aboutsummaryrefslogtreecommitdiff
diff options
context:
space:
mode:
Diffstat (limited to 'sci-biology')
-rw-r--r--sci-biology/ABI-connectivity-data/ABI-connectivity-data-0.1-r1.ebuild2
-rw-r--r--sci-biology/ABI-connectivity-data/ABI-connectivity-data-0.2.ebuild2
-rw-r--r--sci-biology/ABI-expression-data/ABI-expression-data-0.2.ebuild2
-rw-r--r--sci-biology/GAL/GAL-0.2.2_p20200508.ebuild19
-rw-r--r--sci-biology/GAL/files/Build.PL.patch24
-rw-r--r--sci-biology/LINKS/LINKS-1.8.7.ebuild50
-rw-r--r--sci-biology/LINKS/LINKS-2.0.1.ebuild21
-rw-r--r--sci-biology/LINKS/Manifest2
-rw-r--r--sci-biology/MolBioLib/Manifest1
-rw-r--r--sci-biology/MolBioLib/MolBioLib-5.ebuild40
-rw-r--r--sci-biology/MolBioLib/metadata.xml15
-rw-r--r--sci-biology/OBO-Edit/Manifest1
-rw-r--r--sci-biology/OBO-Edit/OBO-Edit-2.3.1.ebuild73
-rw-r--r--sci-biology/OBO-Edit/files/response.varfile10
-rw-r--r--sci-biology/OBO-Edit/metadata.xml15
-rw-r--r--sci-biology/SOAPdenovo2/Manifest1
-rw-r--r--sci-biology/SOAPdenovo2/SOAPdenovo2-242.ebuild40
-rw-r--r--sci-biology/SOAPdenovo2/files/SOAPdenovo2-r241-Makefile.patch204
-rw-r--r--sci-biology/SOAPdenovo2/files/soapdenovo2.122
-rw-r--r--sci-biology/SOAPdenovo2/metadata.xml12
-rw-r--r--sci-biology/SPAdes/Manifest8
-rw-r--r--sci-biology/SPAdes/SPAdes-3.15.1.ebuild55
-rw-r--r--sci-biology/SPAdes/SPAdes-3.15.3.ebuild36
-rw-r--r--sci-biology/Trinotate/Manifest2
-rw-r--r--sci-biology/Trinotate/Trinotate-3.2.2.ebuild (renamed from sci-biology/Trinotate/Trinotate-3.2.1.ebuild)9
-rw-r--r--sci-biology/afni/Manifest2
-rw-r--r--sci-biology/afni/afni-20.1.16.ebuild14
-rw-r--r--sci-biology/afni/afni-20.3.03.ebuild20
-rw-r--r--sci-biology/afni/afni-22.0.21.ebuild (renamed from sci-biology/afni/afni-19.3.12.ebuild)45
-rw-r--r--sci-biology/afni/afni-9999.ebuild70
-rw-r--r--sci-biology/afni/files/afni-20.1.16-python.patch2
-rw-r--r--sci-biology/afni/files/afni-20.3.03-python.patch11
-rw-r--r--sci-biology/aghermann/aghermann-1.1.2-r2.ebuild4
-rw-r--r--sci-biology/ants/ants-2.3.4.ebuild2
-rw-r--r--sci-biology/arachne/Manifest1
-rw-r--r--sci-biology/arachne/arachne-46233.ebuild39
-rw-r--r--sci-biology/arachne/metadata.xml12
-rw-r--r--sci-biology/bambus/bambus-2.33-r2.ebuild (renamed from sci-biology/bambus/bambus-2.33.ebuild)30
-rw-r--r--sci-biology/behaviopy/Manifest2
-rw-r--r--sci-biology/behaviopy/behaviopy-0.2.ebuild (renamed from sci-biology/behaviopy/behaviopy-0.1.ebuild)18
-rw-r--r--sci-biology/behaviopy/behaviopy-9999.ebuild46
-rw-r--r--sci-biology/blasr/Manifest1
-rw-r--r--sci-biology/blasr/blasr-5.3.5.ebuild (renamed from sci-biology/blasr/blasr-9999.ebuild)14
-rw-r--r--sci-biology/canu/canu-2.1.1.ebuild5
-rw-r--r--sci-biology/chiron/chiron-0.6.1.1.ebuild6
-rw-r--r--sci-biology/conrad/Manifest1
-rw-r--r--sci-biology/conrad/conrad-1.ebuild52
-rw-r--r--sci-biology/conrad/metadata.xml15
-rw-r--r--sci-biology/cortex_var/Manifest2
-rw-r--r--sci-biology/cortex_var/cortex_var-1.0.5.21.ebuild51
-rw-r--r--sci-biology/cortex_var/metadata.xml15
-rw-r--r--sci-biology/cramtools/Manifest1
-rw-r--r--sci-biology/cramtools/cramtools-3.0.ebuild34
-rw-r--r--sci-biology/cramtools/metadata.xml15
-rw-r--r--sci-biology/dargcc_bidsdata/dargcc_bidsdata-1.0.ebuild3
-rw-r--r--sci-biology/drlfom_bidsdata/drlfom_bidsdata-1.1.ebuild3
-rw-r--r--sci-biology/fsl/files/fsl-6.0.2-fsldir_redux-p1.patch240
-rw-r--r--sci-biology/fsl/files/fsl-6.0.2-fsldir_redux-p2.patch255
-rw-r--r--sci-biology/fsl/fsl-6.0.4.ebuild6
-rw-r--r--sci-biology/fsl/fsl-6.0.5.ebuild4
-rw-r--r--sci-biology/gffread/Manifest4
-rw-r--r--sci-biology/gffread/gffread-0.12.7.ebuild (renamed from sci-biology/gffread/gffread-0.11.0.ebuild)10
-rw-r--r--sci-biology/irsabi_bidsdata/irsabi_bidsdata-1.4.ebuild3
-rw-r--r--sci-biology/jigsaw/Manifest1
-rw-r--r--sci-biology/jigsaw/jigsaw-3.2.10m.ebuild28
-rw-r--r--sci-biology/jigsaw/metadata.xml12
-rw-r--r--sci-biology/jtreeview-bin/jtreeview-bin-1.2.0.ebuild10
-rw-r--r--sci-biology/jtreeview/Manifest2
-rw-r--r--sci-biology/jtreeview/jtreeview-1.2.0.ebuild39
-rw-r--r--sci-biology/jtreeview/jtreeview-9999.ebuild30
-rw-r--r--sci-biology/jtreeview/metadata.xml16
-rw-r--r--sci-biology/libblasr/Manifest1
-rw-r--r--sci-biology/libblasr/libblasr-5.3.5.ebuild (renamed from sci-biology/libblasr/libblasr-9999.ebuild)15
-rw-r--r--sci-biology/longstitch/longstitch-1.0.1.ebuild9
-rw-r--r--sci-biology/manatee-igs/Manifest1
-rw-r--r--sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild65
-rw-r--r--sci-biology/manatee-igs/metadata.xml15
-rw-r--r--sci-biology/manatee-jcvi/Manifest1
-rw-r--r--sci-biology/manatee-jcvi/manatee-jcvi-2.4.3.ebuild54
-rw-r--r--sci-biology/manatee-jcvi/metadata.xml15
-rw-r--r--sci-biology/mappy/Manifest2
-rw-r--r--sci-biology/mappy/mappy-2.24.ebuild (renamed from sci-biology/mappy/mappy-2.17.ebuild)6
-rw-r--r--sci-biology/mmseqs2/Manifest1
-rw-r--r--sci-biology/mmseqs2/files/mmseqs2-13.0-properly-handle-cpuflags.patch40
-rw-r--r--sci-biology/mmseqs2/metadata.xml22
-rw-r--r--sci-biology/mmseqs2/mmseqs2-13.0-r1.ebuild55
-rw-r--r--sci-biology/mouse-brain-atlases/mouse-brain-atlases-0.5.3.ebuild4
-rw-r--r--sci-biology/mouse-brain-templates/mouse-brain-templates-0.5.3.ebuild4
-rw-r--r--sci-biology/mrsfast/Manifest1
-rw-r--r--sci-biology/mrsfast/metadata.xml11
-rw-r--r--sci-biology/mrsfast/mrsfast-3.4.2.ebuild28
-rw-r--r--sci-biology/ncbi-blast+/ncbi-blast+-2.11.0.ebuild5
-rw-r--r--sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild5
-rw-r--r--sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild5
-rw-r--r--sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild5
-rw-r--r--sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild5
-rw-r--r--sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild5
-rw-r--r--sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild5
-rw-r--r--sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild5
-rw-r--r--sci-biology/nilearn/Manifest3
-rw-r--r--sci-biology/nilearn/files/nilearn-0.9.1-tests.patch10
-rw-r--r--sci-biology/nilearn/nilearn-0.8.1.ebuild (renamed from sci-biology/nilearn/nilearn-0.8.0.ebuild)4
-rw-r--r--sci-biology/nilearn/nilearn-0.9.1.ebuild52
-rw-r--r--sci-biology/nilearn/nilearn-9999.ebuild42
-rw-r--r--sci-biology/oases/Manifest2
-rw-r--r--sci-biology/oases/files/Makefile.patch15
-rw-r--r--sci-biology/oases/metadata.xml12
-rw-r--r--sci-biology/oases/oases-0.2.08.ebuild40
-rw-r--r--sci-biology/oases/oases-9999.ebuild40
-rw-r--r--sci-biology/open-ephys-gui/Manifest1
-rw-r--r--sci-biology/open-ephys-gui/files/open-ephys-gui-0.5.2.2.patch12
-rw-r--r--sci-biology/open-ephys-gui/open-ephys-gui-0.5.2.2.ebuild82
-rw-r--r--sci-biology/opfvta_bidsdata/opfvta_bidsdata-2.0.ebuild3
-rw-r--r--sci-biology/pbbam/Manifest2
-rw-r--r--sci-biology/pbbam/pbbam-1.8.1.ebuild (renamed from sci-biology/pbbam/pbbam-1.6.0.ebuild)3
-rw-r--r--sci-biology/pbbam/pbbam-9999.ebuild26
-rw-r--r--sci-biology/pbcopper/Manifest2
-rw-r--r--sci-biology/pbcopper/pbcopper-1.9.5.ebuild (renamed from sci-biology/pbcopper/pbcopper-1.9.0.ebuild)2
-rw-r--r--sci-biology/pilon-bin/Manifest1
-rw-r--r--sci-biology/pilon-bin/metadata.xml12
-rw-r--r--sci-biology/pilon-bin/pilon-bin-1.24.ebuild29
-rw-r--r--sci-biology/primerD/Manifest1
-rw-r--r--sci-biology/primerD/metadata.xml12
-rw-r--r--sci-biology/primerD/primerD-1.0.0.ebuild42
-rw-r--r--sci-biology/pufferfish/Manifest4
-rw-r--r--sci-biology/pufferfish/files/pufferfish-do-not-fetch.patch31
-rw-r--r--sci-biology/pufferfish/metadata.xml11
-rw-r--r--sci-biology/pufferfish/pufferfish-1.4.0.ebuild35
-rw-r--r--sci-biology/quorum/Manifest1
-rw-r--r--sci-biology/quorum/files/quorum-0.2.1-use-jellyfish1.patch74
-rw-r--r--sci-biology/quorum/metadata.xml12
-rw-r--r--sci-biology/quorum/quorum-1.1.1.ebuild28
-rw-r--r--sci-biology/rat-brain-templates/rat-brain-templates-0.2.ebuild2
-rw-r--r--sci-biology/sailfish/Manifest5
-rw-r--r--sci-biology/sailfish/files/sailfish-0.9.2-no-boost-static.patch20
-rw-r--r--sci-biology/sailfish/files/sailfish-allow-newer-boost.patch13
-rw-r--r--sci-biology/sailfish/files/sailfish-no-curl.patch121
-rw-r--r--sci-biology/sailfish/metadata.xml15
-rw-r--r--sci-biology/sailfish/sailfish-0.10.0.ebuild83
