diff options
Diffstat (limited to 'sci-biology')
298 files changed, 1567 insertions, 9026 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 4b5476138..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://resources.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 4b5476138..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://resources.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 e28aa18be..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://resources.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/BlastToSam/metadata.xml b/sci-biology/BEP032tools/metadata.xml index 5a3c7d51d..8d24d17e7 100644 --- a/sci-biology/BlastToSam/metadata.xml +++ b/sci-biology/BEP032tools/metadata.xml @@ -2,14 +2,15 @@ <!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>gentoo@chymera.eu</email> + <name>Horea Christian</name> </maintainer> <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> </maintainer> <upstream> - <remote-id type="github">AstrorEnales/BlastToSam</remote-id> + <remote-id type="github">INT-NIT/BEP032tools</remote-id> + <remote-id type="pypi">BEP032tools</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="${RDEPEND} - >=virtual/jdk-1.5:* - dev-java/ant-core - dev-java/jython -" - -src_compile() { - ant compile || die -} - -src_install() { - java-pkg_dojar build/jar/BlastToSam.jar - java-pkg_dolauncher - dodoc README.md -} diff --git a/sci-biology/CAT/CAT-1.3.ebuild b/sci-biology/CAT/CAT-1.3.ebuild index a2c4233c9..508ca4c36 100644 --- a/sci-biology/CAT/CAT-1.3.ebuild +++ b/sci-biology/CAT/CAT-1.3.ebuild @@ -4,9 +4,7 @@ EAPI=7 DESCRIPTION="Codon usage bias (composition) and its statistical significance" -HOMEPAGE=" - https://bigd.big.ac.cn/tools/cat - http://cbb.big.ac.cn/Software" +HOMEPAGE="https://bigd.big.ac.cn/tools/cat" SRC_URI="ftp://download.big.ac.cn/bigd/tools/${PN}${PV}.tar.gz -> ${P}.tar.gz" LICENSE="GPL-3+" diff --git a/sci-biology/FLASH/metadata.xml b/sci-biology/FLASH/metadata.xml index 0f267b755..7dc91092f 100644 --- a/sci-biology/FLASH/metadata.xml +++ b/sci-biology/FLASH/metadata.xml @@ -10,6 +10,6 @@ <name>Gentoo Biology Project</name> </maintainer> <upstream> - <remote-id type="sourceforge">downloads</remote-id> + <remote-id type="sourceforge">flashpage</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/MaSuRCA/MaSuRCA-4.0.1.ebuild b/sci-biology/MaSuRCA/MaSuRCA-4.0.1.ebuild index 8e6d2925e..7b070e595 100644 --- a/sci-biology/MaSuRCA/MaSuRCA-4.0.1.ebuild +++ b/sci-biology/MaSuRCA/MaSuRCA-4.0.1.ebuild @@ -1,17 +1,19 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 DESCRIPTION="de Bruijn and OLC assembler for Sanger, Roche 454, Illumina, Pacbio, Nanopore" HOMEPAGE="http://www.genome.umd.edu/masurca.html http://bioinformatics.oxfordjournals.org/content/29/21/2669 - https://biorxiv.org/content/biorxiv/early/2016/07/26/066100.full.pdf" + https://github.com/alekseyzimin/masurca" SRC_URI="https://github.com/alekseyzimin/masurca/releases/download/v${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/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/SPAdes/Manifest b/sci-biology/SPAdes/Manifest index 57f4fc569..cf724a82a 100644 --- a/sci-biology/SPAdes/Manifest +++ b/sci-biology/SPAdes/Manifest @@ -1,4 +1,4 @@ -DIST SPAdes-3.15.3.tar.gz 13687286 BLAKE2B d1c2204889ecd4e95306f10ca1bc4c1243369737822ba882ed141aa203005ce5240698b421e6f9c867684567abe971afb7562b837ad5464cfd91ce572d5e7af4 SHA512 e1b454c03f1edc857b552ebca9b5f4cd842d8e23caebdf11bb0cd05cb16a45e45421a03c67a5ecb04ea6dba0f30ec2652f0bf07afded39e823563518dc8080f4 -DIST SPAdes-3.15.3_manual.html 80507 BLAKE2B 14510ed5ff2ee1b7a6643f7e39761479180a022c6bae7b1bfac7a07fdf8d5f7889e619fc8bbd6c8354aa7b775241a34b0ab14aa6bf92c0b5af2d0e1588d5c4a7 SHA512 73538e487da7056b42715ec46dacd41e8abef0e268d3a4fe2997b49d208db402367913f3a86acd9643c8ff6a9cadd6d1ff109a2bc511ffb63de059633fe3255b -DIST SPAdes-3.15.3_rnaspades_manual.html 8624 BLAKE2B b549a6cae6b02c98cae08fd5d8975210f3593c47f2b4757f19a9445a759e332229620885a6fa2f1dc0662096974548e3d0362079d12c47e6738c0261d755a2af SHA512 2d0b169efd8aa7064d59bed8ad406477c72150f23ae0438227903645071c8f66f26fe062f7dd44b584edf8ef7c709ad6c220237e68917ec23c63cfb3139666b8 -DIST SPAdes-3.15.3_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-3.15.3.ebuild b/sci-biology/SPAdes/SPAdes-3.15.5.ebuild index 002004bca..026dd0476 100644 --- a/sci-biology/SPAdes/SPAdes-3.15.3.ebuild +++ b/sci-biology/SPAdes/SPAdes-3.15.5.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_10 ) +PYTHON_COMPAT=( python3_{10..12} ) inherit python-single-r1 DESCRIPTION="De novo de Bruijn genome assembler overcoming uneven coverage" @@ -27,7 +27,13 @@ DEPEND=" ${PYTHON_DEPS} " RDEPEND="${DEPEND}" -BDEPEND="dev-util/cmake" +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 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 cb1b89168..000000000 --- a/sci-biology/Trinotate/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST Trinotate-3.2.2.tar.gz 12902856 BLAKE2B 741b5b7386c5de646a4a1f3aa4ffc7ed9c4891e64a977efc5cd482eb0cd9315fbddc1db35f20f6fbbf136e28942542f72d33c078524971968a932f5af5d6551b SHA512 9e302eee948974c647fdcc6a352b17d55f3bd1331f6d3ddc49e0fc35f5603dcc370e9c6020e7b33dcd57324a954eab2ed3e81f2e34ef83af2fd97c793f1dfc48 diff --git a/sci-biology/Trinotate/Trinotate-3.2.2.ebuild b/sci-biology/Trinotate/Trinotate-3.2.2.ebuild deleted file mode 100644 index 794de03ae..000000000 --- a/sci-biology/Trinotate/Trinotate-3.2.2.ebuild +++ /dev/null @@ -1,43 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -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 -> ${P}.tar.gz" -S="${WORKDIR}/${PN}-${PN}-v${PV}" - -LICENSE="BSD-BroadInstitute" -SLOT="0" -KEYWORDS="~amd64" - -DEPEND="" -RDEPEND="${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 -# $HMMSEARCH_BINARY = "/path/to/hmmsearch2"; - -src_install(){ - perl_set_version - dobin Trinotate - insinto /usr/share/"${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="${WORKDIR}"/net/sf/varscan diff --git a/sci-biology/abacas/abacas-1.3.1.ebuild b/sci-biology/abacas/abacas-1.3.1.ebuild index 9abddf036..c347b508b 100644 --- a/sci-biology/abacas/abacas-1.3.1.ebuild +++ b/sci-biology/abacas/abacas-1.3.1.ebuild @@ -6,8 +6,8 @@ EAPI=7 inherit optfeature DESCRIPTION="Order and orientate DNA contigs even via 6-frame protein alignments" -HOMEPAGE="http://abacas.sourceforge.net" -SRC_URI="https://downloads.sourceforge.net/project/abacas/abacas.1.3.1.pl" +HOMEPAGE="https://abacas.sourceforge.net" +SRC_URI="https://downloads.sourceforge.net/project/abacas/abacas.${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 e8caa43d1..d1e783ff1 100644 --- a/sci-biology/afni/Manifest +++ b/sci-biology/afni/Manifest @@ -1,3 +1,4 @@ -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-22.0.21.tar.gz 43934548 BLAKE2B 3efd5b7fcbbb7b98000e8de51c363ec936a691fcbd505871ff406824ba6ecd5fef358102f6dd2e4d0991b0a40589db6416c1ef14966138c5c36499d7efa3b089 SHA512 1c741e36227075bd8b4f9983510eef95528084cbc4971f9d6d028726ffc2bb211da7a74df98991538d8f6caed041633fdceb0c4366e04d6594faa0160a0e6d2b +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-20.1.16.ebuild b/sci-biology/afni/afni-20.1.16.ebuild deleted file mode 100644 index e3e16f834..000000000 --- a/sci-biology/afni/afni-20.1.16.ebuild +++ /dev/null @@ -1,73 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -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 -> ${P}.tar.gz" - -LICENSE="GPL-3+" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -RDEPEND="dev-libs/expat - media-libs/glu - media-libs/netpbm - media-libs/qhull - media-video/mpeg-tools - sci-libs/gsl - sys-devel/llvm:* - media-libs/libjpeg-turbo:0 - x11-libs/libGLw - x11-libs/libXft - x11-libs/libXi - x11-libs/libXpm - x11-libs/motif[-static-libs]" - -# x11-libs/motif[static-libs] breaks the build. -# See upstream discussion -# http://afni.nimh.nih.gov/afni/community/board/read.php?1,85348,85348#msg-85348 - -DEPEND="${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/~${EPREFIX}/usr/~g;" -i - default -} - -src_compile() { - emake -j1 all plugins suma_exec -} - -src_install() { - emake INSTALLDIR="${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/${CONFLICT}" - done -} diff --git a/sci-biology/afni/afni-20.3.03.ebuild b/sci-biology/afni/afni-20.3.03.ebuild deleted file mode 100644 index 1d9043ebb..000000000 --- a/sci-biology/afni/afni-20.3.03.ebuild +++ /dev/null @@ -1,73 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -inherit toolchain-funcs - -DESCRIPTION="An open-source environment for processing and displaying functional MRI data" -HOMEPAGE="http://afni.nimh.nih.gov/" -SRC_URI="https://github.com/afni/afni/archive/AFNI_${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="GPL-3+" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -RDEPEND="dev-libs/expat - media-libs/glu - media-libs/netpbm - media-libs/qhull - media-video/mpeg-tools - sci-libs/gsl - sys-devel/llvm:* - media-libs/libjpeg-turbo:0 - x11-libs/libGLw - x11-libs/libXft - x11-libs/libXi - x11-libs/libXpm - x11-libs/motif[-static-libs]" - -# x11-libs/motif[static-libs] breaks the build. -# See upstream discussion -# http://afni.nimh.nih.gov/afni/community/board/read.php?1,85348,85348#msg-85348 - -DEPEND="${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}/${PN}-20.1.16-python.patch" || die - find -type f -exec sed -i -e "s/-lXp //g" {} + - cp other_builds/Makefile.