.ebuild b/sci-biology/tigmint/tigmint-1.2.4-r1.ebuild index 84b582151..c5f630a96 100644 --- a/sci-biology/tigmint/tigmint-1.2.4-r1.ebuild +++ b/sci-biology/tigmint/tigmint-1.2.4-r1.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 -PYTHON_COMPAT=( python3_{8..9} ) +PYTHON_COMPAT=( python3_{10..10} ) DISTUTILS_USE_SETUPTOOLS=no inherit distutils-r1 diff --git a/sci-biology/tigr-foundation-libs/tigr-foundation-libs-2.0-r1.ebuild b/sci-biology/tigr-foundation-libs/tigr-foundation-libs-2.0-r2.ebuild index a03a130c2..18eec4e53 100644 --- a/sci-biology/tigr-foundation-libs/tigr-foundation-libs-2.0-r1.ebuild +++ b/sci-biology/tigr-foundation-libs/tigr-foundation-libs-2.0-r2.ebuild @@ -1,7 +1,7 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 DESCRIPTION="TIGR Foundation for C++" HOMEPAGE="https://sourceforge.net/projects/amos/" @@ -20,11 +20,7 @@ PATCHES=( "${FILESDIR}/TigrFoundation-all-patches.patch" ) -src_prepare(){ - sed -i "s:/export/usr/local:${ED}/usr:g" Makefile || die - default -} - src_install(){ - emake install DESTDIR="${ED}/usr" # Makefile does not respect DESTDIR + sed -i "s:/export/usr/local:${ED}/usr:g" Makefile || die + DESTDIR="${ED}/usr" emake install # Makefile does not respect DESTDIR } diff --git a/sci-biology/tmhmm/Manifest b/sci-biology/tmhmm/Manifest deleted file mode 100644 index 875ce562e..000000000 --- a/sci-biology/tmhmm/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST tmhmm-2.0c.Linux.tar.gz 191561 SHA256 761a87ca82c174e0e6660c5065f257ef0b201fab98f934e1342291e4e673ca40 diff --git a/sci-biology/tmhmm/metadata.xml b/sci-biology/tmhmm/metadata.xml deleted file mode 100644 index 8417d1580..000000000 --- a/sci-biology/tmhmm/metadata.xml +++ /dev/null @@ -1,8 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-biology/tmhmm/tmhmm-2.0c.ebuild b/sci-biology/tmhmm/tmhmm-2.0c.ebuild deleted file mode 100644 index dc50101fa..000000000 --- a/sci-biology/tmhmm/tmhmm-2.0c.ebuild +++ /dev/null @@ -1,39 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -DESCRIPTION="Prediction of transmembrane helices in proteins" -HOMEPAGE="http://www.cbs.dtu.dk/services/TMHMM/" -SRC_URI="${P}.Linux.tar.gz" - -LICENSE="tmhmm" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -RESTRICT="fetch" - -S="TMHMM${PV}" - -pkg_nofetch() { - einfo "Please visit ${HOMEPAGE} and obtain the file" - einfo "\"${SRC_URI}\", then place it into your DISTDIR folder" -} - -src_prepare() { - default - sed -i '1 i #!/usr/bin/env perl' "${S}"/bin/tmhmm* || die - sed -i '1 a $opt_basedir = "/opt/tmhmm";' "${S}"/bin/tmhmm || die -} - -src_install() { - exeinto /opt/${PN}/bin - doexe bin/* - - insinto /opt/${PN}/lib - doins lib/* - - dosym ../${PN}/bin/tmhmm /opt/bin/tmhmm - - dodoc README TMHMM2.0.html -} diff --git a/sci-biology/trans-abyss/Manifest b/sci-biology/trans-abyss/Manifest deleted file mode 100644 index 9addb1899..000000000 --- a/sci-biology/trans-abyss/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST trans-abyss-2.0.1.tar.gz 359063 BLAKE2B 