-rw-r--r--sci-biology/sailfish/sailfish-9999.ebuild62
-rw-r--r--sci-biology/salmon/Manifest4
-rw-r--r--sci-biology/salmon/files/salmon-1.6.0-find-boost.patch116
-rw-r--r--sci-biology/salmon/salmon-1.4.0.ebuild38
-rw-r--r--sci-biology/salmon/salmon-1.6.0.ebuild70
-rw-r--r--sci-biology/salmon/salmon-9999.ebuild32
-rw-r--r--sci-biology/sambamba/Manifest2
-rw-r--r--sci-biology/sambamba/metadata.xml15
-rw-r--r--sci-biology/sambamba/sambamba-0.8.0.ebuild36
-rw-r--r--sci-biology/sambamba/sambamba-9999.ebuild28
-rw-r--r--sci-biology/samri/Manifest1
-rw-r--r--sci-biology/samri/samri-0.4.1.ebuild58
-rw-r--r--sci-biology/samri/samri-0.5.ebuild25
-rw-r--r--sci-biology/samri/samri-9999.ebuild71
-rw-r--r--sci-biology/samri_bidsdata/samri_bidsdata-0.3.ebuild3
-rw-r--r--sci-biology/samri_bindata/samri_bindata-0.4.ebuild3
-rw-r--r--sci-biology/ssaha2-bin/ssaha2-bin-2.5.5-r1.ebuild (renamed from sci-biology/ssaha2-bin/ssaha2-bin-2.5.5.ebuild)14
-rw-r--r--sci-biology/stacks/Manifest2
-rw-r--r--sci-biology/stacks/stacks-2.60.ebuild (renamed from sci-biology/stacks/stacks-2.55.ebuild)31
-rw-r--r--sci-biology/staden/files/staden-2.0.0_beta10-ldflags.patch30
-rw-r--r--sci-biology/staden/files/staden-2.0.0_beta10-zlib.patch16
-rw-r--r--sci-biology/staden/staden-9999.ebuild69
-rw-r--r--sci-biology/subread/Manifest2
-rw-r--r--sci-biology/subread/files/subread-2.0.1-fno-common.patch11
-rw-r--r--sci-biology/subread/subread-2.0.3.ebuild (renamed from sci-biology/subread/subread-2.0.1.ebuild)10
-rw-r--r--sci-biology/symap/Manifest1
-rw-r--r--sci-biology/symap/metadata.xml8
-rw-r--r--sci-biology/symap/symap-5.0.6.ebuild40
-rw-r--r--sci-biology/tigr-foundation-libs/tigr-foundation-libs-2.0-r2.ebuild (renamed from sci-biology/tigr-foundation-libs/tigr-foundation-libs-2.0-r1.ebuild)12
-rw-r--r--sci-biology/trinityrnaseq/Manifest2
-rw-r--r--sci-biology/trinityrnaseq/trinityrnaseq-2.11.0.ebuild70
-rw-r--r--sci-biology/trinityrnaseq/trinityrnaseq-2.13.2.ebuild45
-rw-r--r--sci-biology/vcflib/Manifest2
-rw-r--r--sci-biology/vcflib/vcflib-1.0.3.ebuild (renamed from sci-biology/vcflib/vcflib-1.0.2.ebuild)15
-rw-r--r--sci-biology/wcd/Manifest3
-rw-r--r--sci-biology/wcd/files/wcd-0.6.3-impl-decl.patch15
-rw-r--r--sci-biology/wcd/files/wcd-0.6.3-ldflags.patch16
-rw-r--r--sci-biology/wcd/metadata.xml12
-rw-r--r--sci-biology/wcd/wcd-0.6.3_p20180430.ebuild46
178 files changed, 691 insertions, 3502 deletions
diff --git a/sci-biology/ABI-connectivity-data/ABI-connectivity-data-0.1-r1.ebuild b/sci-biology/ABI-connectivity-data/ABI-connectivity-data-0.1-r1.ebuild
index b882373e2..4b5476138 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
@@ -7,7 +7,7 @@ inherit check-reqs
DESCRIPTION="Connectivity data from the Allen Mouse Brain data portal"
HOMEPAGE="https://github.com/IBT-FMI/ABI-connectivity-data_generator"
-SRC_URI="http://chymera.eu/distfiles/${P}.tar.xz"
+SRC_URI="http://resources.chymera.eu/distfiles/${P}.tar.xz"
LICENSE="fairuse"
SLOT="0"
diff --git a/sci-biology/ABI-connectivity-data/ABI-connectivity-data-0.2.ebuild b/sci-biology/ABI-connectivity-data/ABI-connectivity-data-0.2.ebuild
index b882373e2..4b5476138 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
@@ -7,7 +7,7 @@ inherit check-reqs
DESCRIPTION="Connectivity data from the Allen Mouse Brain data portal"
HOMEPAGE="https://github.com/IBT-FMI/ABI-connectivity-data_generator"
-SRC_URI="http://chymera.eu/distfiles/${P}.tar.xz"
+SRC_URI="http://resources.chymera.eu/distfiles/${P}.tar.xz"
LICENSE="fairuse"
SLOT="0"
diff --git a/sci-biology/ABI-expression-data/ABI-expression-data-0.2.ebuild b/sci-biology/ABI-expression-data/ABI-expression-data-0.2.ebuild
index 0d53f2a90..e28aa18be 100644
--- a/sci-biology/ABI-expression-data/ABI-expression-data-0.2.ebuild
+++ b/sci-biology/ABI-expression-data/ABI-expression-data-0.2.ebuild
@@ -8,7 +8,7 @@ inherit check-reqs
DESCRIPTION="Gene expression data form the Allen Mouse Brain data portal"
HOMEPAGE="https://github.com/IBT-FMI/ABI-expression-data_generator"
SRC_URI="
- http://chymera.eu/distfiles/${P}.tar.xz
+ http://resources.chymera.eu/distfiles/${P}.tar.xz
"
LICENSE="fairuse"
diff --git a/sci-biology/GAL/GAL-0.2.2_p20200508.ebuild b/sci-biology/GAL/GAL-0.2.2_p20200508.ebuild
index 1aa7e99be..f02907368 100644
--- a/sci-biology/GAL/GAL-0.2.2_p20200508.ebuild
+++ b/sci-biology/GAL/GAL-0.2.2_p20200508.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
inherit perl-module
@@ -10,16 +10,15 @@ COMMIT="94af39622aab5ba48eb693f2327f6e90f1d202ed"
DESCRIPTION="Genome Annotation Library (incl. fasta_tool)"
HOMEPAGE="https://github.com/The-Sequence-Ontology/GAL"
SRC_URI="https://github.com/The-Sequence-Ontology/GAL/archive/${COMMIT}.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}/${PN}-${COMMIT}"
LICENSE="( GPL-1+ Artistic )"
SLOT="0"
-KEYWORDS=""
+KEYWORDS="~amd64"
RESTRICT="test"
DEPEND="
- >=dev-lang/perl-5.6.1
- dev-perl/Module-Build
dev-perl/Config-Std
virtual/perl-Data-Dumper
dev-perl/Data-Types
@@ -29,6 +28,7 @@ DEPEND="
dev-perl/Number-Format
virtual/perl-Scalar-List-Utils
dev-perl/Set-IntSpan-Fast
+ dev-perl/Statistics-Descriptive
dev-perl/Statistics-Descriptive-Discrete
dev-perl/Template-Toolkit
dev-perl/Text-Graph
@@ -36,7 +36,12 @@ DEPEND="
dev-perl/Text-Table
dev-perl/Exception-Class
dev-perl/Test-Warn
- dev-perl/URI"
+ dev-perl/URI
+ sci-biology/fasta
+"
RDEPEND="${DEPEND}"
+BDEPEND="dev-perl/Module-Build"
-S="${WORKDIR}/${PN}-${COMMIT}"
+PATCHES=(
+ "${FILESDIR}/Build.PL.patch"
+)
diff --git a/sci-biology/GAL/files/Build.PL.patch b/sci-biology/GAL/files/Build.PL.patch
index 6d881f249..eee4fb60d 100644
--- a/sci-biology/GAL/files/Build.PL.patch
+++ b/sci-biology/GAL/files/Build.PL.patch
@@ -1,16 +1,11 @@
-diff -ruN GAL_0.2.2.orig/Build.PL GAL_0.2.2/Build.PL
---- GAL_0.2.2.orig/Build.PL 2014-01-30 01:35:11.000000000 +0100
-+++ GAL_0.2.2/Build.PL 2016-01-02 12:09:16.212623256 +0100
-@@ -6,26 +6,6 @@
- my $class = Module::Build->subclass
- (
- class => 'Module::Build::Custom',
-- code => q{
-- sub ACTION_build {
-- my $self = shift;
-- $self->SUPER::ACTION_build;
-- $self->dispatch('installdeps');
-- }
+diff --git a/Build.PL b/Build.PL
+index 5915ca8..61eceb3 100644
+--- a/Build.PL
++++ b/Build.PL
+@@ -12,19 +12,6 @@ my $class = Module::Build->subclass
+ $self->SUPER::ACTION_build;
+ $self->dispatch('installdeps');
+ }
- sub ACTION_install {
- my $self = shift;
- print "\n\nGAL does not do a system wide install\n\n";
@@ -24,7 +19,6 @@ diff -ruN GAL_0.2.2.orig/Build.PL GAL_0.2.2/Build.PL
- print "remove the entire subroutine (ACTION_install) where this message\n";
- print "is printed run Build realclean and re-install.\n\n";
- }
-- },
+ },
);
- my $builder = $class->new(
diff --git a/sci-biology/LINKS/LINKS-1.8.7.ebuild b/sci-biology/LINKS/LINKS-1.8.7.ebuild
deleted file mode 100644
index 898898b94..000000000
--- a/sci-biology/LINKS/LINKS-1.8.7.ebuild
+++ /dev/null
@@ -1,50 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DESCRIPTION="Scaffold genome assemblies by Chromium/PacBio/Nanopore reads"
-HOMEPAGE="https://github.com/bcgsc/LINKS"
-SRC_URI="https://github.com/bcgsc/LINKS/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS=""
-
-RESTRICT="test"
-
-RDEPEND="
- >=dev-lang/perl-1.6
- dev-lang/swig
- dev-util/cppcheck
-"
-# sci-biology/btl_bloomfilter
-
-src_compile(){
- cd btllib | die "Cannot chdir to bundled btllib/"
- ./compile-wrappers || die "Failed to compile bundled btllib"
- # baah, this also does some kind of install
- # SUCCESS: sdsl was installed successfully!
- # The sdsl include files are located in $foo'/LINKS/btllib/external/sdsl-lite/installdir/include'.
- # The library files are located in $foo'/LINKS/btllib/external/sdsl-lite/installdir/lib'.
- #
- # Sample programs can be found in the examples-directory.
- # A program 'example.cpp' can be compiled with the command:
- # g++ -std=c++11 -DNDEBUG -O3 [-msse4.2] \
- # -I$foo/LINKS/btllib/external/sdsl-lite/installdir/include -L$foo/LINKS/btllib/external/sdsl-lite/installdir/lib \
- # example.cpp -lsdsl -ldivsufsort -ldivsufsort64
- #
- # Tests in the test-directory
- # A cheat sheet in the extras/cheatsheet-directory.
- # Have fun!
- # [2/3] Installing files.