${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/~${EPREFIX}/usr/~g;" -i - default -} - -src_compile() { - emake -j1 all plugins suma_exec -} - -src_install() { - emake INSTALLDIR="${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/${CONFLICT}" - done -} diff --git a/sci-biology/afni/afni-22.0.21.ebuild b/sci-biology/afni/afni-22.0.21.ebuild deleted file mode 100644 index 149deede8..000000000 --- a/sci-biology/afni/afni-22.0.21.ebuild +++ /dev/null @@ -1,75 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -inherit toolchain-funcs - -DESCRIPTION="An open-source environment for processing and displaying functional MRI data" -HOMEPAGE="http://afni.nimh.nih.gov/" -SRC_URI="https://github.com/afni/afni/archive/AFNI_${PV}.tar.gz -> ${P}.tar.gz" -S="${WORKDIR}/${PN}-AFNI_${PV}/src" - -LICENSE="GPL-3+" -SLOT="0" -# SUMA error: https://ppb.chymera.eu/4223de.log -KEYWORDS="" - -RDEPEND=" - dev-libs/libf2c - dev-libs/expat - media-libs/freeglut - media-libs/glu - media-libs/netpbm - media-libs/qhull - media-video/mpeg-tools - sci-libs/gsl - sys-devel/llvm:* - media-libs/libjpeg-turbo:0 - x11-libs/libGLw - x11-libs/libXft - x11-libs/libXi - x11-libs/libXpm - x11-libs/motif -" - -DEPEND="${RDEPEND} - app-shells/tcsh -" - -BUILD="linux_fedora_19_64" -BIN_CONFLICTS=(qdelaunay whirlgif djpeg cjpeg qhull rbox count) - -src_prepare() { - # more easily applied here than via PATCHES at phase end. - eapply "${FILESDIR}/${PN}-20.1.16-python.patch" || die - find -type f -exec sed -i -e "s/-lXp //g" {} + || die - cp other_builds/Makefile.${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/~${EPREFIX}/usr/~g;" -i || die - default -} - -src_compile() { - emake -j1 all plugins suma_exec -} - -src_install() { - emake INSTALLDIR="${ED}/usr/bin" install install_plugins - emake INSTALLDIR="${ED}/usr/$(get_libdir)" install_lib - for CONFLICT in ${BIN_CONFLICTS[@]}; do - rm "${ED}/usr/bin/${CONFLICT}" || die - done -} diff --git a/sci-biology/afni/afni-24.0.04-r1.ebuild b/sci-biology/afni/afni-24.0.04-r1.ebuild new file mode 100644 index 000000000..557fbd579 --- /dev/null +++ b/sci-biology/afni/afni-24.0.04-r1.ebuild @@ -0,0 +1,110 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..12} ) + +DISTUTILS_USE_PEP517=setuptools +inherit cmake distutils-r1 toolchain-funcs + +GTS_HASH="962155a01f5a1b87bd64e3e3d880b4dbc2347ac7" +NIFTI_HASH="da476fd27f46098f37f5c9c4c1baee01e559572c" +GIFTI_HASH="d3e873d8539d9b469daf7db04093da1d7e73d4f7" + +DESCRIPTION="Advanced Normalitazion Tools for neuroimaging" +HOMEPAGE="http://stnava.github.io/ANTs/" +SRC_URI=" + https://github.com/afni/afni/archive/refs/tags/AFNI_${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/files/afni-20.1.16-python.patch b/sci-biology/afni/files/afni-20.1.16-python.patch deleted file mode 100644 index 8c3e859f5..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-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 cbb8a4299..39ec69d08 100644 --- a/sci-biology/afni/metadata.xml +++ b/sci-biology/afni/metadata.xml @@ -13,6 +13,9 @@ 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> diff --git a/sci-biology/ants/Manifest b/sci-biology/ants/Manifest index c00c77f25..ef2d97caf 100644 --- a/sci-biology/ants/Manifest +++ b/sci-biology/ants/Manifest @@ -1 +1,2 @@ -DIST ants-2.4.1.tar.gz 2473738 BLAKE2B 9abe2ade15bd8348452a23e15d8c862771ca2c8f971c44f185febfb1ee725b1ceb7e89359c8dfee31bd9c4087f10104831fe56bd1528ea7f5a81d52c1a4a4709 SHA512 533ca8adb934e8fe4e24425b3f8a9a8f0b67999d9593f8c8842e0298087d5bc58f65d1fcbfe78ac7dc17d0e786badc4a65bbde80d82d21c277ee6c1b3af7eae4 +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-2.4.1-r1.ebuild b/sci-biology/ants/ants-2.4.3.ebuild index 70d5d8873..2dfa2a56d 100644 --- a/sci-biology/ants/ants-2.4.1-r1.ebuild +++ b/sci-biology/ants/ants-2.4.3.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=8 @@ -10,40 +10,49 @@ MY_PN="ANTs" DESCRIPTION="Advanced Normalitazion Tools for neuroimaging" HOMEPAGE="https://stnava.github.io/ANTs/" -SRC_URI="https://github.com/ANTsX/ANTs/archive/v${PV}.tar.gz -> ${P}.tar.gz" +SRC_URI=" + https://github.com/ANTsX/ANTs/archive/v${PV}.tar.gz -> ${P}.tar.gz + test? ( + https://resources.chymera.eu/distfiles/ants_testdata-${PV}.tar.xz + ) +" S="${WORKDIR}/${MY_PN}-${PV}" SLOT="0" LICENSE="BSD" KEYWORDS="~amd64 ~x86" IUSE="test vtk" -RESTRICT="test" +RESTRICT="!test? ( test )" DEPEND=" - !vtk? ( =sci-libs/itk-5.2*[fftw,-vtkglue] ) + !vtk? ( =sci-libs/itk-5.3*[fftw,-vtkglue] ) vtk? ( - =sci-libs/itk-5.2*[fftw,vtkglue] - =sci-libs/vtk-9.1* + =sci-libs/itk-5.3*[fftw,vtkglue] + =sci-libs/vtk-9.2* ) " RDEPEND="${DEPEND}" -PATCHES=( - "${FILESDIR}/${P}-fix-compile.patch" -) +src_unpack() { + default + if use test; then + 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_USE_SYSTEM_FFTW=ON - -DITK_DIR="${EPREFIX}/usr/include/ITK-5.2/" + -DITK_DIR="${EPREFIX}/usr/include/ITK-5.3/" -DBUILD_TESTING="$(usex test ON OFF)" -DUSE_VTK=$(usex vtk ON OFF) -DUSE_SYSTEM_VTK=$(usex vtk ON OFF) ) use vtk && mycmakeargs+=( - -DVTK_DIR="${EPREFIX}/usr/include/vtk-9.1/" + -DVTK_DIR="${EPREFIX}/usr/include/vtk-9.2/" ) cmake_src_configure } diff --git a/sci-biology/ants/files/ants-2.4.1-fix-compile.patch b/sci-biology/ants/files/ants-2.4.1-fix-compile.patch deleted file mode 100644 index bd7eecbcf..000000000 --- a/sci-biology/ants/files/ants-2.4.1-fix-compile.patch +++ /dev/null @@ -1,13 +0,0 @@ -diff --git a/Examples/PrintHeader.cxx b/Examples/PrintHeader.cxx -index d1e7586..048d934 100644 ---- a/Examples/PrintHeader.cxx -+++ b/Examples/PrintHeader.cxx -@@ -281,7 +281,7 @@ PrintHeader(int argc, char * argv[]) - // Get the metadata as a generic object - string key = itMeta->first, v_string; - itk::SpatialOrientation::ValidCoordinateOrientationFlags v_oflags = -- itk::SpatialOrientationEnums::ValidCoordinateOrientations::ITK_COORDINATE_ORIENTATION_INVALID; -+ itk::SpatialOrientation::ITK_COORDINATE_ORIENTATION_INVALID; - - if (itk::ExposeMetaData<string>(mdd, key, v_string)) - { diff --git a/sci-biology/bambus/bambus-2.33-r2.ebuild b/sci-biology/bambus/bambus-2.33-r2.ebuild index 475c7f0b1..1cb7aad1b 100644 --- a/sci-biology/bambus/bambus-2.33-r2.ebuild +++ b/sci-biology/bambus/bambus-2.33-r2.ebuild @@ -11,7 +11,7 @@ HOMEPAGE=" https://sourceforge.net/projects/amos/files/bambus" SRC_URI=" https://sourceforge.net/projects/amos/files/bambus/${PV}/${P}.tar.gz - http://mira-assembler.sourceforge.net/docs/scaffolding_MIRA_BAMBUS.pdf" # no https + https://mira-assembler.sourceforge.net/docs/scaffolding_MIRA_BAMBUS.pdf" LICENSE="Artistic" SLOT="0" diff --git a/sci-biology/barrnap/barrnap-0.9.ebuild b/sci-biology/barrnap/barrnap-0.9.ebuild index 999f065c1..6b7176e14 100644 --- a/sci-biology/barrnap/barrnap-0.9.ebuild +++ b/sci-biology/barrnap/barrnap-0.9.ebuild @@ -6,7 +6,7 @@ EAPI=7 inherit perl-module DESCRIPTION="Predict Bacterial and Archaeal rRNA genes and output in GFF3 format" -HOMEPAGE="https://vicbioinformatics.com/software.barrnap.shtml" +HOMEPAGE="https://github.com/tseemann/barrnap" SRC_URI="https://github.com/tseemann/barrnap/archive/${PV}.tar.gz -> ${P}.tar.gz" LICENSE="GPL-3" diff --git a/sci-biology/behaviopy/Manifest b/sci-biology/behaviopy/Manifest deleted file mode 100644 index 916b93320..000000000 --- a/sci-biology/behaviopy/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST behaviopy-0.2.tar.gz 36812 BLAKE2B 099f245027ddbbd38478bc48df1746e25e5a2b8d32a381f3352cb4c1339f9aa7a101ff0a3b797bceb543db1656044470911dd2e3addd44f5d2cd8d661e20a0cf SHA512 b7939ac3dcbbc445b5459a2bb96e413ca71e720c14e441d3d9864422be13c6b78178c5a1006f851d141c70a3f1ab9635ea636841610e0f210ca3f35a0f12f9bc diff --git a/sci-biology/behaviopy/behaviopy-0.2.ebuild b/sci-biology/behaviopy/behaviopy-0.2.ebuild deleted file mode 100644 index dc875e7a5..000000000 --- a/sci-biology/behaviopy/behaviopy-0.2.ebuild +++ /dev/null @@ -1,42 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_10 ) - -inherit distutils-r1 - -DESCRIPTION="Neuroimaging tools for Python" -HOMEPAGE="https://github.com/TheChymera/behaviopy" -SRC_URI="https://github.com/TheChymera/behaviopy/archive/${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="GPL-3" -SLOT="0" -IUSE="evaluation" -KEYWORDS="~amd64 ~x86" - -RDEPEND=" - dev-python/matplotlib[${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}] -" - -python_prepare_all() { - if ! use evaluation; then - rm behaviopy/evaluation.py || die - fi - distutils-r1_python_prepare_all -} - -python_test() { - cd behaviopy/examples || die - 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 index ab53258d3..283f2cedf 100644 --- a/sci-biology/bidsschematools/Manifest +++ b/sci-biology/bidsschematools/Manifest @@ -1,3 +1,3 @@ -DIST bidsschematools-0.4.0.tar.gz 1158341 BLAKE2B a47ad610936e8bb9f91ade6f234f258535364d5cd3c188544dbb25f2540138596455656a25f167b1b6417cd896e15b4e1baf140999d0dbccdfa01432b2e88783 SHA512 