9b3f19b883e2616b05bc0677b9161e8c997596b288af7e570a83129549edd517a941f765d39dfb83638160e611df3f2acfc32eb944c7cca63c8350e77fb96246 SHA512 5362665a2758a76c579d8086f8904cf0e40c8dff0dfa1c82368b38af25e37f2f2852f60c3001db254e5f06400e9e2e7f6f6c301133b7806d47cee189f84a0f0f diff --git a/sci-biology/trans-abyss/metadata.xml b/sci-biology/trans-abyss/metadata.xml deleted file mode 100644 index 138cb7705..000000000 --- a/sci-biology/trans-abyss/metadata.xml +++ /dev/null @@ -1,12 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-biology/trans-abyss/trans-abyss-2.0.1.ebuild b/sci-biology/trans-abyss/trans-abyss-2.0.1.ebuild deleted file mode 100644 index cf10dd3b9..000000000 --- a/sci-biology/trans-abyss/trans-abyss-2.0.1.ebuild +++ /dev/null @@ -1,35 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7,8,9} ) - -inherit python-r1 - -DESCRIPTION="Analyze and combine multiple assemblies from abyss" -HOMEPAGE="https://www.bcgsc.ca/resources/software/trans-abyss" -SRC_URI="https://github.com/bcgsc/transabyss/archive/${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="GPL-3" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -DEPEND="${PYTHON_DEPS} - dev-lang/perl - dev-python/python-igraph[${PYTHON_USEDEP}] - sci-biology/abyss - sci-biology/blat -" -RDEPEND="${DEPEND}" - -S="${WORKDIR}/transabyss-${PV}" - -src_install() { - einstalldocs - python_foreach_impl python_domodule utilities - dobin transabyss - dobin transabyss-merge -} diff --git a/sci-biology/trim_galore/Manifest b/sci-biology/trim_galore/Manifest deleted file mode 100644 index d49ab113e..000000000 --- a/sci-biology/trim_galore/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST trim_galore-0.6.6.tar.gz 26829185 BLAKE2B b783d5b8fcf831c5b652cbfed82a42ad55e911aac1b16ac367d27ff6c07f298cd8fd797d4ac4b4213e7c9188ee02e7a2bab97799cc2c9eeba88244556b006832 SHA512 3714f89cee439cf2ef2c88c1f505507c00e426345ff59bdb48fadcc56fe78617d7641da9b6deb5f122fb1d41449fdc4b3f79ee336ec4bf240edbe071aeffc025 diff --git a/sci-biology/trim_galore/metadata.xml b/sci-biology/trim_galore/metadata.xml deleted file mode 100644 index 138cb7705..000000000 --- a/sci-biology/trim_galore/metadata.xml +++ /dev/null @@ -1,12 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-biology/trim_galore/trim_galore-0.6.6.ebuild b/sci-biology/trim_galore/trim_galore-0.6.6.ebuild deleted file mode 100644 index c99dcfcc6..000000000 --- a/sci-biology/trim_galore/trim_galore-0.6.6.ebuild +++ /dev/null @@ -1,26 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -DESCRIPTION="Perl wrapper around Cutadapt and FastQC to adapter and quality trimming" -HOMEPAGE="https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ https://github.com/FelixKrueger/TrimGalore" -SRC_URI="https://github.com/FelixKrueger/TrimGalore/archive/${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="GPL-3" -SLOT="0" -KEYWORDS="~amd64" - -DEPEND="" -RDEPEND=" - dev-lang/perl - sci-biology/cutadapt - sci-biology/fastqc - ${DEPEND}" - -S="${WORKDIR}/TrimGalore-${PV}" - -src_install(){ - dobin trim_galore - dodoc -r Docs -} diff --git a/sci-biology/trinityrnaseq/Manifest b/sci-biology/trinityrnaseq/Manifest index 815ffe565..153f208fd 100644 --- a/sci-biology/trinityrnaseq/Manifest +++ b/sci-biology/trinityrnaseq/Manifest @@ -1 +1 @@ -DIST trinityrnaseq-2.11.0.tar.gz 320752461 BLAKE2B 53327a49d31f7350e8fe820ac106f1cbe0577097852a63ea2154004d1945079f737f646c09d9907cfd45fb011845ea5e21eedf8fcda09e1db17d563fbdd0fd66 SHA512 9e9af2a16423ff8c063522c7acb6c8fc9386a95a7b58e01c94cd97971f71c3080cd5b2d34133bb501505d35cae05b77ff8423ad948324f49f9d4ddbb16629d20 +DIST trinityrnaseq-2.13.2.tar.gz 310355363 BLAKE2B 63055e11976a8d70b2c10b4859b25c8a27f23c05d1f5196eca137f281812aa54558b7eda343498a61af0c5aaa0e8d255e5d0a81e53c906859b455e0725180f95 SHA512 8399e12516d6d3cfde6803323b3bfb9ae249528fc79c08a6b290f42e7498783e6b300b89f9890570b28b2847ebe0f7894f59a888bf47d51190aad9e7c1ce54b7 diff --git a/sci-biology/trinityrnaseq/trinityrnaseq-2.11.0.ebuild b/sci-biology/trinityrnaseq/trinityrnaseq-2.11.0.ebuild deleted file mode 100644 index 9ecaf24f2..000000000 --- a/sci-biology/trinityrnaseq/trinityrnaseq-2.11.0.ebuild +++ /dev/null @@ -1,70 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit perl-module - -# Butterfly should not require any special compilation, as its written in Java and already provided as portable precompiled software ... - -DESCRIPTION="Transcriptome assembler for RNA-seq reads" -HOMEPAGE="https://github.com/Trinotate/Trinotate.github.io/wiki" -SRC_URI="https://github.com/trinityrnaseq/trinityrnaseq/releases/download/v${PV}/${PN}-v${PV}.FULL_with_extendedTestData.tar.gz -> ${P}.tar.gz" - -LICENSE="BSD-BroadInstitute" -SLOT="0" -KEYWORDS="" # PERL5INC path is wrong when /usr/bin/Trinity is executed - -DEPEND="" -RDEPEND="${DEPEND} - sci-biology/parafly - >=sci-biology/jellyfish-2.2.6:2 - >=sci-libs/htslib-1.2.1 - >=sci-biology/samtools-1.3:0 - >=sci-biology/trimmomatic-0.36 - >=sci-biology/GAL-0.2.1 - dev-perl/IO-All - sci-biology/seqtools" -# optionally install https://github.com/HpcGridRunner/HpcGridRunner/releases -# has the following "plugins" (aka bundled 3rd-party code) -# slclust -# DEXseq_util -# COLLECTL -# ParaFly-0.1.0 - -S="${WORKDIR}/${PN}-v${PV}" - -PATCHES=( - "${FILESDIR}/${PN}-2.11.0-fix-compilation.patch" -) - -src_compile(){ - emake all - emake plugins # bundled copies of TransDecoder, trimmomatic, fastool, parafly -} - -src_install(){ - dodoc Chrysalis/chrysalis.notes - dodoc Changelog.txt - perl_set_version - dobin Trinity - perl_domodule util/*.pl - dobin Inchworm/bin/* - cd Chrysalis/bin || die - dobin BubbleUpClustering Chrysalis CreateIwormFastaBundle GraphFromFasta QuantifyGraph ReadsToTranscripts - cd ../../util/R || die - insinto /usr/share/"${PN}"/R - doins *.R - cd ../PBS || die - insinto /usr/share/"${PN}"/PBS - doins * - cd .. || die - cp -rp support_scripts misc "${ED}"/usr/share/"${PN}"/ || die - cd "${S}" || die - perl_domodule util/misc/PerlLib/*.pm PerlLib/*.pm - perl_domodule PerlLib/KmerGraphLib/*.pm - perl_domodule PerlLib/CDNA/*.pm - perl_domodule