- # Installing extras/python/_btllib.so to $foo/LINKS/btllib/python
- # Installing $foo/LINKS/btllib/extras/python/btllib.py to $foo/LINKS/btllib/python
-}
-
-src_install(){
- sed -e 's#$(bin)/../src/##' -i bin/LINKS-make || die
- sed -e 's#perl $(bin)/##' -i bin/LINKS-make || die
- dobin bin/LINKS bin/LINKS-make src/LINKS_CPP bin/*.pl tools/*.pl
- dodoc README.md
-}
diff --git a/sci-biology/LINKS/LINKS-2.0.1.ebuild b/sci-biology/LINKS/LINKS-2.0.1.ebuild
new file mode 100644
index 000000000..c1c9cc5d8
--- /dev/null
+++ b/sci-biology/LINKS/LINKS-2.0.1.ebuild
@@ -0,0 +1,21 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DESCRIPTION="Scaffold genome assemblies by Chromium/PacBio/Nanopore reads"
+HOMEPAGE="https://github.com/bcgsc/LINKS"
+SRC_URI="https://github.com/bcgsc/LINKS/releases/download/v${PV}/links-v${PV}.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}/links-${PV}"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+ >=dev-lang/perl-1.6
+ dev-util/cppcheck
+"
+DEPEND="${RDEPEND}
+ dev-lang/swig
+"
diff --git a/sci-biology/LINKS/Manifest b/sci-biology/LINKS/Manifest
index bc5133d76..e57aae29d 100644
--- a/sci-biology/LINKS/Manifest
+++ b/sci-biology/LINKS/Manifest
@@ -1 +1 @@
-DIST LINKS-1.8.7.tar.gz 13550877 BLAKE2B ee77f295b0dfc70494b985075c1be794492178c050117f7d775d9cfb2a0dc2ab96030fae2b05075955b03ed99683586fd1b0688a99cd741671be762021bc06e8 SHA512 1b869229275eddc7cb9ae2df1d4f9422741b845df50d438761a8afd4ea172244ded1a70e4fba42045e09a0ae23f8a64e2233d66a261698c13aba1b231576015c
+DIST LINKS-2.0.1.tar.gz 4566466 BLAKE2B 0713278c17b5d6fce3d6c0bbfffd2decd71599464b9d4c7da5b82997dfc6f2e1be7435dc26bc96eb6ce23ba0bd8136f8ca714e327de465137e0435ebdaa19d9c SHA512 2bbcc264da6dbe361d8224e2a123983c4f09a4b051490d599f193e3f02463e4e8ff2fadf72b8be2df6adee6db886b76d59eee179648cfed6a025c31d7fe2c696
diff --git a/sci-biology/MolBioLib/Manifest b/sci-biology/MolBioLib/Manifest
deleted file mode 100644
index fcfe68414..000000000
--- a/sci-biology/MolBioLib/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST MolBioLib_public.version5.tar.gz 2414384 BLAKE2B 845ac366ed41886cc0d3d96376dc9a97bae3d84bfc41d5f9e5be4fa274a6d64a981fcbcc12de28e1518212313af12330b08cac5488e7db9a2738c7846b981cb7 SHA512 056c38bcb65b845b32678fb8c5d758023154c07085414194e98e58281e61e475dca7321c8d684955c88bf459bc92c9d39f8b6091d0b804581e6f6e6ecabe3832
diff --git a/sci-biology/MolBioLib/MolBioLib-5.ebuild b/sci-biology/MolBioLib/MolBioLib-5.ebuild
deleted file mode 100644
index bbbbeb605..000000000
--- a/sci-biology/MolBioLib/MolBioLib-5.ebuild
+++ /dev/null
@@ -1,40 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DOCS_BUILDER="doxygen"
-DOCS_DEPEND="media-gfx/graphviz"
-
-inherit docs
-
-DESCRIPTION="C++11 framework for bioinformatics tasks"
-HOMEPAGE="https://sourceforge.net/projects/molbiolib"
-SRC_URI="https://sourceforge.net/projects/molbiolib/files/MolBioLib_public.version${PV}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="" # does not build
-
-# contains bundled samtools-0.1.18 and bamtools (pezmaster31-bamtools-d553a62)
-# which contains jsoncpp, also needs app-doc/doxygen
-DEPEND="
- dev-lang/perl
- sys-devel/gcc:*
- sys-devel/clang:*
- >=sci-biology/samtools-0.1.18:0.1-legacy
- <sci-biology/samtools-1:0.1-legacy"
-RDEPEND="${DEPEND}"
-CDEPEND="doc? ( app-doc/doxygen )"
-
-S="${WORKDIR}"/MolBioLib
-
-src_compile(){
- perl MakeAllApps.pl || die
- docs_compile
-}
-
-src_install() {
- einstalldocs
- # TODO: install this
-}
diff --git a/sci-biology/MolBioLib/metadata.xml b/sci-biology/MolBioLib/metadata.xml
deleted file mode 100644
index 3b9e38617..000000000
--- a/sci-biology/MolBioLib/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>mmokrejs@fold.natur.cuni.cz</email>
- <name>Martin Mokrejs</name>
- </maintainer>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
- <upstream>
- <remote-id type="sourceforge">molbiolib</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/sci-biology/OBO-Edit/Manifest b/sci-biology/OBO-Edit/Manifest
deleted file mode 100644
index 328ce0bca..000000000
--- a/sci-biology/OBO-Edit/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST OBO-Edit_unix_install4j-2.3.1.sh 44841394 BLAKE2B cdde5fa8bd3ce505bc18471a3924f35f6bdcac426a260c65568cdc0a70027c86d095c05e85441e770b4a6d3d0d8de3da1a3808bc3c3758e51e708e60864c0ab4 SHA512 3a48c20c02727057e3dfc7e94cf5e414942a63a9b2339e2bc6bb19e8f45ac0289904e1e6cf7b83efa53bf32b7f188c36d0deb539e169710ea2f326c5ea323603
diff --git a/sci-biology/OBO-Edit/OBO-Edit-2.3.1.ebuild b/sci-biology/OBO-Edit/OBO-Edit-2.3.1.ebuild
deleted file mode 100644
index 321d3901c..000000000
--- a/sci-biology/OBO-Edit/OBO-Edit-2.3.1.ebuild
+++ /dev/null
@@ -1,73 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit java-pkg-2
-
-MY_PV="${PV//./_}"
-
-DESCRIPTION="Java-based editor optimized for the OBO biological ontology file format"
-HOMEPAGE="http://www.oboedit.org/" # no https, invalid certificate
-SRC_URI="https://downloads.sourceforge.net/project/geneontology/OBO-Edit%202%20%5BLatest%20versions%5D/OBO-Edit%20${PV}/oboedit_${MY_PV}_unix_install4j.sh -> ${PN}_unix_install4j-${PV}.sh"
-
-LICENSE="OBO-Edit" # Artistic-like
-SLOT="0"
-KEYWORDS=""
-
-DEPEND="app-arch/rpm2targz"
-RDEPEND="virtual/jre"
-
-S="${WORKDIR}"
-
-pkg_setup() {
- einfo "Fixing java access violations ..."
- # learned from bug #387227
- # opened a bug #402507 to get this .systemPrefs directory pre-created for everybody
- addpredict /opt/icedtea-bin-7.2.0/jre/.systemPrefs
- addpredict /usr/local/bin/OBO-Edit
-}
-
-src_prepare(){
- default
- dodir /opt/OBO-Edit2/.install4j /usr/bin
- cp "${DISTDIR}"/"${PN}"_unix_install4j-"${PV}".sh "${WORKDIR}" || die
-
- # /var/tmp/portage/sci-biology/OBO-Edit-2.1.1.6/image//opt/OBO-Edit2/.install4j/response.varfile
- sed -e "s#\"\${D}\"#"${D}"#g" "${FILESDIR}"/response.varfile | \
- sed -e "s#\"\${HOME}\"#"${HOME}"#g" | \
- sed -e "s@sys.symlinkDir=/usr/local/bin@#sys.symlinkDir=/usr/local/bin@" \
- > "${D}"/opt/OBO-Edit2/.install4j/response.varfile || die "sed failed"
- cp -r "${D}"/opt/OBO-Edit2/.install4j "${HOME}" || die
-
- # for user root install4j writes into /opt/icedtea-bin-7.2.0/jre/.systemPrefs or whatever it
- # found via JAVA_HOME or similar variables
- # for other users it writes into $HOME/.java/.userPrefs/
-
- # trick setting -Djava.util.prefs.systemRoot="${TMPDIR}" does not work
- sed \
- -e "s@/bin/java\" -Dinstall4j.jvmDir=\"\$app_java_home\"@/bin/java\" -Duser.home="${HOME}" -Dinstall4j.jvmDir="${HOME}" -Dsys.symlinkDir="${D}"/usr/bin -Djava.util.prefs.systemRoot="${HOME}"@" \
- -i "${WORKDIR}"/"${PN}"_unix_install4j-"${PV}".sh \
- || die "failed to set userHome and jvmDir where JAVA .systemPrefs can be found"
-
- chmod u+rx "${WORKDIR}/${PN}"_unix_install4j-"${PV}".sh || die
-}
-
-src_install(){
- # it looks install4j removes the target installation direcotry before writing into it :((
- #
- # cat "${TMPDIR}"/.install4j/response.varfile
- # chmod a-w "${TMPDIR}"/.install4j/response.varfile
-
- INSTALL4J_KEEP_TEMP="yes" \
- sh "${WORKDIR}"/"${PN}"_unix_install4j-"${PV}".sh -q \
- --varfile="${HOME}"/.install4j/response.varfile \
- --destination="${D}"/opt/OBO-Edit2 \
- -dir "${D}"/opt/OBO-Edit2 \
- || die "Failed to run the self-extracting ${WORKDIR}/${PN}_unix_install4j-${PV}.sh file"
-
- find . -name firstrun -delete || die
-
- echo "PATH=/opt/OBO-Edit2" > 99OBO-Edit || die
- doenvd 99OBO-Edit
-}
diff --git a/sci-biology/OBO-Edit/files/response.varfile b/sci-biology/OBO-Edit/files/response.varfile
deleted file mode 100644
index 8c4361d01..000000000
--- a/sci-biology/OBO-Edit/files/response.varfile
+++ /dev/null
@@ -1,10 +0,0 @@
-#install4j response file for OBO-Edit2 2.1.1-b6
-#Tue Feb 07 03:08:04 MET 2012
-sys.component.89$Boolean=false
-createDesktopLinkAction$Boolean=false
-oboedit.memoryAlloc$Integer=3456
-sys.programGroupDisabled$Boolean=true
-sys.component.61$Boolean=true
-sys.symlinkDir="${D}"usr/bin
-sys.languageId=en
-sys.installationDir="${D}"opt/OBO-Edit2
diff --git a/sci-biology/OBO-Edit/metadata.xml b/sci-biology/OBO-Edit/metadata.xml
deleted file mode 100644
index acbbc35a4..000000000
--- a/sci-biology/OBO-Edit/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>mmokrejs@fold.natur.cuni.cz</email>
- <name>Martin Mokrejs</name>
- </maintainer>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
- <upstream>
- <remote-id type="sourceforge">geneontology</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/sci-biology/SOAPdenovo2/Manifest b/sci-biology/SOAPdenovo2/Manifest
deleted file mode 100644
index f732ff7a8..000000000