c42dd337a0f2402de2c4794b85382b0e422ffbd9dbc814e943f32bc95cb1d7d2bc31dc40aeef6fd792d14ec09617de289ecdb794c0d22f1154f23e2f04bd5fdd -DIST bidsschematools-0.5.1.tar.gz 1159308 BLAKE2B a53355b24e87ea7008fa64ca4f7e71c7bf29effc52f4aa3f855af633ce83817d5551eead4224d39f8cd46693dc48a7d9325a7ad8698e159b468e902982c5a940 SHA512 f1d9ab6b37c8fd4fd6a6aa821ef718c1af7f3d453d44c2c76c104f5601d40e5a328b0332255a591d8431e8c0ca3406dccd852c6c1fc8d832657b27a6b0076adc 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 index 13aabaa37..96b6cd57f 100644 --- a/sci-biology/bidsschematools/bidsschematools-0.6.0.ebuild +++ b/sci-biology/bidsschematools/bidsschematools-0.6.0.ebuild @@ -1,4 +1,4 @@ -# Copyright 2022 Gentoo Authors +# Copyright 2022-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 @@ -6,11 +6,10 @@ EAPI=8 DISTUTILS_USE_PEP517=setuptools PYTHON_COMPAT=( python3_{10..11} ) -inherit distutils-r1 +inherit distutils-r1 pypi DESCRIPTION="A Python library for working with the BIDS schema" HOMEPAGE="https://github.com/bids-standard/bids-specification" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" LICENSE="MIT" SLOT="0" diff --git a/sci-biology/bidsschematools/bidsschematools-0.4.0.ebuild b/sci-biology/bidsschematools/bidsschematools-0.7.0.ebuild index 0e62efa42..98b773243 100644 --- a/sci-biology/bidsschematools/bidsschematools-0.4.0.ebuild +++ b/sci-biology/bidsschematools/bidsschematools-0.7.0.ebuild @@ -1,4 +1,4 @@ -# Copyright 2022 Gentoo Authors +# Copyright 2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 @@ -6,20 +6,23 @@ EAPI=8 DISTUTILS_USE_PEP517=setuptools PYTHON_COMPAT=( python3_{10..11} ) -inherit distutils-r1 +inherit distutils-r1 pypi DESCRIPTION="A Python library for working with the BIDS schema" HOMEPAGE="https://github.com/bids-standard/bids-specification" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" LICENSE="MIT" SLOT="0" KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" IUSE="render" +# Documented upstream: +# https://github.com/conda-forge/bidsschematools-feedstock/pull/2 +#RESTRICT="test" RDEPEND=" dev-python/pyyaml[${PYTHON_USEDEP}] render? ( + dev-python/markdown-it-py[${PYTHON_USEDEP}] dev-python/pandas[${PYTHON_USEDEP}] dev-python/tabulate[${PYTHON_USEDEP}] ) @@ -28,6 +31,12 @@ DEPEND="" distutils_enable_tests pytest +# Reported upstream: +# https://github.com/bids-standard/bids-specification/issues/1500 +EPYTEST_DESELECT=( + "bidsschematools/tests/test_validator.py::test_bids_datasets[ds000248]" +) + src_prepare() { if ! use render; then rm "${S}/bidsschematools/render.py" diff --git a/sci-biology/bidsschematools/bidsschematools-0.5.1-r1.ebuild b/sci-biology/bidsschematools/bidsschematools-0.7.1.ebuild index 13aabaa37..b5b12165d 100644 --- a/sci-biology/bidsschematools/bidsschematools-0.5.1-r1.ebuild +++ b/sci-biology/bidsschematools/bidsschematools-0.7.1.ebuild @@ -1,4 +1,4 @@ -# Copyright 2022 Gentoo Authors +# Copyright 2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 @@ -6,11 +6,10 @@ EAPI=8 DISTUTILS_USE_PEP517=setuptools PYTHON_COMPAT=( python3_{10..11} ) -inherit distutils-r1 +inherit distutils-r1 pypi DESCRIPTION="A Python library for working with the BIDS schema" HOMEPAGE="https://github.com/bids-standard/bids-specification" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" LICENSE="MIT" SLOT="0" diff --git a/sci-biology/blasr/Manifest b/sci-biology/blasr/Manifest deleted file mode 100644 index 7819d5a37..000000000 --- a/sci-biology/blasr/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST blasr-5.3.5.tar.gz 2709986 BLAKE2B 48a8d12e4a47159c00d5febab4222dec5e2f4e5ce4d7a481243b4b62e0ba693eb9e1aa2a11b5de36606ec977db3947178cfdd0a1a09ccfea213e1a1567402e74 SHA512 79155f29076e4a9fe1d66d9e8310d38d3b6690fe1959be923627607ed4d7dfe97c020ff9f9134a3cffcb8e1cd5eb1b3a861d10cb476f9c3866c87e85e6ae93e7 diff --git a/sci-biology/blasr/blasr-5.3.5.ebuild b/sci-biology/blasr/blasr-5.3.5.ebuild deleted file mode 100644 index 85e4ea66d..000000000 --- a/sci-biology/blasr/blasr-5.3.5.ebuild +++ /dev/null @@ -1,24 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -inherit meson - -DESCRIPTION="The PacBio long read aligner" -HOMEPAGE="http://www.smrtcommunity.com/SMRT-Analysis/Algorithms/BLASR" -SRC_URI="https://github.com/PacificBiosciences/blasr/archive/${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="blasr" -SLOT="0" -KEYWORDS="~amd64" - -BDEPEND=" - dev-util/cmake - virtual/pkgconfig -" -DEPEND=" - sci-biology/libblasr - dev-libs/boost:= -" -RDEPEND="${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 a94c2be48..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 1999-2022 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 DISTUTILS_USE_SETUPTOOLS="rdepend" -PYTHON_COMPAT=( python3_10 ) +PYTHON_COMPAT=( python3_{10..11} ) inherit distutils-r1 diff --git a/sci-biology/bx-python/metadata.xml b/sci-biology/bx-python/metadata.xml index 80a22b44a..f1fc4360e 100644 --- a/sci-biology/bx-python/metadata.xml +++ b/sci-biology/bx-python/metadata.xml @@ -10,8 +10,7 @@ <name>Gentoo Biology Project</name> </maintainer> <upstream> - <remote-id type="bitbucket">james_taylor/bx-python</remote-id> - <remote-id type="pypi">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/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 987fb99f2..000000000 --- a/sci-biology/canu/canu-2.1.1.ebuild +++ /dev/null @@ -1,70 +0,0 @@ -# Copyright 1999-2022 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="${RDEPEND} - >=virtual/jdk-1.8:* - dev-java/ant-core -" - -# Detected file collision(s): -# * sci-biology/wgs-assembler-8.3_rc2:0::science -# * /usr/bin/bogart -# * /usr/bin/bogus -# * /usr/bin/fastqAnalyze -# * /usr/bin/fastqSample -# * /usr/bin/fastqSimulate -# * /usr/bin/fastqSimulate-sort -# * /usr/bin/meryl -# * /usr/bin/overlapInCore -# * /usr/bin/utgcns - -# Perl 5.12.0, or File::Path 2.08 -# Java SE 8 -# https://github.com/marbl/MHAP uses Apache maven - -# contains bundled mhap-2.1.3.jar, kmer, pbutgcns, FALCON - -src_compile(){ - cd src || die - emake -} - -src_install(){ - # installs - # /usr/bin - # /usr/lib/libcanu.a - # /usr/lib64/perl5/vendor_perl/5.28.0/lib/site_perl/canu - # /usr/share/java/classes/mhap-2.1.3.jar - rm -rf Linux-amd64/obj - insinto /usr - doins -r Linux-amd64/{bin,share} - insinto /usr/$(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/canu/metadata.xml b/sci-biology/canu/metadata.xml deleted file mode 100644 index 138cb7705..000000000 --- a/sci-biology/canu/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/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 162a03129..000000000 --- a/sci-biology/chiron/chiron-0.6.1.1.ebuild +++ /dev/null @@ -1,29 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{8..9} ) -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/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/dcmstack/Manifest b/sci-biology/dcmstack/Manifest index c542a92a3..ab8414c4e 100644 --- a/sci-biology/dcmstack/Manifest +++ b/sci-biology/dcmstack/Manifest @@ -1,2 +1 @@ -DIST dcmstack-0.8-pytest.patch 90212 BLAKE2B dd2ddff15b590a19f991ab07a00cdb4facb1d18a9dc3556e85094e95dd8e31a0c49c801a1bc9dca040902d120c3a608c07ebd8f1fab1a350e6ffe0c2f0f52176 SHA512 b02108d77a10fe0e318621cf4e8babdc64b70a210700b286e972c5084a4fbcd44c6d750de77f547881c2d51a844efb10cc7be03e80b48e78d6cbdd99c4abf2f6 -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 8ec65b7b8..d207526c0 100644 --- a/sci-biology/dcmstack/dcmstack-0.8.ebuild +++ b/sci-biology/dcmstack/dcmstack-0.9.ebuild @@ -1,19 +1,16 @@ -# 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_10 ) +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 -> ${P}.tar.gz - https://resources.chymera.eu/patches/dcmstack-0.8-pytest.patch -" -EGIT_REPO_URI="https://github.com/moloney/dcmstack" +SRC_URI="https://github.com/moloney/dcmstack/archive/v${PV}.tar.gz -> ${P}.gh.tar.gz" LICENSE="MIT" SLOT="0" @@ -25,6 +22,4 @@ RDEPEND=" sci-libs/pydicom[${PYTHON_USEDEP}] " -PATCHES=( "${DISTDIR}/${P}-pytest.patch" ) - distutils_enable_tests pytest 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/deeptools-3.5.0.ebuild b/sci-biology/deeptools/deeptools-3.5.0.ebuild index fc48e2224..7c2eaa739 100644 --- a/sci-biology/deeptools/deeptools-3.5.0.ebuild +++ b/sci-biology/deeptools/deeptools-3.5.0.ebuild @@ -3,7 +3,8 @@ EAPI=8 -PYTHON_COMPAT=( python3_{10..10} ) +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 -> ${P}.tar LICENSE="BSD" SLOT="0" -KEYWORDS="~amd64 ~x86" +KEYWORDS="~amd64" # TODO: fix this RESTRICT="test" @@ -32,5 +33,5 @@ RDEPEND=" S="${WORKDIR}/deepTools-${PV}" -distutils_enable_sphinx docs dev-python/sphinx_rtd_theme dev-python/sphinx-argparse +distutils_enable_sphinx docs dev-python/sphinx-rtd-theme dev-python/sphinx-argparse #distutils_enable_tests nose diff --git a/sci-biology/deeptools/deeptools-3.5.1.ebuild b/sci-biology/deeptools/deeptools-3.5.1.ebuild index fc48e2224..7c2eaa739 100644 --- a/sci-biology/deeptools/deeptools-3.5.1.ebuild +++ b/sci-biology/deeptools/deeptools-3.5.1.ebuild @@ -3,7 +3,8 @@ EAPI=8 -PYTHON_COMPAT=( python3_{10..10} ) +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..11} ) inherit distutils-r1 @@ -13,7 +14,7 @@ SRC_URI="https://github.com/deeptools/deepTools/archive/${PV}.tar.gz -> ${P}.tar LICENSE="BSD" SLOT="0" -KEYWORDS="~amd64 ~x86" +KEYWORDS="~amd64" # TODO: fix this RESTRICT="test" @@ -32,5 +33,5 @@ RDEPEND=" S="${WORKDIR}/deepTools-${PV}" -distutils_enable_sphinx docs dev-python/sphinx_rtd_theme dev-python/sphinx-argparse +distutils_enable_sphinx docs dev-python/sphinx-rtd-theme dev-python/sphinx-argparse #distutils_enable_tests nose diff --git a/sci-biology/drlfom_bidsdata/drlfom_bidsdata-1.1.ebuild b/sci-biology/drlfom_bidsdata/drlfom_bidsdata-1.1.ebuild index 227aafd54..8ddd4007e 100644 --- a/sci-biology/drlfom_bidsdata/drlfom_bidsdata-1.1.ebuild +++ b/sci-biology/drlfom_bidsdata/drlfom_bidsdata-1.1.ebuild @@ -1,12 +1,12 @@ -# Copyright 1999-2022 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 inherit check-reqs DESCRIPTION="BIDS data files released with the DRLFOM publication" -HOMEPAGE="http://www.aic-fmi.ethz.ch/" +HOMEPAGE="https://chymera.eu/docs/focus/open-science/" SRC_URI=" https://zenodo.org/record/3598424/files/${P}.tar.xz " @@ -15,9 +15,6 @@ 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/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/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-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 ${OBJS} mist/mist.o mist/mist || echo "CLEAN could not locate some files scheduled for deletion." - - .PHONY: all clean installdata --- -2.24.1 - diff --git a/sci-biology/fsl/fsl-6.0.4.ebuild b/sci-biology/fsl/fsl-6.0.4.ebuild index cd91cf192..6e5d6e779 100644 --- a/sci-biology/fsl/fsl-6.0.4.ebuild +++ b/sci-biology/fsl/fsl-6.0.4.ebuild @@ -151,8 +151,8 @@ src_compile() { # define the default build system to match upstream official standard # -> individual projects may overwrite the '-std=' flag - export ANSI_CFLAGS="-std=c99" - export ANSI_CXXFLAGS="-std=c++98" + export ANSI_CFLAGS="-std=c11" + export ANSI_CXXFLAGS="-std=c++11" export USERLDFLAGS="${LDFLAGS}" export USERCFLAGS="${CFLAGS}" diff --git a/sci-biology/gemini/Manifest b/sci-biology/gemini/Manifest deleted file mode 100644 index e85205a03..000000000 --- a/sci-biology/gemini/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST gemini-0.30.2.tar.gz 1629220 BLAKE2B cbcbcb367817550d39f5385617fa577895d13a084ef2f7e8be2aa3895f9f22e9df2d453673993962819cdfa1705b1a8fa5f7f899d836f055eff753a7f6c5ae2f SHA512 08f88cc54631bc6f9fca72eaa996457dff1f19e4a5791b5ce11a2c2983e3ca23101aa572d2dcbd2fb1340d4e3ed1ea87d99e88530b25f2bfc533f879ac584b6d diff --git a/sci-biology/gemini/gemini-0.30.2.ebuild b/sci-biology/gemini/gemini-0.30.2.ebuild deleted file mode 100644 index 25ec22946..000000000 --- a/sci-biology/gemini/gemini-0.30.2.ebuild +++ /dev/null @@ -1,45 +0,0 @@ -# Copyright 1999-2023 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{10..10} ) - -inherit distutils-r1 - -DESCRIPTION="Lightweight VCF to DB framework for disease and population genetics" -HOMEPAGE="https://github.com/arq5x/gemini - http://gemini.readthedocs.org/en/latest" -SRC_URI="mirror://pypi/${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 $@ - - # C/C++ linker - diff --git a/sci-biology/gffutils/Manifest b/sci-biology/gffutils/Manifest index a697f0784..e8b006cbf 100644 --- a/sci-biology/gffutils/Manifest +++ b/sci-biology/gffutils/Manifest @@ -1,2 +1 @@ -DIST gffutils-0.10.1.tar.gz 1636628 BLAKE2B ca539bdcf2a2e199d264194e23c3d1b52e1f4b141d2a43a1346024c008020ff531d5b642c63bd4c3a34cd97de2a399975eea430163f16218f5a1d671521e69b6 SHA512 21f56e013abdf1368756db97afcea0be6d0edc56cb0636e9e796603959570c7c3ba0cecf1bf90a69ab7afd2c4c831d3d42b92960a8c34f9b645be7e47d42190a -DIST gffutils-0.8.7.1.tar.gz 1541112 BLAKE2B 65676cf0b910ad0fee478315409dba808a13d11922d0ab254694939ebd01f10b62c2237ae517d941999c6cf9bcb08d903bde8b9055bcf7a67116e14439ec4cca SHA512 4739dd402963d402f34a5e3da9cca7ba9586dcbbe62efbad89bf85c5dbb0feff0e260eea20563340911756e6817289c1556c261ef973a61f4e66e50efdfc8aa8 +DIST gffutils-0.11.1.tar.gz 1646787 BLAKE2B 96e573cf366844c8a348aff062362aeaea1a46360c74ae75a2d8d730d37cd69f0e6c658d1d0f348ca8f8e8c49d9a7c923c52619341e8d2dabd92a329fb43b677 SHA512 1844e9d7626a800549def2ba09b4d97e60c8a1a0fce2da60d7841cf4c4347da50aea850e8c1a67b07de08d4e6cf737b0d5c2bf8eb5fc87900427866282e82bdb diff --git a/sci-biology/gffutils/gffutils-0.10.1.ebuild b/sci-biology/gffutils/gffutils-0.11.1.ebuild index c7a437264..8ee8fd4b5 100644 --- a/sci-biology/gffutils/gffutils-0.10.1.ebuild +++ b/sci-biology/gffutils/gffutils-0.11.1.ebuild @@ -1,19 +1,23 @@ -# Copyright 1999-2020 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 -PYTHON_COMPAT=( python3_{7..9} ) +PYTHON_COMPAT=( python3_{10..11} ) inherit distutils-r1 DESCRIPTION="GFF and GTF file manipulation and interconversion" -HOMEPAGE="https://pythonhosted.org/gffutils/" +HOMEPAGE="https://gffutils.readthedocs.io/en/latest/" SRC_URI="https://github.com/daler/gffutils/archive/v${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 d50ebf927..021929bad 100644 --- a/sci-biology/irsabi_bidsdata/irsabi_bidsdata-1.4.ebuild +++ b/sci-biology/irsabi_bidsdata/irsabi_bidsdata-1.4.ebuild @@ -6,7 +6,7 @@ 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=" 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}/${P}.tar.gz" # older version is hidden in trinityrnaseq_r20140413p1/trinity-plugins/jellyfish-1.1.11 diff --git a/sci-biology/jellyfish/metadata.xml b/sci-biology/jellyfish/metadata.xml index 138cb7705..f2c1cd819 100644 --- a/sci-biology/jellyfish/metadata.xml +++ b/sci-biology/jellyfish/metadata.xml @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">gmarcais/Jellyfish</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/jtreeview-bin/jtreeview-bin-1.2.0.ebuild b/sci-biology/jtreeview-bin/jtreeview-bin-1.2.0.ebuild index d146efd5a..63ec84d2f 100644 --- a/sci-biology/jtreeview-bin/jtreeview-bin-1.2.0.ebuild +++ b/sci-biology/jtreeview-bin/jtreeview-bin-1.2.0.ebuild @@ -8,7 +8,7 @@ inherit java-pkg-2 java-ant-2 perl-module S="${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 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="${DEPEND}" diff --git a/sci-biology/kraken/Manifest b/sci-biology/kraken/Manifest deleted file mode 100644 index bb9fb5722..000000000 --- a/sci-biology/kraken/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -DIST kraken-1.1.1.tar.gz 76541 BLAKE2B 74a302196c9e40757981094838a4a31b24f803ce49941b11be955f7fafc1f89a0e63ab2d8661a7c099c82058959744206c057d047c852693c80df627efa66ba8 SHA512 9f4897d7738b8aed2839581b4f629eff9229ce8333e2a99aa0d2a90fee34036a9f8dd89b4aecbdaf46b785b7d1080b3a014cf89f88efa4d49acf1d36638dedcb -DIST kraken-2.1.1.tar.gz 193878 BLAKE2B d5494038f715e0bb9bd7325a7a0f5430ff3062b0589f0cbd154d671a98aadbd85ce3334f7f3c7844b6becaafdc06889893f427d2da76db71bca71cb8dd7073a5 SHA512 3b5c24955deff63d23017ee5e798648ebd2319a1ead77e85d285b6a1735d38155799f5988c6d1c69121bd7902dde1aaa03782a7d72b841b74c93e314f8a81bfe diff --git a/sci-biology/kraken/kraken-1.1.1-r2.ebuild b/sci-biology/kraken/kraken-1.1.1-r2.ebuild deleted file mode 100644 index 3dd599b83..000000000 --- a/sci-biology/kraken/kraken-1.1.1-r2.ebuild +++ /dev/null @@ -1,51 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit perl-functions - -DESCRIPTION="Detect sequencing project contaminants by mapping reads to taxonomic groups" -HOMEPAGE="https://ccb.jhu.edu/software/kraken" -SRC_URI="https://github.com/DerrickWood/kraken/archive/v${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/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${PV}.tar.gz" LICENSE="Artistic" diff --git a/sci-biology/mappy/Manifest b/sci-biology/mappy/Manifest index c39d0ea60..ff114e6ea 100644 --- a/sci-biology/mappy/Manifest +++ b/sci-biology/mappy/Manifest @@ -1 +1,2 @@ DIST mappy-2.24.tar.gz 140859 BLAKE2B af8ecf8f00c33951b2c7e81bec1e45fe39b7b41da1692fc8c4804b3ad5465320f453e2d53f771c09ce88fa681ad60c0c3706334ace8a682eee8b6f4ebccb02fc SHA512 5500b76ffb0f530aa8f1433c01f1805f5b95e329445ab103847e6ec6e0977a54e5c0dabe405869c7dd8d9103646db0b3cff0ef13b79d7021752ed266002a1dd4 +DIST mappy-2.26.tar.gz 135105 BLAKE2B 26c4c94eae3b719cfaadf2fe31a84faeaef4894b8b8c9ad6bbba46dbb17f609c62c61ecfd42e3be07a7eace38545d029ab03d1fee611868ac6839b3d3362698d SHA512 75949b705561455c317713bfb4bca2de24368881e6c0bb3bf2d11841db9f9e792c7eef0e46f00a7b27e38fe143db5b00be5f281fe058dca32130b745057dcb75 diff --git a/sci-biology/mappy/mappy-2.24.ebuild b/sci-biology/mappy/mappy-2.24.ebuild index f8d964df4..0fa703188 100644 --- a/sci-biology/mappy/mappy-2.24.ebuild +++ b/sci-biology/mappy/mappy-2.24.ebuild @@ -1,15 +1,15 @@ -# Copyright 1999-2022 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 -PYTHON_COMPAT=( python3_10 ) +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..11} ) -inherit distutils-r1 +inherit distutils-r1 pypi DESCRIPTION="Minimap2 python binding" HOMEPAGE="https://github.com/haotianteng/chiron" -SRC_URI="mirror://pypi/${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/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 0709fb65d..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://resources.chymera.eu/distfiles/${P}.tar.xz - hires? ( http://resources.chymera.eu/distfiles/${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 79c042a2a..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://resources.chymera.eu/distfiles/${P}.tar.xz - hires? ( http://resources.chymera.eu/distfiles/${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/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/multiqc/metadata.xml b/sci-biology/multiqc/metadata.xml new file mode 100644 index 000000000..09bd2b6e6 --- /dev/null +++ b/sci-biology/multiqc/metadata.xml @@ -0,0 +1,12 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>mschu.dev@gmail.com</email> + <name>Michael Schubert</name> + </maintainer> + <upstream> + <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 $(NCBI_C_ncbi)