PerlLib/Simulate/*.pm - perl_domodule PerlLib/CanvasXpress/*.pm - chmod a+rx -R "${ED}/${VENDOR_LIB}/${PN}" -} diff --git a/sci-biology/trinityrnaseq/trinityrnaseq-2.13.2.ebuild b/sci-biology/trinityrnaseq/trinityrnaseq-2.13.2.ebuild new file mode 100644 index 000000000..3b94d9713 --- /dev/null +++ b/sci-biology/trinityrnaseq/trinityrnaseq-2.13.2.ebuild @@ -0,0 +1,45 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit perl-module + +DESCRIPTION="Transcriptome assembler for RNA-seq reads" +HOMEPAGE="https://github.com/Trinotate/Trinotate.github.io/wiki" +SRC_URI="https://github.com/${PN}/${PN}/releases/download/Trinity-v${PV}/${PN}-v${PV}.FULL_with_extendedTestData.tar.gz -> ${P}.tar.gz" +S="${WORKDIR}/${PN}-v${PV}" + +LICENSE="BSD-BroadInstitute" +SLOT="0" +KEYWORDS="~amd64" + +DEPEND="" +RDEPEND="${DEPEND} + sci-biology/parafly + >=sci-biology/jellyfish-2.2.6:2 + >=sci-libs/htslib-1.2.1 + >=sci-biology/samtools-1.3:0 + >=sci-biology/trimmomatic-0.36 + >=sci-biology/GAL-0.2.1 + dev-perl/IO-All + sci-biology/seqtools +" + +PATCHES=( + "${FILESDIR}/${PN}-2.11.0-fix-compilation.patch" +) + +src_compile(){ + # missing submodule for bamsifter + emake no_bamsifter + emake plugins +} + +src_install(){ + # fix the install path + sed -e "s:/usr/local/bin:${ED}/usr/bin:g" \ + -i util/support_scripts/trinity_installer.py || die + dodir /usr/bin + default +} diff --git a/sci-biology/ugene/metadata.xml b/sci-biology/ugene/metadata.xml index a3daeebd2..36e8936e5 100644 --- a/sci-biology/ugene/metadata.xml +++ b/sci-biology/ugene/metadata.xml @@ -9,4 +9,7 @@ <email>sci@gentoo.org</email> <name>Gentoo Science Project</name> </maintainer> + <upstream> + <remote-id type="github">ugeneunipro/ugene</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/vcflib/Manifest b/sci-biology/vcflib/Manifest index 57b3d1f2b..a535ea547 100644 --- a/sci-biology/vcflib/Manifest +++ b/sci-biology/vcflib/Manifest @@ -1 +1 @@ -DIST vcflib-1.0.2-src.tar.gz 20881031 BLAKE2B 67e8fd60db3171fa05cac36306852134cc8c37a3e4715d141547773c3252569a01363298297978d89c015b1120ad0f0d05eb2b67b5ee7d01728f27f0049bc748 SHA512 7dadd2398d4054a1d7e7b520f192243f63c98a4fa184f7c6750dce9296356f4b45bdbb50f7de270a6c4c3aa76deec45980c363e19b22bea64590de711fdb7d71 +DIST vcflib-1.0.3.tar.gz 19213097 BLAKE2B 142685d494759d61e7b0ed40e9d91b78d7856038b6fb73f7f26f80152b0a85006bd6f3e9b5e7422e74841eb9a21e3a86efc3f63545e3fea7545fb91a7475b409 SHA512 16c7b3932fd4e6a985adbc1131dd0b48028501be3023d85fd57b4efccaf071a11ba6f49219df723f6eacc2787218e8f3f2b318e016633ce3e829139b698154a2 diff --git a/sci-biology/vcflib/vcflib-1.0.2.ebuild b/sci-biology/vcflib/vcflib-1.0.3.ebuild index 272e69483..d4cf1e02f 100644 --- a/sci-biology/vcflib/vcflib-1.0.2.ebuild +++ b/sci-biology/vcflib/vcflib-1.0.3.ebuild @@ -1,18 +1,17 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 inherit cmake toolchain-funcs DESCRIPTION="VCF/BED utils, Genotype Phenotype Association Toolkit (GPAT++)" HOMEPAGE="https://github.com/vcflib/vcflib" -SRC_URI="https://github.com/vcflib/vcflib/releases/download/v${PV}/${P}-src.tar.gz" - -# vcflib