--- a/sci-biology/SOAPdenovo2/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST SOAPdenovo2-242.tar.gz 1534059 BLAKE2B e72b8b8005a807e1f949d092a1b582ed75ddbd3f4a1f014f86754ae69e279b93758693f36942e16183095fcfcc843a637fab39b08cfa6b8cbeffaf8b07c3050a SHA512 eaa2020aa9054588805bd69bb2e1d70be5bfcad31d52a33ed8f7accd4006db1ec980b20f846a6e1c0ee0ec8a493c38febb9022ce6a59c14d03fe43a3ca50569b
diff --git a/sci-biology/SOAPdenovo2/SOAPdenovo2-242.ebuild b/sci-biology/SOAPdenovo2/SOAPdenovo2-242.ebuild
deleted file mode 100644
index 33fd4a2a3..000000000
--- a/sci-biology/SOAPdenovo2/SOAPdenovo2-242.ebuild
+++ /dev/null
@@ -1,40 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DESCRIPTION="Whole genome shotgun assembler (sparse de Bruijn graph) (now MEGAHIT)"
-HOMEPAGE="https://github.com/aquaskyline/SOAPdenovo2
- https://gigascience.biomedcentral.com/articles/10.1186/2047-217X-1-18"
-SRC_URI="https://github.com/aquaskyline/SOAPdenovo2/archive/r${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="" # fails to compile
-
-DEPEND="dev-libs/libaio
- sci-biology/samtools:0.1-legacy"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/"${PN}"-r"${PV}" # version is 2.04-r241
-
-src_prepare(){
- #eapply "${FILESDIR}"/SOAPdenovo2-r241-Makefile.patch
- # this will be partly covered by
- # https://github.com/aquaskyline/SOAPdenovo2/pull/44
- #
- for f in Makefile standardPregraph/Makefile sparsePregraph/Makefile; do
- sed -e 's#^INCLUDES =#INCLUDES = -I/usr/include/bam-0.1-legacy -I./inc#;s#-lbam#-lbam-0.1-legacy#' -i $f || die
- done
- rm -f standardPregraph/*.a standardPregraph/inc/sam.h standardPregraph/inc/bam.h standardPregraph/inc/bgzf.h \
- sparsePregraph/inc/sam.h sparsePregraph/inc/bam.h sparsePregraph/inc/bgzf.h standardPregraph/inc/zlib.h \
- standardPregraph/inc/zconf.h sparsePregraph/inc/zlib.h sparsePregraph/inc/zconf.h standardPregraph/inc/*.so \
- sparsePregraph/*.a || die
- find -type f -name "*.h" -exec sed -i -e 's/#include "sam.h"/#include "bam-0.1-legacy\/sam.h"/g' {} + || die
- find -type f -name "*.h" -exec sed -i -e 's/#include "bgzf.h"/#include "bam-0.1-legacy\/bgzf.h"/g' {} + || die
- find -type f -name "*.h" -exec sed -i -e 's/#include "sam.h"/#include "bam-0.1-legacy\/sam.h"/g' {} + || die
- find -type f -name "*.c*" -exec sed -i -e 's/#include "bam.h"/#include "bam-0.1-legacy\/bam.h"/g' {} + || die
- find -type f -name "*.c*" -exec sed -i -e 's/#include "bgzf.h"/#include "bam-0.1-legacy\/bgzf.h"/g' {} + || die
- find -type f -name "*.c*" -exec sed -i -e 's/#include "sam.h"/#include "bam-0.1-legacy\/sam.h"/g' {} + || die
- default
-}
diff --git a/sci-biology/SOAPdenovo2/files/SOAPdenovo2-r241-Makefile.patch b/sci-biology/SOAPdenovo2/files/SOAPdenovo2-r241-Makefile.patch
deleted file mode 100644
index a710c2d86..000000000
--- a/sci-biology/SOAPdenovo2/files/SOAPdenovo2-r241-Makefile.patch
+++ /dev/null
@@ -1,204 +0,0 @@
---- sparsePregraph/Makefile.ori 2017-01-03 21:34:59.000000000 +0100
-+++ sparsePregraph/Makefile 2018-04-22 22:07:47.303546845 +0200
-@@ -1,28 +1,28 @@
--CC= g++
-+CXX ?= g++
- ifdef debug
--CFLAGS= -O0 -g -fomit-frame-pointer
-+CXXFLAGS ?= -O0 -g -fomit-frame-pointer
- else
--CFLAGS= -O3 -fomit-frame-pointer -w
-+CXXFLAGS ?= -O3 -fomit-frame-pointer -w
- endif
-
--DFLAGS=
--OBJS= build_graph.o build_edge.o multi_threads.o \
-- build_preArc.o pregraph_sparse.o io_func.o\
-- global.o convert_soapdenovo.o
--PROG=
--INCLUDES= -I./inc
--SUBDIRS= .
--LIBPATH= -L/usr/lib64
--LIBS= -pthread -lz -L./inc
-+DFLAGS =
-+OBJS = build_graph.o build_edge.o multi_threads.o \
-+ build_preArc.o pregraph_sparse.o io_func.o\
-+ global.o convert_soapdenovo.o
-+PROG =
-+INCLUDES = -I./inc
-+SUBDIRS = .
-+LIBPATH = -L/usr/lib64
-+LIBS = -pthread -lz -L./inc
- EXTRA_FLAGS=
--VERSION = 1.0.3
-+VERSION = 1.0.3
-
- ifdef 127mer
--CFLAGS += -D_127MER_
-+CXXFLAGS += -D_127MER_
- PROG = pregraph_sparse_127mer.v$(VERSION)
-
- else
--CFLAGS += -D_63MER_
-+CXXFLAGS += -D_63MER_
- PROG = pregraph_sparse_63mer.v$(VERSION)
- endif
-
-@@ -38,22 +38,22 @@
- endif
-
- ifneq (,$(findstring $(shell uname -m), x86_64))
--CFLAGS += -m64
-+CXXFLAGS += -m64
- endif
-
- ifneq (,$(findstring $(shell uname -m), ia64))
--CFLAGS +=
-+CXXFLAGS +=
- endif
-
- ifneq (,$(findstring $(shell uname -m), ppc64))
--CFLAGS += -mpowerpc64
-+CXXFLAGS += -mpowerpc64
- endif
-
- .SUFFIXES:.cpp .o
-
- .cpp.o:
- @printf "Compiling $<... \r"
-- @$(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< || echo "Error in command: $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $<"
-+ @$(CXX) -c $(CXXFLAGS) $(DFLAGS) $(INCLUDES) $< || echo "Error in command: $(CXX) -c $(CXXFLAGS) $(DFLAGS) $(INCLUDES) $<"
-
- all: $(OBJS)
- @printf "$(PROG) objects generated. \n"
-@@ -66,7 +66,7 @@
-
- pregraph_sparse: clean envTest $(OBJS)
- @printf "Linking... \r"
-- @$(CC) $(CFLAGS)$(INCLUDES) -o $(PROG) $(OBJS) $(LIBPATH) $(LIBS) $(ENTRAFLAGS)
-+ @$(CXX) $(CXXFLAGS)$(INCLUDES) -o $(PROG) $(OBJS) $(LIBPATH) $(LIBS) $(ENTRAFLAGS)
- @printf "$(PROG) compilation done. \n"
-
- clean:
---- Makefile.ori 2017-01-03 21:34:59.000000000 +0100
-+++ Makefile 2018-04-22 22:09:16.526124921 +0200
-@@ -1,17 +1,17 @@
- MAKEFLAGS += --no-print-directory
--CC = g++
-+CXX ?= g++
- ifdef debug
--CFLAGS= -O0 -g -fomit-frame-pointer
-+CXXFLAGS ?= -O0 -g -fomit-frame-pointer
- else
--CFLAGS= -O3 -fomit-frame-pointer
-+CXXFLAGS ?= -O3 -fomit-frame-pointer
- endif
-
- SUBDIRS = sparsePregraph standardPregraph fusion
--PROG= SOAPdenovo-63mer SOAPdenovo-127mer SOAPdenovo-fusion
--INCLUDES= -I./sparsePregraph/inc -I./standardPregraph/inc
-+PROG = SOAPdenovo-63mer SOAPdenovo-127mer SOAPdenovo-fusion
-+INCLUDES = -I./sparsePregraph/inc -I./standardPregraph/inc
-
--LIBPATH= -L/lib64 -L/usr/lib64 -L./sparsePregraph/inc -L./standardPregraph/inc
--LIBS= -pthread -lz -lm
-+LIBPATH = -L./sparsePregraph/inc -L./standardPregraph/inc
-+LIBS = -pthread -lz -lm
- EXTRA_FLAGS=
-
- BIT_ERR = 0
-@@ -25,15 +25,15 @@
- endif
-
- ifneq (,$(findstring $(shell uname -m), x86_64))
--CFLAGS += -m64
-+CXXFLAGS += -m64
- endif
-
- ifneq (,$(findstring $(shell uname -m), ia64))
--CFLAGS +=
-+CXXFLAGS +=
- endif
-
- ifneq (,$(findstring $(shell uname -m), ppc64))
--CFLAGS += -mpowerpc64
-+CXXFLAGS += -mpowerpc64
- endif
-
-
-@@ -46,20 +46,20 @@
- SOAPdenovo-63mer:
- @cd sparsePregraph;make 63mer=1 debug=1;cd ..;
- @cd standardPregraph;make 63mer=1 debug=1;cd ..;
-- @$(CC) sparsePregraph/*.o standardPregraph/*.o $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-63mer
-+ @$(CXX) sparsePregraph/*.o standardPregraph/*.o $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-63mer
- SOAPdenovo-127mer:
- @cd sparsePregraph;make 127mer=1 debug=1;cd ..;
- @cd standardPregraph;make 127mer=1 debug=1;cd ..;
-- @$(CC) sparsePregraph/*.o standardPregraph/*.o $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-127mer
-+ @$(CXX) sparsePregraph/*.o standardPregraph/*.o $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-127mer
- else
- SOAPdenovo-63mer:
- @cd sparsePregraph;make 63mer=1;cd ..;
- @cd standardPregraph;make 63mer=1;cd ..;
-- @$(CC) sparsePregraph/*.o standardPregraph/*.o $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-63mer
-+ @$(CXX) sparsePregraph/*.o standardPregraph/*.o $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-63mer
- SOAPdenovo-127mer:
- @cd sparsePregraph;make 127mer=1;cd ..;
- @cd standardPregraph;make 127mer=1;cd ..;
-- @$(CC) sparsePregraph/*.o standardPregraph/*.o $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-127mer
-+ @$(CXX) sparsePregraph/*.o standardPregraph/*.o $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-127mer
- endif
-
- clean:
---- standardPregraph/Makefile.ori 2017-01-03 21:34:59.000000000 +0100
-+++ standardPregraph/Makefile 2018-04-22 22:10:33.108337752 +0200
-@@ -5,13 +5,13 @@
- #
- ###################################
-
--CC= gcc
-+CC ?= gcc
- GCCVERSIONMAJOR := $(shell expr `$(CC) -dumpversion | cut -f1 -d.` \>= 4)
- GCCVERSIONMINOR := $(shell expr `$(CC) -dumpversion | cut -f2 -d.` \>= 4)
- ifdef debug
--CFLAGS= -O0 -g -fomit-frame-pointer #-msse4.2
-+CFLAGS ?= -O0 -g -fomit-frame-pointer #-msse4.2
- else
--CFLAGS= -O3 -fomit-frame-pointer -w #-msse4.2
-+CFLAGS ?= -O3 -fomit-frame-pointer -w #-msse4.2
- endif
- DFLAGS=
- OBJS= arc.o attachPEinfo.o bubble.o check.o compactEdge.o \
-@@ -24,12 +24,12 @@
- prlRead2path.o prlReadFillGap.o read2scaf.o readInterval.o stack.o\
- readseq1by1.o scaffold.o searchPath.o seq.o splitReps.o \
- cutTip_graph2.o linearEdge.o kmerhash.o read2edge.o iterate.o
--PROG= SOAPdenovo-63mer
--INCLUDES= -Iinc
--SUBDIRS= .
--LIBPATH= -L/lib64 -L/usr/lib64 -L./inc
--LIBS= -pthread -lz -lm
--EXTRA_FLAGS=
-+PROG = SOAPdenovo-63mer
-+INCLUDES = -Iinc
-+SUBDIRS = .