--xblast includes blast
-+xblast needs blast
- xblast needs xalgoblastdbindex
- xblast needs xalgodustmask
- xblast needs xalgowinmask
diff --git a/sci-biology/ncbi-blast+/metadata.xml b/sci-biology/ncbi-blast+/metadata.xml deleted file mode 100644 index 93556eaa7..000000000 --- a/sci-biology/ncbi-blast+/metadata.xml +++ /dev/null @@ -1,23 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <use> - <flag name="boost">Undocumented USE</flag> - <flag name="cppunit">Undocumented USE</flag> - <flag name="freetype">Undocumented USE</flag> - <flag name="mesa">Undocumented USE</flag> - <flag name="muparser">Undocumented USE</flag> - <flag name="sablotron">Undocumented USE</flag> - <flag name="xerces">Undocumented USE</flag> - <flag name="xalan">Undocumented USE</flag> - <flag name="xslt">Undocumented USE</flag> - </use> -</pkgmetadata> diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.11.0.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.11.0.ebuild deleted file mode 100644 index 527acfadf..000000000 --- a/sci-biology/ncbi-blast+/ncbi-blast+-2.11.0.ebuild +++ /dev/null @@ -1,360 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7,8,9} ) - -inherit python-single-r1 toolchain-funcs - -MY_P="ncbi-blast-${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++ - 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? ( ${PYTHON_DEPS} ) - cppunit? ( dev-util/cppunit ) - icu? ( dev-libs/icu ) - expat? ( dev-libs/expat ) - sablotron? ( app-text/sablotron ) - xml? ( dev-libs/libxml2 ) - xslt? ( dev-libs/libxslt ) - xerces? ( dev-libs/xerces-c ) - xalan? ( dev-libs/xalan-c ) - muparser? ( dev-cpp/muParser ) - hdf5? ( sci-libs/hdf5[cxx] ) - gif? ( media-libs/giflib ) - jpeg? ( media-libs/libjpeg-turbo:0= ) - png? ( media-libs/libpng:0= ) - tiff? ( media-libs/tiff:0= ) - xpm? ( x11-libs/libXpm ) - dev-libs/lzo - app-arch/bzip2 - dev-libs/libpcre - dev-db/lmdb" -# USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC OEChem sge -# Intentionally omitted USE flags: -# ftds? ( dev-db/freetds ) # support for outside FreeTDS installations is currently broken. -# The default (heavily patched) embedded copy should work, or you can -# leave it off altogether -- the only public apps that make use of it are -# samples and tests, since NCBI's database servers are of course firewalled. - -# seems muParser is required, also glew is required. configure exits otherwise if these are explicitly passed to it (due to USE flag enabled) - -RDEPEND="${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 e90652f38..000000000 --- a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild +++ /dev/null @@ -1,350 +0,0 @@ -# Copyright 1999-2022 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++ - 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? ( media-libs/libjpeg-turbo: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 ddeeac07d..000000000 --- a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild +++ /dev/null @@ -1,350 +0,0 @@ -# Copyright 1999-2022 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++ - 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? ( media-libs/libjpeg-turbo: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 976ea3804..000000000 --- a/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild +++ /dev/null @@ -1,355 +0,0 @@ -# Copyright 1999-2022 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++ - 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? ( media-libs/libjpeg-turbo: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 527acfadf..000000000 --- a/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild +++ /dev/null @@ -1,360 +0,0 @@ -# Copyright 1999-2022 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++ - 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? ( ${PYTHON_DEPS} ) - cppunit? ( dev-util/cppunit ) - icu? ( dev-libs/icu ) - expat? ( dev-libs/expat ) - sablotron? ( app-text/sablotron ) - xml? ( dev-libs/libxml2 ) - xslt? ( dev-libs/libxslt ) - xerces? ( dev-libs/xerces-c ) - xalan? ( dev-libs/xalan-c ) - muparser? ( dev-cpp/muParser ) - hdf5? ( sci-libs/hdf5[cxx] ) - gif? ( media-libs/giflib ) - jpeg? ( media-libs/libjpeg-turbo:0= ) - png? ( media-libs/libpng:0= ) - tiff? ( media-libs/tiff:0= ) - xpm? ( x11-libs/libXpm ) - dev-libs/lzo - app-arch/bzip2 - dev-libs/libpcre - dev-db/lmdb" -# USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC OEChem sge -# Intentionally omitted USE flags: -# ftds? ( dev-db/freetds ) # support for outside FreeTDS installations is currently broken. -# The default (heavily patched) embedded copy should work, or you can -# leave it off altogether -- the only public apps that make use of it are -# samples and tests, since NCBI's database servers are of course firewalled. - -# seems muParser is required, also glew is required. configure exits otherwise if these are explicitly passed to it (due to USE flag enabled) - -RDEPEND="${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 $FAST_LDFLAGS" -+ fi - fi - fi - diff --git a/sci-biology/ncbi-tools++/metadata.xml b/sci-biology/ncbi-tools++/metadata.xml deleted file mode 100644 index fbf79d9b7..000000000 --- a/sci-biology/ncbi-tools++/metadata.xml +++ /dev/null @@ -1,19 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <use> - <flag name="boost">Undocumented USE</flag> - <flag name="cppunit">Undocumented USE</flag> - <flag name="freetype">Undocumented USE</flag> - <flag name="mesa">Undocumented USE</flag> - <flag name="muparser">Undocumented USE</flag> - <flag name="sablotron">Undocumented USE</flag> - <flag name="xerces">Undocumented USE</flag> - <flag name="xalan">Undocumented USE</flag> - <flag name="xslt">Undocumented USE</flag> - </use> -</pkgmetadata> diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild deleted file mode 100644 index 009085d15..000000000 --- a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild +++ /dev/null @@ -1,364 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit toolchain-funcs - -MY_TAG="Jun_15_2010" -MY_Y="${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:= - 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? ( media-libs/libjpeg-turbo: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 604c9c638..000000000 --- a/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild +++ /dev/null @@ -1,383 +0,0 @@ -# Copyright 1999-2022 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:= - 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? ( ${PYTHON_DEPS} ) - cppunit? ( dev-util/cppunit ) - icu? ( dev-libs/icu ) - expat? ( dev-libs/expat ) - sablotron? ( app-text/sablotron ) - xml? ( dev-libs/libxml2 ) - xslt? ( dev-libs/libxslt ) - xerces? ( dev-libs/xerces-c ) - xalan? ( dev-libs/xalan-c ) - muparser? ( dev-cpp/muParser ) - hdf5? ( sci-libs/hdf5[cxx] ) - gif? ( media-libs/giflib ) - jpeg? ( media-libs/libjpeg-turbo:0= ) - png? ( media-libs/libpng:0= ) - tiff? ( media-libs/tiff:0= ) - xpm? ( x11-libs/libXpm ) - dev-libs/lzo - app-arch/bzip2 - dev-libs/libpcre" -# USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC OEChem sge -# Intentionally omitted USE flags: -# ftds? ( dev-db/freetds ) # support for outside FreeTDS installations is currently broken. -# The default (heavily patched) embedded copy should work, or you can -# leave it off altogether -- the only public apps that make use of it are -# samples and tests, since NCBI's database servers are of course firewalled. - -# seems muParser is required, also glew is required. configure exits otherwise if these are explicitly passed to it (due to USE flag enabled) - -RDEPEND="${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 4d0d6363e..000000000 --- a/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild +++ /dev/null @@ -1,388 +0,0 @@ -# Copyright 1999-2022 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:= - 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? ( ${PYTHON_DEPS} ) - cppunit? ( dev-util/cppunit ) - icu? ( dev-libs/icu ) - expat? ( dev-libs/expat ) - sablotron? ( app-text/sablotron ) - xml? ( dev-libs/libxml2 ) - xslt? ( >=dev-libs/libxslt-1.1.14 ) - xerces? ( dev-libs/xerces-c ) - xalan? ( dev-libs/xalan-c ) - muparser? ( dev-cpp/muParser ) - hdf5? ( sci-libs/hdf5[cxx] ) - gif? ( media-libs/giflib ) - jpeg? ( media-libs/libjpeg-turbo:0= ) - png? ( media-libs/libpng:0= ) - tiff? ( media-libs/tiff:0= ) - xpm? ( x11-libs/libXpm ) - >=dev-libs/lzo-2.0 - app-arch/bzip2 - dev-libs/libpcre" -# USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC OEChem sge -# Intentionally omitted USE flags: -# ftds? ( dev-db/freetds ) # support for outside FreeTDS installations is currently broken. -# The default (heavily patched) embedded copy should work, or you can -# leave it off altogether -- the only public apps that make use of it are -# samples and tests, since NCBI's database servers are of course firewalled. - -# seems muParser is required, also glew is required. configure exits otherwise if these are explicitly passed to it (due to USE flag enabled) - -RDEPEND="${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/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/nilearn/Manifest b/sci-biology/nilearn/Manifest index 5dd197214..550ed1f0f 100644 --- a/sci-biology/nilearn/Manifest +++ b/sci-biology/nilearn/Manifest @@ -1,2 +1,2 @@ -DIST nilearn-0.8.1.tar.gz 11305317 BLAKE2B adefde80f5bce5ef115299326d212a7771a6ca1fc1ed7afc20fdd5b099882cfe37cc2d163807677450328916704d44e8f4044229b1470f764c75ee12d2e72b63 SHA512 4de95caa5c2080665e827310de28efb48a8b2e8161ac62f9e799984dbcd364f45ce486fcd21e9f30ef1fc41f48d2e41e477846acec5f89caf3cc1489373293d4 -DIST nilearn-0.9.1.tar.gz 11660100 BLAKE2B f2031b531faf2b7f77a6128ce2c41d4d8c4c9d5fab79df453ca127228f7ec4784b319107a9e9988b3d3a9ce87358d251e500a88dfb8226a6d4510ae5fe9f3a0c SHA512 f824fc563fd56b25508ee5803963fc98c2048fbab8823a6a6bde39e4b428a871588211649b4ce939f65173f6d4afd019e9fe1445b5cfdd00fba7823d9e23a571 +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/nilearn-0.8.1.ebuild b/sci-biology/nilearn/nilearn-0.8.1.ebuild index 2592a63fb..3064c0ba5 100644 --- a/sci-biology/nilearn/nilearn-0.8.1.ebuild +++ b/sci-biology/nilearn/nilearn-0.8.1.ebuild @@ -1,15 +1,15 @@ -# 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_10 ) +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 -> ${P}.gh.tar.gz" LICENSE="BSD" SLOT="0" diff --git a/sci-biology/nilearn/nilearn-0.9.1.ebuild b/sci-biology/nilearn/nilearn-0.9.1.ebuild index c14c8f665..425e79444 100644 --- a/sci-biology/nilearn/nilearn-0.9.1.ebuild +++ b/sci-biology/nilearn/nilearn-0.9.1.ebuild @@ -1,15 +1,15 @@ -# Copyright 1999-2022 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 -PYTHON_COMPAT=( python3_10 ) +PYTHON_COMPAT=( python3_{10..11} ) inherit distutils-r1 DESCRIPTION="Fast and easy statistical learning on NeuroImaging data" HOMEPAGE="http://nilearn.github.io/" -SRC_URI="https://github.com/nilearn/nilearn/archive/${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" 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[${PYTHON_USEDEP}] + " + +distutils_enable_tests pytest +distutils_enable_sphinx doc diff --git a/sci-biology/nitime/nitime-0.9.ebuild b/sci-biology/nitime/nitime-0.9.ebuild index 7a767390a..cae7fdfea 100644 --- a/sci-biology/nitime/nitime-0.9.ebuild +++ b/sci-biology/nitime/nitime-0.9.ebuild @@ -3,13 +3,12 @@ EAPI=8 -PYTHON_COMPAT=( python3_{10..10} ) +PYTHON_COMPAT=( python3_{10..11} ) -inherit distutils-r1 virtualx +inherit distutils-r1 pypi virtualx DESCRIPTION="Time-series analysis of neuroscience data" HOMEPAGE="http://nipy.org/nitime/index.html" -SRC_URI="mirror://pypi/${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 3e0894c90..ee81c01dc 100644 --- a/sci-biology/nitime/nitime-9999.ebuild +++ b/sci-biology/nitime/nitime-9999.ebuild @@ -3,9 +3,10 @@ EAPI=8 -PYTHON_COMPAT=( python3_{10..10} ) +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/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/open-ephys-gui/Manifest b/sci-biology/open-ephys-gui/Manifest index 53d2e5925..5863b7945 100644 --- a/sci-biology/open-ephys-gui/Manifest +++ b/sci-biology/open-ephys-gui/Manifest @@ -1,2 +1,3 @@ DIST open-ephys-gui-0.5.5.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-0.6.4.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/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-"${Suffix}" +} + +pkg_postinst() { + udev_reload +} + +pkg_postrm() { + udev_reload +} diff --git a/sci-biology/open-ephys-gui/open-ephys-gui-9999.ebuild b/sci-biology/open-ephys-gui/open-ephys-gui-9999.ebuild index 446972aeb..2ab957f40 100644 --- a/sci-biology/open-ephys-gui/open-ephys-gui-9999.ebuild +++ b/sci-biology/open-ephys-gui/open-ephys-gui-9999.ebuild @@ -1,4 +1,4 @@ -# Copyright 2019-2022 Gentoo Authors +# Copyright 2019-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 @@ -36,7 +36,7 @@ DEPEND=" media-libs/alsa-lib media-libs/freeglut media-libs/freetype - net-libs/webkit-gtk + net-libs/webkit-gtk:4 net-misc/curl x11-libs/libXrandr x11-libs/libXcursor @@ -46,7 +46,7 @@ DEPEND=" RDEPEND="${DEPEND}" BUILD_DIR="${S}/Build" -PATCHES=( "${FILESDIR}"/"${PN}"-0.6.1.patch ) +PATCHES=( "${FILESDIR}"/"${PN}"-0.6.4.patch ) QA_PREBUILT="opt/open-ephys-*/shared/*.so" QA_PRESTRIPPED=" diff --git a/sci-biology/open-ephys-gui/open-ephys-gui-99999999.ebuild b/sci-biology/open-ephys-gui/open-ephys-gui-99999999.ebuild index 446972aeb..2ab957f40 100644 --- a/sci-biology/open-ephys-gui/open-ephys-gui-99999999.ebuild +++ b/sci-biology/open-ephys-gui/open-ephys-gui-99999999.ebuild @@ -1,4 +1,4 @@ -# Copyright 2019-2022 Gentoo Authors +# Copyright 2019-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 @@ -36,7 +36,7 @@ DEPEND=" media-libs/alsa-lib media-libs/freeglut media-libs/freetype - net-libs/webkit-gtk + net-libs/webkit-gtk:4 net-misc/curl x11-libs/libXrandr x11-libs/libXcursor @@ -46,7 +46,7 @@ DEPEND=" RDEPEND="${DEPEND}" BUILD_DIR="${S}/Build" -PATCHES=( "${FILESDIR}"/"${PN}"-0.6.1.patch ) +PATCHES=( "${FILESDIR}"/"${PN}"-0.6.4.patch ) QA_PREBUILT="opt/open-ephys-*/shared/*.so" QA_PRESTRIPPED=" diff --git a/sci-biology/opfvta_bidsdata/opfvta_bidsdata-2.0.ebuild b/sci-biology/opfvta_bidsdata/opfvta_bidsdata-2.0.ebuild index c43c10257..d21f85f8c 100644 --- a/sci-biology/opfvta_bidsdata/opfvta_bidsdata-2.0.ebuild +++ b/sci-biology/opfvta_bidsdata/opfvta_bidsdata-2.0.ebuild @@ -6,7 +6,7 @@ EAPI=7 inherit check-reqs DESCRIPTION="BIDS data files released with the OPFVTA publication" -HOMEPAGE="http://www.aic-fmi.ethz.ch/" +HOMEPAGE="http://chymera.eu/docs/focus/open-science/" SRC_URI=" https://zenodo.org/record/3575149/files/${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 8c90b0a8f..000000000 --- a/sci-biology/phusion2/phusion2-3.0.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 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" -# dependency sci-biology/phrap removed from ::gentoo in f3cfb83adfc5dd1b85d0c9dce5ffbf166b25f4e4 -KEYWORDS="" - -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" "${S}/src" || die -} - -src_configure() { - # non-standard configure script - ./configure -} - -src_compile() { - pushd src - emake -j1 - popd -} - -src_install() { - pushd src - default - popd - einstalldocs -} diff --git a/sci-biology/prokka/Manifest b/sci-biology/prokka/Manifest deleted file mode 100644 index e0285e5de..000000000 --- a/sci-biology/prokka/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST prokka-1.14.6.tar.gz 112621657 BLAKE2B 3188d0a9dc6c62fa375a007950eaf91a7ff3fe6d610e89daaa8f8f911dd0035ac976cd3a2f4a14719b5c5e7d9a5bf7fdae64f838d5c54101ca8818cb2d0fd2c0 SHA512 96cc7490072d68242d4444c0842af7618f7ac132d00b008b8c4c1056d45a1f6f25c0599e7b74cd0477794bd88d88897cf57276d29c979ff1104f79f5bbf7c447 diff --git a/sci-biology/prokka/metadata.xml b/sci-biology/prokka/metadata.xml deleted file mode 100644 index 9272f0d9c..000000000 --- a/sci-biology/prokka/metadata.xml +++ /dev/null @@ -1,15 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="github">tseemann/prokka</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-biology/prokka/prokka-1.14.6.ebuild b/sci-biology/prokka/prokka-1.14.6.ebuild deleted file mode 100644 index b56fd143f..000000000 --- a/sci-biology/prokka/prokka-1.14.6.ebuild +++ /dev/null @@ -1,36 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -DESCRIPTION="Prokaryotic whole genome annotation pipeline" -HOMEPAGE="https://vicbioinformatics.com/software.prokka.shtml" -SRC_URI="https://github.com/tseemann/prokka/archive/v${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 ${PN} * - cd ../util/blasr-1.3.1 || die - dobin blasr -} - -pkg_postinst(){ - einfo "Proovread uses its own, modified version of bwa as bwa-proovread" - einfo "with linked in libbwa.a. It also bundles shrimp2 and blasr" -} diff --git a/sci-biology/pybedtools/Manifest b/sci-biology/pybedtools/Manifest index 8cfd1985e..a952ac4b8 100644 --- a/sci-biology/pybedtools/Manifest +++ b/sci-biology/pybedtools/Manifest @@ -1 +1,2 @@ DIST pybedtools-0.8.2.tar.gz 12496355 BLAKE2B f1ff67f524a5a51a6f6a5450bb72ecd6602fe41232c77a38838b9b4051c528abadaa65d561bbef69cb595624a7f2edee8b98927ca0e7a55d5352e56e17f81d64 SHA512 4534c0ff4eeebbe8e3b1f126563700e4ba2b212581a76106d89fa8c61e043974b76649bf68d0b78f45923d66eb63c44bc69994de1f5a42e5069a761a93b8acbe +DIST pybedtools-0.9.0.tar.gz 12497249 BLAKE2B f43c94a7dae773b2ca46c0105d4de57f4e93a095f168b67771a568b64bc088b517e160da27ef68d81fea3df75689cad1a3db2b25dda36a37ed688e4e426fe43a SHA512 