is incorporated into several projects, such as freebayes +SRC_URI="https://github.com/vcflib/vcflib/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz" LICENSE="MIT-with-advertising" SLOT="0" +# No proper release tarball for this release yet KEYWORDS="" IUSE="openmp" @@ -22,10 +21,6 @@ DEPEND=" sci-biology/tabixpp " RDEPEND="${DEPEND}" -# contains bundled sci-biology/htslib ? -# see also ./include for possible traces of other bundled sw - -S="${WORKDIR}/${PN}" src_prepare(){ cmake_src_prepare @@ -47,7 +42,7 @@ src_prepare(){ src_compile(){ mycmakeargs=( -DOPENMP="$(use_enable openmp)" - -DHTSLIB_LOCAL=NO + -DHTSLIB_LOCAL=ON ) cmake_src_compile } diff --git a/sci-biology/wcd/Manifest b/sci-biology/wcd/Manifest deleted file mode 100644 index 5209a3925..000000000 --- a/sci-biology/wcd/Manifest +++ /dev/null @@ -1,3 +0,0 @@ -DIST wcd-0.6.3_p20180430.tar.gz 368654 BLAKE2B c6936964d4dd2602e9fd735ddf70ed79e625b6dfa58972a1ba95532b36968da4345ef40d7ba68355f8f53308d0989124c1bbdce48e11d0240ccabc91787d3b61 SHA512 7c847607fcbeb20cb5dbf023968a9174a5d2fd876127a6008b878274ec2e1a6498e7c0a610e4f75473128236661848d6403f96fc868eec773be3a8e4e7dd7f4f -DIST wcd.html 8448 BLAKE2B d1561925a0f299d12c177f499a95fbc314d558c18106642c49852bd96a104bdef5271b5ea1b4312e70936db6726ea3ea54e3a942d9c9c52e806b48137321cf05 SHA512 11156d4811b7716632fbd7b0330d918ae30b6dcc9ebbd59c95d445ba465504aa68d0fa9863b3ad4b5743c929f4558d1698af03c124fd02299ef13479a80555c2 -DIST wcd.pdf 275513 BLAKE2B 049d0d8b9d6db0e2754322f69903c5680a62c007a9abf5466b21a96f778a9f537a8ec91344d729961317ff6a8b484ca870f5ee0a78fa7cec8ae4ba2d7c5f1939 SHA512 ef2e0e8bbe49a5c5b304a305d8948b253ba2bf789790941600c5d5ba74351fe41e54a66dd189a33846304a8f2a8fa4c70025e516f3b73643da71030cbded63a2 diff --git a/sci-biology/wcd/files/wcd-0.6.3-impl-decl.patch b/sci-biology/wcd/files/wcd-0.6.3-impl-decl.patch deleted file mode 100644 index 15d851577..000000000 --- a/sci-biology/wcd/files/wcd-0.6.3-impl-decl.patch +++ /dev/null @@ -1,15 +0,0 @@ - src/auxcluster.c | 1 + - 1 file changed, 1 insertion(+) - -diff --git a/src/auxcluster.c b/src/auxcluster.c -index ac00a0f..e98f19f 100644 ---- a/src/auxcluster.c -+++ b/src/auxcluster.c -@@ -2,6 +2,7 @@ - - #include "common.h" - #include "strings.h" -+#include <string.h> - #include "assert.h" - - extern SeqInfoPtr seqInfo; diff --git a/sci-biology/wcd/files/wcd-0.6.3-ldflags.patch b/sci-biology/wcd/files/wcd-0.6.3-ldflags.patch deleted file mode 100644 index d697d00b7..000000000 --- a/sci-biology/wcd/files/wcd-0.6.3-ldflags.patch +++ /dev/null @@ -1,16 +0,0 @@ - src/Makefile.am | 2 +- - 1 file changed, 1 insertion(+), 1 deletion(-) - -diff --git a/src/Makefile.am b/src/Makefile.am -index e986a91..ff87e29 100644 ---- a/src/Makefile.am -+++ b/src/Makefile.am -@@ -7,7 +7,7 @@ wcd_CFLAGS += -DMPI - endif - if PTHREADS - wcd_CFLAGS += -DPTHREADS --wcd_LDFLAGS += -lpthread -+wcd_LDADD = -lpthread - endif - if !COMPILER - wcd_CFLAGS += -DNOINLINE diff --git a/sci-biology/wcd/metadata.xml