-+LIBPATH = -L./inc
-+LIBS = -pthread -lz -lm
-+EXTRA_FLAGS =
-
- BIT_ERR = 0
- ifeq (,$(findstring $(shell uname -m), x86_64 ppc64 ia64))
---- fusion/Makefile.ori 2017-01-03 21:34:59.000000000 +0100
-+++ fusion/Makefile 2018-04-22 22:11:21.209727636 +0200
-@@ -6,8 +6,8 @@
- libdir =
- mandir =
-
--CC = gcc
--CCOPT = -O3 -fprefetch-loop-arrays -funroll-loops -fomit-frame-pointer -w
-+CC ?= gcc
-+CCOPT ?= -O3 -fprefetch-loop-arrays -funroll-loops -fomit-frame-pointer -w
- LIBS = -lm -lpthread
- INCDIRS = -Iinc/
- CFLAGS = ${CCOPT} ${INCDIRS}
diff --git a/sci-biology/SOAPdenovo2/files/soapdenovo2.1 b/sci-biology/SOAPdenovo2/files/soapdenovo2.1
deleted file mode 100644
index 337618ace..000000000
--- a/sci-biology/SOAPdenovo2/files/soapdenovo2.1
+++ /dev/null
@@ -1,22 +0,0 @@
-.TH soapdenovo2 1 "February 09, 2013" "version 2.2.3" "USER COMMANDS"
-.SH NAME
-soapdenovo2 \- Short-read assembly method that can build a de novo draft assembly
-.SH SYNOPSIS
-.B soapdenovo_63mer soapdenovo_127mer
-
-.SH Introduction
-
-SOAPdenovo is a novel short-read assembly method that can build a de novo draft assembly for the human-sized genomes. The program is specially designed to assemble Illumina GA short reads. It creates new opportunities for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost effective way.
-
-1) Support large kmer up to 127 to utilize long reads. Three version are provided.
- I. The 31mer version support kmer only <=31.
- II. The 63mer version support kmer only <=63 and doubles the memory consumption than 31mer version, even being used with kmer <=31.
- III. The 127mer version support kmer only <=127 and double the memory consumption than 63mer version, even being used with kmer <=63.
-
-Please notice that, with longer kmer, the quantity of nodes would decrease significantly, thus the memory consumption is usually smaller than double with shifted version.
-
-For more information, look at the MANUAL in /usr/share/doc/soapdenovo2 or on soapdenovo web site.
-
-.SH AUTHOR
-Olivier Sallou (olivier.sallou (at) irisa.fr) - Man page and packaging
-
diff --git a/sci-biology/SOAPdenovo2/metadata.xml b/sci-biology/SOAPdenovo2/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/SOAPdenovo2/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>mmokrejs@fold.natur.cuni.cz</email>
- <name>Martin Mokrejs</name>
- </maintainer>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
-</pkgmetadata>
diff --git a/sci-biology/SPAdes/Manifest b/sci-biology/SPAdes/Manifest
index e10186934..57f4fc569 100644
--- a/sci-biology/SPAdes/Manifest
+++ b/sci-biology/SPAdes/Manifest
@@ -1,4 +1,4 @@
-DIST SPAdes-3.15.1.tar.gz 13686155 BLAKE2B fb0ff0de93302268e1fc28199be3e14ef670aeab91fca82f2e895f899c9cd8d5380c31d4fe2e884737a917ff04a94cf55d25b91a27b47c91aa3e7c7408b9bd87 SHA512 b2ee4719937912f2b6326b67f602dc62f4be319ccf2774380a487da67fc2e32adcfa417ac5fcf4c5494f80152aab561b87e30a2d36abfe50ed1c48396b44d9d9
-DIST SPAdes-3.15.1_manual.html 78200 BLAKE2B b78da09ae94a46fbf4df19ba668276e6129083e7b50f66f86da137f8ed6435a2300b133be58fe25edb0cbb598aeb66e9310425574408bc419a3e3dff18893b15 SHA512 c3571abc87ffea1c54d7f0d42ce73955a7d101a4a61ecd104538832d193eab19c8813cf0a732f2bbe428724c24be283db89165900c2d49a7f3142770de4ca3b6
-DIST SPAdes-3.15.1_rnaspades_manual.html 8624 BLAKE2B b549a6cae6b02c98cae08fd5d8975210f3593c47f2b4757f19a9445a759e332229620885a6fa2f1dc0662096974548e3d0362079d12c47e6738c0261d755a2af SHA512 2d0b169efd8aa7064d59bed8ad406477c72150f23ae0438227903645071c8f66f26fe062f7dd44b584edf8ef7c709ad6c220237e68917ec23c63cfb3139666b8
-DIST SPAdes-3.15.1_truspades_manual.html 10821 BLAKE2B eb466697f774d3421053cf0fd290c82d9b2059cafd787f10c616c1363537c59960cb8ca41a8a02983ec199e0e1a27567c5850009ad6d2173df45e38f7d3120f7 SHA512 1f3bcdbe5397a23ee94820f6aaf3b85c48aca357276f58f66607140d25529c28b31298c5c8e681df3c61dabed478ac67abeb0975885aa9b7e365e14d6aac06fd
+DIST SPAdes-3.15.3.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
diff --git a/sci-biology/SPAdes/SPAdes-3.15.1.ebuild b/sci-biology/SPAdes/SPAdes-3.15.1.ebuild
deleted file mode 100644
index 853524984..000000000
--- a/sci-biology/SPAdes/SPAdes-3.15.1.ebuild
+++ /dev/null
@@ -1,55 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DESCRIPTION="De novo de Bruijn genome assembler overcoming uneven coverage"
-HOMEPAGE="https://cab.spbu.ru/software/spades"
-SRC_URI="
- https://github.com/ablab/spades/releases/download/v${PV}/${P}.tar.gz
- https://cab.spbu.ru/files/release${PV}/manual.html -> ${P}_manual.html
- https://cab.spbu.ru/files/release${PV}/rnaspades_manual.html -> ${P}_rnaspades_manual.html
- https://cab.spbu.ru/files/release${PV}/truspades_manual.html -> ${P}_truspades_manual.html"
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS=""
-
-DEPEND="
- sys-libs/zlib
- app-arch/bzip2
- dev-python/regex"
-RDEPEND="${DEPEND}"
-BDEPEND="dev-util/cmake"
-# BUG:
-# SPAdes uses bundled while modified copy of dev-libs/boost (only headers are used,
-# not *.so or *.a are even used)
-#
-# BUG: "${S}"/ext/src/ contains plenty of bundled 3rd-party tools. Drop them all and properly DEPEND on their
-# existing packages
-# nlopt
-# llvm
-# python_libs
-# bamtools
-# ConsensusCore
-# ssw
-# jemalloc
-# htrie
-# getopt_pp
-# cppformat
-# cityhash
-# samtools
-# bwa
-
-# BUG: "${S}"/ext/tools/ contains even two version of bwa, being installed as bwa-spades binary?
-# bwa-0.7.12
-# bwa-0.6.2
-
-src_compile(){
- PREFIX="${ED}"/usr ./spades_compile.sh || die
-}
-
-src_install(){
- # BUG: move *.py files to standard site-packages/ subdirectories
- insinto /usr/share/"${PN}"
- dodoc "${DISTDIR}"/${P}_*manual.html
-}
diff --git a/sci-biology/SPAdes/SPAdes-3.15.3.ebuild b/sci-biology/SPAdes/SPAdes-3.15.3.ebuild
new file mode 100644
index 000000000..553c21e21
--- /dev/null
+++ b/sci-biology/SPAdes/SPAdes-3.15.3.ebuild
@@ -0,0 +1,36 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..10} )
+inherit python-single-r1
+
+DESCRIPTION="De novo de Bruijn genome assembler overcoming uneven coverage"
+HOMEPAGE="https://cab.spbu.ru/software/spades"
+SRC_URI="
+ https://github.com/ablab/spades/releases/download/v${PV}/${P}.tar.gz
+ https://cab.spbu.ru/files/release${PV}/manual.html -> ${P}_manual.html
+ https://cab.spbu.ru/files/release${PV}/rnaspades_manual.html -> ${P}_rnaspades_manual.html
+ https://cab.spbu.ru/files/release${PV}/truspades_manual.html -> ${P}_truspades_manual.html
+"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64"
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+DEPEND="
+ sys-libs/zlib
+ app-arch/bzip2
+ dev-python/regex
+ ${PYTHON_DEPS}
+"
+RDEPEND="${DEPEND}"
+BDEPEND="dev-util/cmake"
+
+src_install(){
+ einstalldocs
+ # WORKAROUND: This script does both compile and install in one go
+ PREFIX="${ED}"/usr ./spades_compile.sh || die
+}
diff --git a/sci-biology/Trinotate/Manifest b/sci-biology/Trinotate/Manifest
index 30ecd61fa..cb1b89168 100644
--- a/sci-biology/Trinotate/Manifest
+++ b/sci-biology/Trinotate/Manifest
@@ -1 +1 @@
-DIST Trinotate-3.2.1.tar.gz 29794455 BLAKE2B b630b4750540aeefaed598d34038ebc4bf0147f998d9a45038759b1f02cd210835b88cdc7e8e5b8e194ade05b410f8e76ea562c09dcbf09bfa56cfffafa207c3 SHA512 0c2c5021156651644cfcec09bdd19f45c4dd5ab5dd63effbacca3ffc13a32ff3b2050d8fe860e4302ade142f350c895303925542aa730c16abe0721654f8cad7
+DIST Trinotate-3.2.2.tar.gz 12902856 BLAKE2B 741b5b7386c5de646a4a1f3aa4ffc7ed9c4891e64a977efc5cd482eb0cd9315fbddc1db35f20f6fbbf136e28942542f72d33c078524971968a932f5af5d6551b SHA512 9e302eee948974c647fdcc6a352b17d55f3bd1331f6d3ddc49e0fc35f5603dcc370e9c6020e7b33dcd57324a954eab2ed3e81f2e34ef83af2fd97c793f1dfc48
diff --git a/sci-biology/Trinotate/Trinotate-3.2.1.ebuild b/sci-biology/Trinotate/Trinotate-3.2.2.ebuild
index ca61abdf4..794de03ae 100644