aa0cca035d560bd4e4d39f6eac74e677e3bac3266af5b69ceca1c4878742220d576d0db9ebf9c8da490d24259b1153e9999a78d2a5c46f1acb544fa3dba73a18 diff --git a/sci-biology/pybedtools/pybedtools-0.8.2.ebuild b/sci-biology/pybedtools/pybedtools-0.8.2.ebuild index 8f4ae591f..bc02bda6f 100644 --- a/sci-biology/pybedtools/pybedtools-0.8.2.ebuild +++ b/sci-biology/pybedtools/pybedtools-0.8.2.ebuild @@ -1,9 +1,10 @@ -# Copyright 1999-2022 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 -PYTHON_COMPAT=( python3_10 ) +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools inherit distutils-r1 @@ -15,9 +16,6 @@ LICENSE="MIT" SLOT="0" KEYWORDS="~amd64 ~x86" -# ModuleNotFoundError: No module named 'pybedtools.cbedtools' -RESTRICT="test" - RDEPEND=" sci-biology/bedtools sci-biology/pysam[${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/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[${PYTHON_USEDEP}] -" - -distutils_enable_tests --install setup.py diff --git a/sci-biology/rat-brain-templates/metadata.xml b/sci-biology/rat-brain-templates/metadata.xml index ac271f806..5dacf4476 100644 --- a/sci-biology/rat-brain-templates/metadata.xml +++ b/sci-biology/rat-brain-templates/metadata.xml @@ -14,4 +14,7 @@ format oriented in the standard RAS space, with origin at bregma for use in magnetic resonance rat brain imaging. </longdescription> + <upstream> + <remote-id type="gitlab">FOS-FMI/rat-brain-templates_generator</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/rat-brain-templates/rat-brain-templates-0.2.ebuild b/sci-biology/rat-brain-templates/rat-brain-templates-0.2.ebuild index d41c14a11..cab3dec4f 100644 --- a/sci-biology/rat-brain-templates/rat-brain-templates-0.2.ebuild +++ b/sci-biology/rat-brain-templates/rat-brain-templates-0.2.ebuild @@ -7,7 +7,7 @@ inherit check-reqs DESCRIPTION="A collection of rat brain templates in NIfTI format" HOMEPAGE="https://gitlab.com/FOS-FMI/rat-brain-templates_generator" -SRC_URI="http://resources.chymera.eu/distfiles/${P}.tar.xz" +SRC_URI="https://resources.chymera.eu/distfiles/${P}.tar.xz" LICENSE="fairuse" SLOT="0" diff --git a/sci-biology/roiextractors/Manifest b/sci-biology/roiextractors/Manifest new file mode 100644 index 000000000..4db78b7b8 --- /dev/null +++ b/sci-biology/roiextractors/Manifest @@ -0,0 +1 @@ +DIST roiextractors-0.5.1.gh.tar.gz 288765 BLAKE2B 5e1b1931f3da8c1157fc2668c203e3ea9812b94246b85e97848d25ff880b1b6d9433637b9847a28dc53c9d88746d1eaa472c7beffd2593d461a24f98eaddd997 SHA512 6f02decfca12f45c8e18ad9ee07931a5891a2099b046e56a7c415d179d93bc6b9a47a320e4ce500217b1f02abdbbdb59c7e85b4f0a773cbd44ba983f5b7595d6 diff --git a/sci-biology/roiextractors/metadata.xml b/sci-biology/roiextractors/metadata.xml new file mode 100644 index 000000000..000a44418 --- /dev/null +++ b/sci-biology/roiextractors/metadata.xml @@ -0,0 +1,16 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>gentoo@chymera.eu</email> + <name>Horea Christian</name> + </maintainer> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <upstream> + <remote-id type="github">catalystneuro/roiextractors</remote-id> + <remote-id type="pypi">roiextractors</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/roiextractors/roiextractors-0.5.1.ebuild b/sci-biology/roiextractors/roiextractors-0.5.1.ebuild new file mode 100644 index 000000000..1c2fba6ea --- /dev/null +++ b/sci-biology/roiextractors/roiextractors-0.5.1.ebuild @@ -0,0 +1,40 @@ +# Copyright 2021-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools +inherit distutils-r1 + +DESCRIPTION="Optical imaging data handling from several file formats" +HOMEPAGE="https://github.com/catalystneuro/roiextractors" +SRC_URI="https://github.com/catalystneuro/roiextractors/archive/refs/tags/v${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[${PYTHON_USEDEP}] + ) +" + +distutils_enable_tests pytest + +python_test() { + epytest tests/test_internals +} diff --git a/sci-biology/rtg-tools/Manifest b/sci-biology/rtg-tools/Manifest deleted file mode 100644 index 4e0799efc..000000000 --- a/sci-biology/rtg-tools/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST rtg-tools-3.12.tar.gz 32484461 BLAKE2B 3fcee1db9ddcb0d04c34d1252fdf3564aeb255bff36501d0e0bdbe5f6c7d3564581b7fd8aacc90c1a818787c03c3da5478590402cda3cb691be90e816a7ee048 SHA512 2ab7c2a2203e48c74983e89a72b2cf0053e8810a7442931868489f71af6db5f22ca119a5924e7e03bc0f524e41bddff0b20ee8e3c811a21f9168a6b3d6b92d89 diff --git a/sci-biology/rtg-tools/metadata.xml b/sci-biology/rtg-tools/metadata.xml deleted file mode 100644 index 026053b60..000000000 --- a/sci-biology/rtg-tools/metadata.xml +++ /dev/null @@ -1,15 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="github">RealTimeGenomics/rtg-tools</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-biology/rtg-tools/rtg-tools-3.12.ebuild b/sci-biology/rtg-tools/rtg-tools-3.12.ebuild deleted file mode 100644 index a07f55539..000000000 --- a/sci-biology/rtg-tools/rtg-tools-3.12.ebuild +++ /dev/null @@ -1,63 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit java-pkg-2 java-ant-2 - -DESCRIPTION="Manipulate and analyze VCF files" -HOMEPAGE="https://github.com/RealTimeGenomics/rtg-tools" -SRC_URI="https://github.com/RealTimeGenomics/rtg-tools/archive/${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/samri/Manifest b/sci-biology/samri/Manifest index d683d1d3b..26d7dd5ed 100644 --- a/sci-biology/samri/Manifest +++ b/sci-biology/samri/Manifest @@ -1 +1,2 @@ -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 a20c63f61..f632f83a8 100644 --- a/sci-biology/samri/samri-0.5.ebuild +++ b/sci-biology/samri/samri-0.5.3.ebuild @@ -1,20 +1,26 @@ -# 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_10 ) +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 -> ${P}.tar.gz" -S="${WORKDIR}/SAMRI-${PV}" +if [ "$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-${PV}" +fi LICENSE="GPL-3" SLOT="0" -KEYWORDS="~amd64" IUSE="+atlases labbookdb" REQUIRED_USE="test? ( atlases )" @@ -42,7 +48,7 @@ RDEPEND=" >=sci-libs/nipy-0.4.1[${PYTHON_USEDEP}] >=sci-libs/nipype-1.0.0[${PYTHON_USEDEP}] <sci-libs/pybids-0.10.2[${PYTHON_USEDEP}] - sci-libs/scikit-image[${PYTHON_USEDEP}] + dev-python/scikit-image[${PYTHON_USEDEP}] sci-biology/ants sci-biology/afni sci-biology/nilearn[${PYTHON_USEDEP}] diff --git a/sci-biology/samri/samri-0.5.4.ebuild b/sci-biology/samri/samri-0.5.4.ebuild new file mode 100644 index 000000000..f632f83a8 --- /dev/null +++ b/sci-biology/samri/samri-0.5.4.ebuild @@ -0,0 +1,77 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools + +inherit distutils-r1 prefix + +DESCRIPTION="Small Animal Magnetic Resonance Imaging" +HOMEPAGE="https://github.com/IBT-FMI/SAMRI" +if [ "$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-${PV}" +fi + +LICENSE="GPL-3" +SLOT="0" +IUSE="+atlases labbookdb" +REQUIRED_USE="test? ( atlases )" + +DEPEND=" + test? ( + sci-biology/samri_bidsdata + sci-biology/samri_bindata + ) + " +RDEPEND=" + dev-python/argh[${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[${PYTHON_USEDEP}] + >=media-gfx/blender-2.83.4 + >=sci-biology/fsl-5.0.9 + sci-biology/bru2nii + atlases? ( sci-biology/mouse-brain-templates ) + labbookdb? ( sci-libs/labbookdb[${PYTHON_USEDEP}] ) + sci-libs/nibabel[${PYTHON_USEDEP}] + >=sci-libs/nipy-0.4.1[${PYTHON_USEDEP}] + >=sci-libs/nipype-1.0.0[${PYTHON_USEDEP}] + <sci-libs/pybids-0.10.2[${PYTHON_USEDEP}] + dev-python/scikit-image[${PYTHON_USEDEP}] + sci-biology/ants + sci-biology/afni + sci-biology/nilearn[${PYTHON_USEDEP}] +" + +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` || 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:$PATH + export PYTHONIOENCODING=utf-8 + ./test_scripts.sh || die "Test scripts failed." + sed -i -e \ + "/def test_bru2bids():/i@pytest.mark.skip('Removed in full test suite, as this is already tested in `test_scripts.sh`')" \ + samri/pipelines/tests/test_repos.py || die + epytest -k "not longtime" +} diff --git a/sci-biology/samri/samri-9999.ebuild b/sci-biology/samri/samri-9999.ebuild new file mode 100644 index 000000000..f632f83a8 --- /dev/null +++ b/sci-biology/samri/samri-9999.ebuild @@ -0,0 +1,77 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools + +inherit distutils-r1 prefix + +DESCRIPTION="Small Animal Magnetic Resonance Imaging" +HOMEPAGE="https://github.com/IBT-FMI/SAMRI" +if [ "$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-${PV}" +fi + +LICENSE="GPL-3" +SLOT="0" +IUSE="+atlases labbookdb" +REQUIRED_USE="test? ( atlases )" + +DEPEND=" + test? ( + sci-biology/samri_bidsdata + sci-biology/samri_bindata + ) + " +RDEPEND=" + dev-python/argh[${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[${PYTHON_USEDEP}] + >=media-gfx/blender-2.83.4 + >=sci-biology/fsl-5.0.9 + sci-biology/bru2nii + atlases? ( sci-biology/mouse-brain-templates ) + labbookdb? ( sci-libs/labbookdb[${PYTHON_USEDEP}] ) + sci-libs/nibabel[${PYTHON_USEDEP}] + >=sci-libs/nipy-0.4.1[${PYTHON_USEDEP}] + >=sci-libs/nipype-1.0.0[${PYTHON_USEDEP}] + <sci-libs/pybids-0.10.2[${PYTHON_USEDEP}] + dev-python/scikit-image[${PYTHON_USEDEP}] + sci-biology/ants + sci-biology/afni + sci-biology/nilearn[${PYTHON_USEDEP}] +" + +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` || 