b/sci-biology/wcd/metadata.xml deleted file mode 100644 index 138cb7705..000000000 --- a/sci-biology/wcd/metadata.xml +++ /dev/null @@ -1,12 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-biology/wcd/wcd-0.6.3_p20180430.ebuild b/sci-biology/wcd/wcd-0.6.3_p20180430.ebuild deleted file mode 100644 index 6593d97ed..000000000 --- a/sci-biology/wcd/wcd-0.6.3_p20180430.ebuild +++ /dev/null @@ -1,46 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -COMMIT="aee525029bb661b633097e989c6fe2eaa93d2def" - -DESCRIPTION="EST sequence clustering: d2 function, edit distance, common word heuristics" -HOMEPAGE="https://shaze.github.io/wcdest/" -SRC_URI="https://github.com/shaze/wcdest/archive/${COMMIT}.tar.gz -> ${P}.tar.gz - http://www.bioinf.wits.ac.za/~scott/wcd.html - http://www.bioinf.wits.ac.za/~scott/wcd.pdf" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="" - -IUSE="doc mpi threads" - -# This code (0.4.1 at least) has been tested using LAMMPI (RedHat, Suse, -# MacOS X), MPICH (Ubuntu) and MVAPICH (Suse) -DEPEND="mpi? ( sys-cluster/mpich2 )" - -PATCHES=( - "${FILESDIR}"/${PN}-0.6.3-ldflags.patch - "${FILESDIR}"/${PN}-0.6.3-impl-decl.patch -) - -S="${WORKDIR}/${PN}est-${COMMIT}/code" - -src_configure(){ - econf \ - $(use_enable mpi) \ - $(use_enable threads pthreads) -} - -src_compile() { - default - use doc && emake pdf info html -} - -src_install() { - use doc && HTML_DOCS=( doc/wcd.html doc/wcd.pdf doc/wcd.texi ) - emake install PREFIX=/usr LIBDIR="${D}"/usr/$(get_libdir) - dodoc "${DISTDIR}"/wcd.* -} diff --git a/sci-biology/weblogo/Manifest b/sci-biology/weblogo/Manifest deleted file mode 100644 index 264bad9bd..000000000 --- a/sci-biology/weblogo/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST weblogo-3.7.5.tar.gz 817128 BLAKE2B f7619b6ea0c944fb21b8acdfc9593d6223e7d48ac9495c872c3bcadc0187249883b013e44bec70ce126d820abb6281b2e5ef5f04126e7a288c3f5a1026612ab0 SHA512 7fbf71854eee0bcebebe926f2c93653b0b8475462ed5b3dc951947cec67a37bee801d468f893932257f5bdca8c754264c3279695cdb3da747bd82e9353392c0b diff --git a/sci-biology/weblogo/metadata.xml b/sci-biology/weblogo/metadata.xml deleted file mode 100644 index 138cb7705..000000000 --- a/sci-biology/weblogo/metadata.xml +++ /dev/null @@ -1,12 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-biology/weblogo/weblogo-3.7.5.ebuild b/sci-biology/weblogo/weblogo-3.7.5.ebuild deleted file mode 100644 index a8db5bec5..000000000 --- a/sci-biology/weblogo/weblogo-3.7.5.ebuild +++ /dev/null @@ -1,33 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7..9} ) -DISTUTILS_USE_SETUPTOOLS=rdepend -inherit distutils-r1 - -DESCRIPTION="generate consensus sequence logo figures" -HOMEPAGE="http://weblogo.threeplusone.com/" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -RDEPEND=" - dev-python/scipy -" -BDEPEND=" - test? ( - app-text/ghostscript-gpl - dev-python/mypy - ) -" - -distutils_enable_tests pytest - -python_test() { - distutils_install_for_testing - pytest -vv || die "tests failed with ${EPYTHON}" -} |