--- a/sci-biology/Trinotate/Trinotate-3.2.1.ebuild
+++ b/sci-biology/Trinotate/Trinotate-3.2.2.ebuild
@@ -1,17 +1,18 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
inherit perl-module
DESCRIPTION="Annotation and analysis pipeline for de novo assembled transcriptomes"
HOMEPAGE="https://github.com/Trinotate/Trinotate.github.io/wiki"
SRC_URI="https://github.com/Trinotate/Trinotate/archive/${PN}-v${PV}.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}/${PN}-${PN}-v${PV}"
LICENSE="BSD-BroadInstitute"
SLOT="0"
-KEYWORDS=""
+KEYWORDS="~amd64"
DEPEND=""
RDEPEND="${DEPEND}
@@ -32,8 +33,6 @@ RDEPEND="${DEPEND}
# In the 'rnammer' software configuration, edit the rnammer script to point
# $HMMSEARCH_BINARY = "/path/to/hmmsearch2";
-S="${WORKDIR}/${PN}-${PN}-v${PV}"
-
src_install(){
perl_set_version
dobin Trinotate
diff --git a/sci-biology/afni/Manifest b/sci-biology/afni/Manifest
index 2f909b5c4..e8caa43d1 100644
--- a/sci-biology/afni/Manifest
+++ b/sci-biology/afni/Manifest
@@ -1,3 +1,3 @@
-DIST afni-19.3.12.tar.gz 42337320 BLAKE2B f8f3347e38b7c4b3d720c3c49d5bc50f1057b1d3945e6a33b8415e84e7e539577e5eb351cfc61c53269b6a465619f900b9edcb25830ea056a53f54beb683b0ad SHA512 c4f9303312a89a6e87285646f58223df40b07329cf155bf251a48e8e63302988f103a97363d0666ddd8e9f62f762cf0c219bfc995265b4fe1f1ff5f782025371
DIST afni-20.1.16.tar.gz 43355499 BLAKE2B ad7750e64dd9f4c2ca7e5c67bd99faeb8595a41d8a16192e77202f3d307e912083affc11dcbb5da3530079b9e3cf3c2b6b470050f57d5d7af2bb35cc2322772f SHA512 e6fdb8baea6165865bae5bb186375bd65e862564c48470523a8fe026a12f00715fd21bd852bd77c4077ea444a97642c4c3d2ca8060640ba5ddd57bd7883901a6
DIST afni-20.3.03.tar.gz 43263734 BLAKE2B 7fdaf3de874edff9b32950a2724ba8b4cbcdda538b09effb12658a042326d5c8badf48f1a4dfb4555eb069347099cf3cdb08c4fe1a12999e6eca3ca6f8dca639 SHA512 3c5007f59d6c46093d38f9419c72aa36fb5701314690811f757d9568561b386cf3cd602ddf910ae08fd071ea7ae1e51f5762081217f7a29b23e32f1490f5db65
+DIST afni-22.0.21.tar.gz 43934548 BLAKE2B 3efd5b7fcbbb7b98000e8de51c363ec936a691fcbd505871ff406824ba6ecd5fef358102f6dd2e4d0991b0a40589db6416c1ef14966138c5c36499d7efa3b089 SHA512 1c741e36227075bd8b4f9983510eef95528084cbc4971f9d6d028726ffc2bb211da7a74df98991538d8f6caed041633fdceb0c4366e04d6594faa0160a0e6d2b
diff --git a/sci-biology/afni/afni-20.1.16.ebuild b/sci-biology/afni/afni-20.1.16.ebuild
index e2ed432c8..e3e16f834 100644
--- a/sci-biology/afni/afni-20.1.16.ebuild
+++ b/sci-biology/afni/afni-20.1.16.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
inherit toolchain-funcs
@@ -21,7 +21,7 @@ RDEPEND="dev-libs/expat
media-video/mpeg-tools
sci-libs/gsl
sys-devel/llvm:*
- virtual/jpeg:0
+ media-libs/libjpeg-turbo:0
x11-libs/libGLw
x11-libs/libXft
x11-libs/libXi
@@ -46,17 +46,17 @@ src_prepare() {
# 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)~" \
+ 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~LD = /usr/bin/gcc~LD = $(tc-getCC)~" \
+ -e "s~AR = /usr/bin/ar~AR = $(tc-getAR)~" \
-e "s~RANLIB = /usr/bin/ranlib~RANLIB = $(tc-getRANLIB)~" \
-i Makefile || die "Could not edit Makefile"
# they provide somewhat problematic makefiles :(
sed -e "s~ifeq ($(CC),gcc)~ifeq (1,1)~"\
-i SUMA/SUMA_Makefile || die "Could not edit SUMA/SUMA_Makefile"
# upstream checks if $CC is EXACTLY gcc, else sets variables for Mac
- find "${S}" -iname "*Makefile*" | xargs sed -e "s~/usr/~${EROOT}/usr/~g;" -i
+ find "${S}" -iname "*Makefile*" | xargs sed -e "s~/usr/~${EPREFIX}/usr/~g;" -i
default
}
diff --git a/sci-biology/afni/afni-20.3.03.ebuild b/sci-biology/afni/afni-20.3.03.ebuild
index 3185a297a..1d9043ebb 100644
--- a/sci-biology/afni/afni-20.3.03.ebuild
+++ b/sci-biology/afni/afni-20.3.03.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
inherit toolchain-funcs
@@ -21,7 +21,7 @@ RDEPEND="dev-libs/expat
media-video/mpeg-tools
sci-libs/gsl
sys-devel/llvm:*
- virtual/jpeg:0
+ media-libs/libjpeg-turbo:0
x11-libs/libGLw
x11-libs/libXft
x11-libs/libXi
@@ -39,28 +39,24 @@ S="${WORKDIR}/${PN}-AFNI_${PV}/src"
BUILD="linux_fedora_19_64"
BIN_CONFLICTS=(qdelaunay whirlgif djpeg cjpeg qhull rbox count mpeg_encode)
-#PATCHES=(
-# "${FILESDIR}/${P}-python.patch"
-#)
-
src_prepare() {
- eapply "${FILESDIR}/${P}-python.patch" || die
+ 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)~" \
+ 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~LD = /usr/bin/gcc~LD = $(tc-getCC)~" \
+ -e "s~AR = /usr/bin/ar~AR = $(tc-getAR)~" \
-e "s~RANLIB = /usr/bin/ranlib~RANLIB = $(tc-getRANLIB)~" \
-i Makefile || die "Could not edit Makefile"
# they provide somewhat problematic makefiles :(
sed -e "s~ifeq ($(CC),gcc)~ifeq (1,1)~"\
-i SUMA/SUMA_Makefile || die "Could not edit SUMA/SUMA_Makefile"
# upstream checks if $CC is EXACTLY gcc, else sets variables for Mac
- find "${S}" -iname "*Makefile*" | xargs sed -e "s~/usr/~${EROOT}/usr/~g;" -i
+ find "${S}" -iname "*Makefile*" | xargs sed -e "s~/usr/~${EPREFIX}/usr/~g;" -i
default
}
diff --git a/sci-biology/afni/afni-19.3.12.ebuild b/sci-biology/afni/afni-22.0.21.ebuild
index db19930fd..149deede8 100644
--- a/sci-biology/afni/afni-19.3.12.ebuild
+++ b/sci-biology/afni/afni-22.0.21.ebuild
@@ -1,46 +1,49 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
inherit toolchain-funcs
DESCRIPTION="An open-source environment for processing and displaying functional MRI data"
HOMEPAGE="http://afni.nimh.nih.gov/"
SRC_URI="https://github.com/afni/afni/archive/AFNI_${PV}.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}/${PN}-AFNI_${PV}/src"
LICENSE="GPL-3+"
SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
+# SUMA error: https://ppb.chymera.eu/4223de.log
+KEYWORDS=""
-RDEPEND="dev-libs/expat
+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:*
- virtual/jpeg:0
+ 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
+ x11-libs/motif
+"
DEPEND="${RDEPEND}
- app-shells/tcsh"
+ app-shells/tcsh
+"
-S="${WORKDIR}/${PN}-AFNI_${PV}/src"
BUILD="linux_fedora_19_64"
-BIN_CONFLICTS=(qdelaunay whirlgif djpeg cjpeg qhull rbox count mpeg_encode)
+BIN_CONFLICTS=(qdelaunay whirlgif djpeg cjpeg qhull rbox count)
src_prepare() {
- find -type f -exec sed -i -e "s/-lXp //g" {} +
+ # 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" \
@@ -52,11 +55,11 @@ src_prepare() {
-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)~"\
+ sed -e "s~ifeq (\$(CC),gcc)~ifeq (1,1)~"\
-i SUMA/SUMA_Makefile || die "Could not edit SUMA/SUMA_Makefile"
# upstream checks if $CC is EXACTLY gcc, else sets variables for Mac
- find "${S}" -iname "*Makefile*" | xargs sed -e "s~/usr/~${EROOT}/usr/~g;" -i
- eapply_user
+ find "${S}" -iname "*Makefile*" | xargs sed -e "s~/usr/~${EPREFIX}/usr/~g;" -i || die
+ default
}
src_compile() {
@@ -64,9 +67,9 @@ src_compile() {
}
src_install() {
- emake INSTALLDIR="${ED}/usr/bin" -j1 install install_plugins
- emake INSTALLDIR="${ED}/usr/$(get_libdir)" -j1 install_lib
+ 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/${CONFLICT}"
+ rm "${ED}/usr/bin/${CONFLICT}" || die
done
}
diff --git a/sci-biology/afni/afni-9999.ebuild b/sci-biology/afni/afni-9999.ebuild
deleted file mode 100644
index c6e4c669b..000000000
--- a/sci-biology/afni/afni-9999.ebuild
+++ /dev/null
@@ -1,70 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit git-r3 toolchain-funcs
-
-DESCRIPTION="An open-source environment for processing and displaying functional MRI data"
-HOMEPAGE="http://afni.nimh.nih.gov/"
-SRC_URI=""
-EGIT_REPO_URI="https://github.com/AFNI/AFNI"
-
-LICENSE="GPL-3+"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-RDEPEND="dev-libs/expat
- media-libs/glu
- media-libs/netpbm
- media-libs/qhull
- media-video/mpeg-tools
- sci-libs/gsl
- sys-devel/llvm:*
- virtual/jpeg:0
- x11-libs/libGLw
- x11-libs/libXft
- x11-libs/libXi
- x11-libs/libXpm
- x11-libs/motif[-static-libs]"
-
-# x11-libs/motif[static-libs] breaks the build.