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:$PATH + export PYTHONIOENCODING=utf-8 + ./test_scripts.sh || die "Test scripts failed." + sed -i -e \ + "/def test_bru2bids():/i@pytest.mark.skip('Removed in full test suite, as this is already tested in `test_scripts.sh`')" \ + samri/pipelines/tests/test_repos.py || die + epytest -k "not longtime" +} diff --git a/sci-biology/screed/Manifest b/sci-biology/screed/Manifest deleted file mode 100644 index ff390a90d..000000000 --- a/sci-biology/screed/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST screed-1.0.4.tar.gz 121589 BLAKE2B 0d234e1b03247dca1515c7a6e03d297b75d708dfc6303124c28a0cd936704eb921d76560fd06956d190b8f8277ed301f27e776b6a3642209655d9218e32a3fe3 SHA512 6176029f7efa0319e4a7bf03727aad1729733859445fd0df51f39edfa660f44057e1849d487fe37c34289b023f1e85bc6f29b5f7ece189aea861637afd5fa516 diff --git a/sci-biology/screed/metadata.xml b/sci-biology/screed/metadata.xml deleted file mode 100644 index 297401f3d..000000000 --- a/sci-biology/screed/metadata.xml +++ /dev/null @@ -1,12 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="github">ged-lab/screed</remote-id> - <remote-id type="pypi">screed</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-biology/screed/screed-1.0.4.ebuild b/sci-biology/screed/screed-1.0.4.ebuild deleted file mode 100644 index eab1748f4..000000000 --- a/sci-biology/screed/screed-1.0.4.ebuild +++ /dev/null @@ -1,26 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7,8,9} ) - -inherit distutils-r1 - -DESCRIPTION="Short read sequence utilities" -HOMEPAGE="https://pypi.python.org/pypi/screed https://github.com/ged-lab/screed/" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -SLOT="0" -LICENSE="BSD" -KEYWORDS="~amd64 ~x86" - -distutils_enable_tests --install pytest - -RDEPEND="dev-python/bz2file[${PYTHON_USEDEP}]" - -python_prepare_all() { - # do not depend on pytest-runner - sed -i "/pytest-runner/d" setup.py || die - distutils-r1_python_prepare_all -} diff --git a/sci-biology/signalp/Manifest b/sci-biology/signalp/Manifest deleted file mode 100644 index 4f4d96631..000000000 --- a/sci-biology/signalp/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST signalp-3.0.Linux.tar.Z 1216617 SHA256 260c2e5bd945b386e833a7b7326cff6d7332302868e99c0aeae306212047c0c2 diff --git a/sci-biology/signalp/metadata.xml b/sci-biology/signalp/metadata.xml deleted file mode 100644 index 8417d1580..000000000 --- a/sci-biology/signalp/metadata.xml +++ /dev/null @@ -1,8 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-biology/signalp/signalp-3.0.ebuild b/sci-biology/signalp/signalp-3.0.ebuild deleted file mode 100644 index dcd83d920..000000000 --- a/sci-biology/signalp/signalp-3.0.ebuild +++ /dev/null @@ -1,46 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -DESCRIPTION="Prediction of signal peptide cleavage sites in amino acid sequences" -HOMEPAGE="http://www.cbs.dtu.dk/services/SignalP/" -SRC_URI="${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/${P}/how - doexe how/* - doman signalp.1 - dodoc *readme -} diff --git a/sci-biology/snapgene-viewer/Manifest b/sci-biology/snapgene-viewer/Manifest new file mode 100644 index 000000000..2e6582002 --- /dev/null +++ b/sci-biology/snapgene-viewer/Manifest @@ -0,0 +1 @@ +DIST snapgene_7.0.3_linux.deb 129706720 BLAKE2B 539257921cc36c8770f5786e3af37502a6e958636ed32f861dcb2fd4621dfbac19d39c9a0772e0d08a532226f9b1875964bf657638917b52c606ff448a03b6f3 SHA512 b902d2bc229e697c4409b09b4f8e2a0ef6583a1958e7a38ef8321b453cdda687e33bc42adb14133d7320cc18791ec1b79409701efbfc5f6be0bbcce2f4e6e87f diff --git a/sci-biology/kmergenie/metadata.xml b/sci-biology/snapgene-viewer/metadata.xml index 138cb7705..5c83ce208 100644 --- a/sci-biology/kmergenie/metadata.xml +++ b/sci-biology/snapgene-viewer/metadata.xml @@ -2,11 +2,11 @@ <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> + <email>pacho@gentoo.org</email> + <name>Pacho Ramos</name> </maintainer> <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> </maintainer> </pkgmetadata> diff --git a/sci-biology/snapgene-viewer/snapgene-viewer-7.0.3.ebuild b/sci-biology/snapgene-viewer/snapgene-viewer-7.0.3.ebuild new file mode 100644 index 000000000..d117fbc14 --- /dev/null +++ b/sci-biology/snapgene-viewer/snapgene-viewer-7.0.3.ebuild @@ -0,0 +1,65 @@ +# Copyright 2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 +inherit unpacker wrapper xdg + +DESCRIPTION="Software for plasmid mapping, primer design, and restriction site analysis" +HOMEPAGE="https://www.snapgene.com/features" +SRC_URI="snapgene_${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/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/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 ../${PN}/bin/tmhmm /opt/bin/tmhmm - - dodoc README TMHMM2.0.html -} diff --git a/sci-biology/trans-abyss/Manifest b/sci-biology/trans-abyss/Manifest deleted file mode 100644 index 9addb1899..000000000 --- a/sci-biology/trans-abyss/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST trans-abyss-2.0.1.tar.gz 359063 BLAKE2B 9b3f19b883e2616b05bc0677b9161e8c997596b288af7e570a83129549edd517a941f765d39dfb83638160e611df3f2acfc32eb944c7cca63c8350e77fb96246 SHA512 5362665a2758a76c579d8086f8904cf0e40c8dff0dfa1c82368b38af25e37f2f2852f60c3001db254e5f06400e9e2e7f6f6c301133b7806d47cee189f84a0f0f diff --git a/sci-biology/trans-abyss/metadata.xml b/sci-biology/trans-abyss/metadata.xml deleted file mode 100644 index 079fb5aae..000000000 --- a/sci-biology/trans-abyss/metadata.xml +++ /dev/null @@ -1,15 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="github">bcgsc/transabyss</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-biology/trans-abyss/trans-abyss-2.0.1.ebuild b/sci-biology/trans-abyss/trans-abyss-2.0.1.ebuild deleted file mode 100644 index cf10dd3b9..000000000 --- a/sci-biology/trans-abyss/trans-abyss-2.0.1.ebuild +++ /dev/null @@ -1,35 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7,8,9} ) - -inherit python-r1 - -DESCRIPTION="Analyze and combine multiple assemblies from abyss" -HOMEPAGE="https://www.bcgsc.ca/resources/software/trans-abyss" -SRC_URI="https://github.com/bcgsc/transabyss/archive/${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-${PV}" - -src_install() { - einstalldocs - python_foreach_impl python_domodule utilities - dobin transabyss - dobin transabyss-merge -} diff --git a/sci-biology/trim_galore/Manifest b/sci-biology/trim_galore/Manifest deleted file mode 100644 index d49ab113e..000000000 --- a/sci-biology/trim_galore/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST trim_galore-0.6.6.tar.gz 26829185 BLAKE2B b783d5b8fcf831c5b652cbfed82a42ad55e911aac1b16ac367d27ff6c07f298cd8fd797d4ac4b4213e7c9188ee02e7a2bab97799cc2c9eeba88244556b006832 SHA512 3714f89cee439cf2ef2c88c1f505507c00e426345ff59bdb48fadcc56fe78617d7641da9b6deb5f122fb1d41449fdc4b3f79ee336ec4bf240edbe071aeffc025 diff --git a/sci-biology/trim_galore/metadata.xml b/sci-biology/trim_galore/metadata.xml deleted file mode 100644 index ac0e44aa7..000000000 --- a/sci-biology/trim_galore/metadata.xml +++ /dev/null @@ -1,15 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="github">FelixKrueger/TrimGalore</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-biology/trim_galore/trim_galore-0.6.6.ebuild b/sci-biology/trim_galore/trim_galore-0.6.6.ebuild deleted file mode 100644 index c99dcfcc6..000000000 --- a/sci-biology/trim_galore/trim_galore-0.6.6.ebuild +++ /dev/null @@ -1,26 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -DESCRIPTION="Perl wrapper around Cutadapt and FastQC to adapter and quality trimming" -HOMEPAGE="https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ https://github.com/FelixKrueger/TrimGalore" -SRC_URI="https://github.com/FelixKrueger/TrimGalore/archive/${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-${PV}" - -src_install(){ - dobin trim_galore - dodoc -r Docs -} diff --git a/sci-biology/weblogo/Manifest b/sci-biology/weblogo/Manifest deleted file mode 100644 index 264bad9bd..000000000 --- a/sci-biology/weblogo/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST weblogo-3.7.5.tar.gz 817128 BLAKE2B f7619b6ea0c944fb21b8acdfc9593d6223e7d48ac9495c872c3bcadc0187249883b013e44bec70ce126d820abb6281b2e5ef5f04126e7a288c3f5a1026612ab0 SHA512 7fbf71854eee0bcebebe926f2c93653b0b8475462ed5b3dc951947cec67a37bee801d468f893932257f5bdca8c754264c3279695cdb3da747bd82e9353392c0b diff --git a/sci-biology/weblogo/metadata.xml b/sci-biology/weblogo/metadata.xml deleted file mode 100644 index 138cb7705..000000000 --- a/sci-biology/weblogo/metadata.xml +++ /dev/null @@ -1,12 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-biology/weblogo/weblogo-3.7.5.ebuild b/sci-biology/weblogo/weblogo-3.7.5.ebuild deleted file mode 100644 index a8db5bec5..000000000 --- a/sci-biology/weblogo/weblogo-3.7.5.ebuild +++ /dev/null @@ -1,33 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7..9} ) -DISTUTILS_USE_SETUPTOOLS=rdepend -inherit distutils-r1 - -DESCRIPTION="generate consensus sequence logo figures" -HOMEPAGE="http://weblogo.threeplusone.com/" -SRC_URI="mirror://pypi/${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}" -} |