-# See upstream discussion
-# http://afni.nimh.nih.gov/afni/community/board/read.php?1,85348,85348#msg-85348
-
-DEPEND="${RDEPEND}
- app-shells/tcsh"
-
-S="${WORKDIR}/${P}/src"
-BUILD="linux_fedora_19_64"
-BIN_CONFLICTS=(qdelaunay whirlgif djpeg cjpeg qhull rbox count mpeg_encode)
-
-src_prepare() {
- find -type f -exec sed -i -e "s/-lXp //g" {} +
- cp other_builds/Makefile.${BUILD} Makefile || die "Could not copy Makefile"
- sed -e "s~CC = /usr/bin/gcc -O2 -m64~CC = $(tc-getCC) \$(CFLAGS)~" \
- -e "s~CCMIN = /usr/bin/gcc -m64~CCMIN = $(tc-getCC) \$(CFLAGS)~" \
- -e "s~LD = /usr/bin/gcc~LD = $(tc-getCC)~" \
- -e "s~AR = /usr/bin/ar~AR = $(tc-getAR)~" \
- -e "s~RANLIB = /usr/bin/ranlib~RANLIB = $(tc-getRANLIB)~" \
- -i Makefile || die "Could not edit Makefile"
- # they provide somewhat problematic makefiles :(
- sed -e "s~ifeq ($(CC),gcc)~ifeq (1,1)~"\
- -i SUMA/SUMA_Makefile || die "Could not edit SUMA/SUMA_Makefile"
- # upstream checks if $CC is EXACTLY gcc, else sets variables for Mac
- find "${S}" -iname "*Makefile*" | xargs sed -e "s~/usr/~${EROOT}/usr/~g;" -i
- eapply_user
-}
-
-src_compile() {
- emake -j1 all plugins suma_exec
-}
-
-src_install() {
- emake INSTALLDIR="${ED}/usr/bin" -j1 install install_plugins
- emake INSTALLDIR="${ED}/usr/$(get_libdir)" -j1 install_lib
- for CONFLICT in ${BIN_CONFLICTS[@]}; do
- rm "${ED}/usr/bin/${CONFLICT}"
- done
-}
diff --git a/sci-biology/afni/files/afni-20.1.16-python.patch b/sci-biology/afni/files/afni-20.1.16-python.patch
index 24ed98405..8c3e859f5 100644
--- a/sci-biology/afni/files/afni-20.1.16-python.patch
+++ b/sci-biology/afni/files/afni-20.1.16-python.patch
@@ -1,5 +1,5 @@
--- a/other_builds/Makefile.linux_fedora_19_64 2020-10-09 07:07:58.348874414 -0400
-+++ b/other_builds/Makefile.linux_fedora_19_64 2020-10-10 01:15:22.337755934 -0400
++++ b/other_builds/Makefile.linux_fedora_19_64 2020-10-10 01:15:22.337755934 -0400
@@ -11,8 +11,6 @@
# ------------------------------
diff --git a/sci-biology/afni/files/afni-20.3.03-python.patch b/sci-biology/afni/files/afni-20.3.03-python.patch
deleted file mode 100644
index 24ed98405..000000000
--- a/sci-biology/afni/files/afni-20.3.03-python.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- a/other_builds/Makefile.linux_fedora_19_64 2020-10-09 07:07:58.348874414 -0400
-+++ b/other_builds/Makefile.linux_fedora_19_64 2020-10-10 01:15:22.337755934 -0400
-@@ -11,8 +11,6 @@
-
- # ------------------------------
- # python from C
--IPYTHON = -DSELENIUM_READY -I/usr/include/python2.7
--LDPYTHON = -lpython2.7
-
- # ----------------------------------------------------------------------
- # X configuration
diff --git a/sci-biology/aghermann/aghermann-1.1.2-r2.ebuild b/sci-biology/aghermann/aghermann-1.1.2-r2.ebuild
index 4606fa9df..b0ac5fe00 100644
--- a/sci-biology/aghermann/aghermann-1.1.2-r2.ebuild
+++ b/sci-biology/aghermann/aghermann-1.1.2-r2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
@@ -13,7 +13,7 @@ SRC_URI="http://johnhommer.com/code/aghermann/source/${P}.tar.xz"
LICENSE="GPL-2+"
SLOT="0"
-KEYWORDS=""
+KEYWORDS="~amd64"
REQUIRED_USE="${LUA_REQUIRED_USE}"
diff --git a/sci-biology/ants/ants-2.3.4.ebuild b/sci-biology/ants/ants-2.3.4.ebuild
index 756fde11d..95eb6355b 100644
--- a/sci-biology/ants/ants-2.3.4.ebuild
+++ b/sci-biology/ants/ants-2.3.4.ebuild
@@ -14,7 +14,7 @@ HOMEPAGE="http://stnava.github.io/ANTs/"
SRC_URI="
https://github.com/ANTsX/ANTs/archive/v${PV}.tar.gz -> ${P}.tar.gz
test? (
- http://chymera.eu/distfiles/ants_testdata-${PV}.tar.xz
+ http://resources.chymera.eu/distfiles/ants_testdata-${PV}.tar.xz
)
"
diff --git a/sci-biology/arachne/Manifest b/sci-biology/arachne/Manifest
deleted file mode 100644
index c70683996..000000000
--- a/sci-biology/arachne/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST arachne-46233.tar.gz 5161566 BLAKE2B dc9381fae80477e4a2439e24cbcf9bc462c7a4effb06c26a9f74ad1740f86a96273c3dae142d0065aad08d6340e9508528c35ee6914a8405b66327bfc4ec89da SHA512 4ab293e7f4477dd6aeba7c6bc1a78d168cbb811d7f67cbcbc1eea094a7b6bd180bdde6fb1b7c8256ff473dba3d748a43bd426d971575f1c0793289a0b200dc2b
diff --git a/sci-biology/arachne/arachne-46233.ebuild b/sci-biology/arachne/arachne-46233.ebuild
deleted file mode 100644
index b34d00134..000000000
--- a/sci-biology/arachne/arachne-46233.ebuild
+++ /dev/null
@@ -1,39 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DESCRIPTION="Whole genome shotgun OLC assembler for Sanger reads (overlap-layout-contig)"
-HOMEPAGE="https://genome.cshlp.org/content/12/1/177.abstract"
-SRC_URI="ftp://ftp.broadinstitute.org/pub/crd/ARACHNE/latest_source_code/${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS=""
-IUSE="doc openmp"
-
-DEPEND="dev-libs/xerces-c
- doc? ( virtual/latex-base app-text/dvipsk )"
-RDEPEND="${DEPEND}"
-
-# needs >=g++-4.7 but does not compile with 5.3.0
-
-# --disable-openmp to disable requirement for OpenMP-capable compiler
-src_configure() {
- local myconf=()
- use openmp || myconf+=( --disable-openmp )
- econf ${myconf[@]}
-}
-
-# set the following environment variables
-# http://www.broadinstitute.org/crd/wiki/index.php/Setup
-#
-# ARACHNE_PRE
-# ARACHNE_BIN_DIR
-# ARACHNE_PRETTY_HELP
-
-pkg_postinst(){
- einfo "Please add these to your ~/.bashrc"
- einfo "limit stacksize 100000"
- einfo "limit datasize unlimited"
-}
diff --git a/sci-biology/arachne/metadata.xml b/sci-biology/arachne/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/arachne/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>mmokrejs@fold.natur.cuni.cz</email>
- <name>Martin Mokrejs</name>
- </maintainer>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
-</pkgmetadata>
diff --git a/sci-biology/bambus/bambus-2.33.ebuild b/sci-biology/bambus/bambus-2.33-r2.ebuild
index e92c8c8da..475c7f0b1 100644
--- a/sci-biology/bambus/bambus-2.33.ebuild
+++ b/sci-biology/bambus/bambus-2.33-r2.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
inherit perl-module toolchain-funcs
@@ -66,28 +66,12 @@ src_prepare() {
einfo "bambus-2.33/src/TIGR_Foundation_CC/OptionResult.cc:/*! Uses same syntax as getopt"
#rm -rf src/TIGR_Foundation_CC || die "Failed to rm -rf src/TIGR_Foundation_CC/, we use it from sci-biology/tigr-foundation-libs"
#sed -i 's:TIGR_Foundation_CC::' src/Makefile || die "Failed to zap last pointer to local copy of tigr-foundation-libs"
- cd src/TIGR_Foundation_CC || die "Failed to cd src/TIGR_Foundation_CC/"
- sed -e "s:/export/usr/local:${ED}/usr:g" -i Makefile || die
-}
-
-src_compile() {
- emake DESTDIR="${ED}/usr"
-
- # TODO:
- #ld -L../TIGR_Foundation_CC/ -shared -fPIC -o grommit grommit.o -L. -lgraph -lTigrFoundation
- # ld: warning: creating a DT_TEXTREL in object.
- #
- # * QA Notice: The following files contain runtime text relocations
- # * Text relocations force the dynamic linker to perform extra
- # * work at startup, waste system resources, and may pose a security
- # * risk. On some architectures, the code may not even function
- # * properly, if at all.
- # * For more information, see http://hardened.gentoo.org/pic-fix-guide.xml
- # * Please include the following list of files in your report:
- # * TEXTREL usr/bin/grommit
}
src_install() {
+ pushd src/TIGR_Foundation_CC || die
+ sed -e "s:/export/usr/local:${ED}/usr:g" -i Makefile || die
+ popd || die
emake DESTDIR="${ED}/usr" install
# cvs HEAD of amos now contains even more updated files: /usr/bin/printScaff /usr/bin/untangle /usr/lib/TIGR/AsmLib.pm
for f in FASTArecord.pm FASTAreader.pm Foundation.pm FASTAgrammar.pm AsmLib.pm; do rm "${ED}"/usr/lib/TIGR/$f; done || die
@@ -102,13 +86,13 @@ src_install() {
done
rm "${ED}"/usr/lib/libTigrFoundation.a || die
- dodir /usr/share/doc/${P}
+ dodir /usr/share/doc/${PF}
mv "${ED}"/usr/doc/* "${ED}"/usr/share/doc/${PF} || die
rmdir "${ED}"/usr/doc || die
dobin "${FILESDIR}"/goBambus.pl
dodoc "${DISTDIR}"/scaffolding_MIRA_BAMBUS.pdf
- rm -rf "${ED}"/usr/lib || die
+ rm -r "${ED}"/usr/lib || die
}
pkg_postinst(){
diff --git a/sci-biology/behaviopy/Manifest b/sci-biology/behaviopy/Manifest
index e5e6f36cd..916b93320 100644
--- a/sci-biology/behaviopy/Manifest
+++ b/sci-biology/behaviopy/Manifest
@@ -1 +1 @@
-DIST behaviopy-0.1.tar.gz 32986 BLAKE2B f0de67a59591f266906d0b21c8fedf1e847df47128f0cb45e10fca849c674cb95d1ef586f407c9775ccaad8a7300aa4d6a67f1a4cc77fa18af28ec0848b77605 SHA512 8cead97a6bf06b31b817999377e5460ec7b05b58a997bcad9c8947f6cd1ab48d2525600c0c6e18bd6e52fccd8a9358b5f36c9911d1fab0fb974dc6581a63949b
+DIST behaviopy-0.2.tar.gz 36812 BLAKE2B 099f245027ddbbd38478bc48df1746e25e5a2b8d32a381f3352cb4c1339f9aa7a101ff0a3b797bceb543db1656044470911dd2e3addd44f5d2cd8d661e20a0cf SHA512 b7939ac3dcbbc445b5459a2bb96e413ca71e720c14e441d3d9864422be13c6b78178c5a1006f851d141c70a3f1ab9635ea636841610e0f210ca3f35a0f12f9bc
diff --git a/sci-biology/behaviopy/behaviopy-0.1.ebuild b/sci-biology/behaviopy/behaviopy-0.2.ebuild
index 35bcaab6b..ca6700729 100644
--- a/sci-biology/behaviopy/behaviopy-0.1.ebuild
+++ b/sci-biology/behaviopy/behaviopy-0.2.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
-PYTHON_COMPAT=( python3_{7,8} )
+PYTHON_COMPAT=( python3_{8..10} )
inherit distutils-r1
@@ -13,11 +13,9 @@ SRC_URI="https://github.com/TheChymera/behaviopy/archive/${PV}.tar.gz -> ${P}.ta
LICENSE="GPL-3"
SLOT="0"
-IUSE="evaluation test"
+IUSE="evaluation"
KEYWORDS="~amd64 ~x86"
-RESTRICT="!test? ( test )"
-DEPEND="dev-python/setuptools[${PYTHON_USEDEP}]"
RDEPEND="
dev-python/matplotlib[${PYTHON_USEDEP}]
dev-python/numpy[${PYTHON_USEDEP}]
@@ -25,17 +23,17 @@ RDEPEND="
dev-python/seaborn[${PYTHON_USEDEP}]
dev-python/statsmodels[${PYTHON_USEDEP}]
dev-python/scipy[${PYTHON_USEDEP}]
- "
+"
-src_prepare() {
+python_prepare_all() {
if ! use evaluation; then
rm behaviopy/evaluation.py || die
fi
- default
+ distutils-r1_python_prepare_all
}
python_test() {
- cd behaviopy/examples
+ cd behaviopy/examples || die
echo "backend : Agg" > matplotlibrc || die
for i in *py; do
echo "Executing $i"
diff --git a/sci-biology/behaviopy/behaviopy-9999.ebuild b/sci-biology/behaviopy/behaviopy-9999.ebuild
deleted file mode 100644
index a4c087764..000000000
--- a/sci-biology/behaviopy/behaviopy-9999.ebuild
+++ /dev/null
@@ -1,46 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7,8} )
-
-inherit distutils-r1 git-r3
-
-DESCRIPTION="Neuroimaging tools for Python"
-HOMEPAGE="https://github.com/TheChymera/behaviopy"
-SRC_URI=""
-EGIT_REPO_URI="https://github.com/TheChymera/behaviopy"
-
-LICENSE="GPL-3"
-SLOT="0"
-IUSE="evaluation test"
-KEYWORDS=""
-RESTRICT="!test? ( test )"
-
-DEPEND="dev-python/setuptools[${PYTHON_USEDEP}]"
-RDEPEND="
- dev-python/matplotlib[${PYTHON_USEDEP}]
- dev-python/numpy[${PYTHON_USEDEP}]
- dev-python/pandas[${PYTHON_USEDEP}]
- dev-python/seaborn[${PYTHON_USEDEP}]
- dev-python/statsmodels[${PYTHON_USEDEP}]
- dev-python/scipy[${PYTHON_USEDEP}]
- "
- #evaluation? ( sci-biology/psychopy[${PYTHON_USEDEP}] )
-
-src_prepare() {
- if ! use evaluation; then
- rm behaviopy/evaluation.py || die
- fi
- default
-}
-
-python_test() {
- cd behaviopy/examples
- echo "backend : Agg" > matplotlibrc || die
- for i in *py; do
- echo "Executing $i"
- ${EPYTHON} $i || die
- done
-}
diff --git a/sci-biology/blasr/Manifest b/sci-biology/blasr/Manifest
new file mode 100644
index 000000000..7819d5a37
--- /dev/null
+++ b/sci-biology/blasr/Manifest
@@ -0,0 +1 @@
+DIST blasr-5.3.5.tar.gz 2709986 BLAKE2B 48a8d12e4a47159c00d5febab4222dec5e2f4e5ce4d7a481243b4b62e0ba693eb9e1aa2a11b5de36606ec977db3947178cfdd0a1a09ccfea213e1a1567402e74 SHA512 79155f29076e4a9fe1d66d9e8310d38d3b6690fe1959be923627607ed4d7dfe97c020ff9f9134a3cffcb8e1cd5eb1b3a861d10cb476f9c3866c87e85e6ae93e7
diff --git a/sci-biology/blasr/blasr-9999.ebuild b/sci-biology/blasr/blasr-5.3.5.ebuild
index cbd012727..85e4ea66d 100644
--- a/sci-biology/blasr/blasr-9999.ebuild
+++ b/sci-biology/blasr/blasr-5.3.5.ebuild
@@ -1,26 +1,24 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
-inherit meson git-r3
+inherit meson
DESCRIPTION="The PacBio long read aligner"
HOMEPAGE="http://www.smrtcommunity.com/SMRT-Analysis/Algorithms/BLASR"
-EGIT_REPO_URI="https://github.com/PacificBiosciences/blasr.git"
-#SRC_URI="https://github.com/PacificBiosciences/blasr/tarball/${PV} -> ${P}.tar.gz"
+SRC_URI="https://github.com/PacificBiosciences/blasr/archive/${PV}.tar.gz -> ${P}.tar.gz"
LICENSE="blasr"
SLOT="0"
-KEYWORDS=""
+KEYWORDS="~amd64"
BDEPEND="
dev-util/cmake
virtual/pkgconfig
"
DEPEND="
- sci-biology/pbbam
sci-biology/libblasr
- dev-libs/boost:=[threads(-)]
+ dev-libs/boost:=
"
RDEPEND="${DEPEND}"
diff --git a/sci-biology/canu/canu-2.1.1.ebuild b/sci-biology/canu/canu-2.1.1.ebuild
index e14efe3af..987fb99f2 100644
--- a/sci-biology/canu/canu-2.1.1.ebuild
+++ b/sci-biology/canu/canu-2.1.1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
@@ -28,8 +28,7 @@ RDEPEND="${PYTHON_DEPS}
DEPEND="${RDEPEND}
>=virtual/jdk-1.8:*
dev-java/ant-core
- !sci-biology/wgs-assembler
- "
+"
# Detected file collision(s):
# * sci-biology/wgs-assembler-8.3_rc2:0::science
diff --git a/sci-biology/chiron/chiron-0.6.1.1.ebuild b/sci-biology/chiron/chiron-0.6.1.1.ebuild
index 645e4ed30..162a03129 100644
--- a/sci-biology/chiron/chiron-0.6.1.1.ebuild
+++ b/sci-biology/chiron/chiron-0.6.1.1.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
-PYTHON_COMPAT=( python3_{7,8} )
+PYTHON_COMPAT=( python3_{8..9} )
DISTUTILS_USE_SETUPTOOLS=rdepend
inherit distutils-r1
diff --git a/sci-biology/conrad/Manifest b/sci-biology/conrad/Manifest
deleted file mode 100644
index 33745ecdd..000000000
--- a/sci-biology/conrad/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST conrad-1.zip 13266670 BLAKE2B bd89175dd02541323bfefeed1c0a9691c46f21ed08041b5f89a7424660a4eeeb469e4695f6345a15544b8affb5a5e3879f3551729299802c0e3454624cd85164 SHA512 804b70442437317276dd4757806ce1dec2deb4f3121ef08c981c955dd0e943d135c98727a956f605a6d42a913c9efb2c72c1c2dab4015e8fce925f10f51118f3
diff --git a/sci-biology/conrad/conrad-1.ebuild b/sci-biology/conrad/conrad-1.ebuild
deleted file mode 100644
index bca495174..000000000
--- a/sci-biology/conrad/conrad-1.ebuild
+++ /dev/null
@@ -1,52 +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="Ab initio- and ad hoc evidence-based (RNA-Seq, BLAST) gene/ORF predictor"
-HOMEPAGE="https://sourceforge.net/projects/conradcrf"
-SRC_URI="https://downloads.sourceforge.net/project/conradcrf/conradcrf/Version%201/conradSrc.zip -> ${P}.zip"
-
-LICENSE="LGPL-2.1"
-SLOT="0"
-KEYWORDS="~amd64"
-
-RDEPEND="
- >=virtual/jre-1.5:*
- <virtual/jdk-1.9:*
- dev-java/commons-logging
- >=dev-java/commons-lang-2.1:*
- dev-java/colt
- dev-java/dom4j
- "
- # spring # see bug #97004
- # dev-java/LBFGS # LBFGS is a numericla library we use internally for the solver
-DEPEND="${RDEPEND}
- >=virtual/jdk-1.5:*
- <virtual/jdk-1.9:*
- dev-java/ant-core
- >=dev-java/jfreechart-1.0.3
- >=dev-java/jcommon-1.0.6
- >=dev-java/commons-math-1.1
- "
-BDEPEND="app-arch/unzip"
-S="${WORKDIR}"
-
-src_prepare(){
- default
- sed -e s'#lib/conrad.jar#/usr/share/conrad/lib/conrad.jar#' -i bin/conrad.sh || die
-}
-
-src_compile(){
- cd dev || die
- ant compile || die
-}
-
-src_install() {
- dobin bin/conrad.sh
- java-pkg_dojar lib/conrad.jar
- java-pkg_dolauncher conrad --jar conrad.jar
- dodoc -r docs models samples trainingFiles
-}
diff --git a/sci-biology/conrad/metadata.xml b/sci-biology/conrad/metadata.xml
deleted file mode 100644
index 814dcabcc..000000000
--- a/sci-biology/conrad/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">conradcrf</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/sci-biology/cortex_var/Manifest b/sci-biology/cortex_var/Manifest
deleted file mode 100644
index 969e60d0a..000000000
--- a/sci-biology/cortex_var/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST CORTEX_release_v1.0.5.21.tgz 26902149 BLAKE2B 397d309fa941fd76ca51f58f20e036dd51548455ae2831738f03fed2293bb3f8dac7443282bba900b3f264a14e6bdacc23ff5460e713c05d4c5e5f11de021080 SHA512 92200cc1e886e519a8e54c9054a2901a03001091654a0534c7a92a5fa7a0ac43aba782b59731d588525902adf749cabca64cdb9cdb25c215be9afb01690215e3
-DIST cortex_var_user_manual.pdf 265899 BLAKE2B 83797183e88f0c17fe3a114c2912263bb84b4c2dca1a0a2a563c82fe377111d24a8ad726581f62b3e44a6cc714bcf58ffd8c18f9f5bd0eb9df6130bd49b296ee SHA512 e4ff442f9280e9eee384c2b82c75493bdb90589b354333fc8b2bee8cf9c9baa432ec09dce5325b2e12c1e1930971616065713858565d56f9a361c573ac0c4f65
diff --git a/sci-biology/cortex_var/cortex_var-1.0.5.21.ebuild b/sci-biology/cortex_var/cortex_var-1.0.5.21.ebuild
deleted file mode 100644
index d368f5db3..000000000
--- a/sci-biology/cortex_var/cortex_var-1.0.5.21.ebuild
+++ /dev/null
@@ -1,51 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit perl-functions
-
-DESCRIPTION="Genotype variant discovery without reference sequence"
-HOMEPAGE="http://cortexassembler.sourceforge.net/index_cortex_var.html" # no https
-SRC_URI="
- https://sourceforge.net/projects/cortexassembler/files/cortex_var/latest/CORTEX_release_v${PV}.tgz
- http://cortexassembler.sourceforge.net/cortex_var_user_manual.pdf"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS=""
-
-# http://www.well.ox.ac.uk/project-stampy
-
-DEPEND="
- sci-biology/vcftools
- sci-libs/gsl
- sci-libs/htslib:0=
- dev-lang/perl"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}/CORTEX_release_v${PV}"
-
-src_prepare(){
- default
- sed -i -e "s/ -O3 / ${CFLAGS} /" Makefile || die
- sed -i -e "s#libs/gsl-1.15#${EPREFIX}/usr/include/gsl#" Makefile || die
-}
-
-src_compile(){
- rm -rf libs/htslib libs/gsl-1.15 || die
- emake -C libs/string_buffer
- emake STRING_BUF_PATH="${S}/libs/string_buffer" HTS_PATH="/usr/include/" -C libs/seq_file
- emake NUM_COLS=1 MAXK=31 cortex_var
-}
-
-src_install(){
- bash install.sh || die
- perl_set_version
- perl_domodule scripts/analyse_variants/bioinf-perl/lib/* scripts/calling/*
- echo \
- "PATH=${EPREFIX}/usr/share/${PN}/scripts/analyse_variants/needleman_wunsch" \
- > "${T}/99${PN}" || die
- doenvd "${T}/99${PN}"
- dodoc "${DISTDIR}"/cortex_var_user_manual.pdf
-}
diff --git a/sci-biology/cortex_var/metadata.xml b/sci-biology/cortex_var/metadata.xml
deleted file mode 100644
index a2867d6fd..000000000
--- a/sci-biology/cortex_var/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>mmokrejs@fold.natur.cuni.cz</email>
- <name>Martin Mokrejs</name>
- </maintainer>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
- <upstream>
- <remote-id type="sourceforge">cortexassembler</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/sci-biology/cramtools/Manifest b/sci-biology/cramtools/Manifest
deleted file mode 100644
index 7d81698d2..000000000
--- a/sci-biology/cramtools/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST cramtools-3.0.tar.gz 7394093 BLAKE2B dc0b21f94b1c3f256a55f4aa324106b6bfb3cd9548ce0aaf589c4da9f95fcbb0007a71c44ed6a915340d86c80555f91ebbf5864e38603f06a73aa132af23772e SHA512 077806ece2e0449f2245e4aefd5ebf5ae91e01f177575a3fed9f7458f8d0ba0a554c368ec56ba305f58ed7f3502a7ac1da1685fb38a19e3230564f4329ecb080
diff --git a/sci-biology/cramtools/cramtools-3.0.ebuild b/sci-biology/cramtools/cramtools-3.0.ebuild
deleted file mode 100644
index b57f4fb26..000000000
--- a/sci-biology/cramtools/cramtools-3.0.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
-
-inherit java-pkg-2 java-ant-2
-
-DESCRIPTION="Java tools and APIs for efficient compression of sequence read data"
-HOMEPAGE="http://www.ebi.ac.uk/ena/software/cram-toolkit
- https://github.com/enasequence/cramtools"
-SRC_URI="https://github.com/enasequence/cramtools/archive/v3.0.tar.gz -> ${P}.tar.gz"
-
-LICENSE="Apache-2.0"
-SLOT="0"
-KEYWORDS="~amd64"
-
-DEPEND="
- >=virtual/jdk-1.7:*
- dev-java/ant-core
- dev-java/htsjdk"
-RDEPEND="
- ${DEPEND}
- >=virtual/jre-1.7:*"
-
-# TODO: zap bundled htsjdk to ensure it uses dev-java/htsjdk?
-# https://github.com/enasequence/cramtools/issues/58
-# https://github.com/enasequence/cramtools/issues/59
-src_compile(){
- ant -f build/build.xml runnable || die
-}
-
-src_install() {
- java-pkg_newjar "${P}.jar" "${PN}.jar"
-}
diff --git a/sci-biology/cramtools/metadata.xml b/sci-biology/cramtools/metadata.xml
deleted file mode 100644
index 5a55ad312..000000000
--- a/sci-biology/cramtools/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>mmokrejs@fold.natur.cuni.cz</email>
- <name>Martin Mokrejs</name>
- </maintainer>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
- <upstream>
- <remote-id type="github">enasequence/cramtools</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/sci-biology/dargcc_bidsdata/dargcc_bidsdata-1.0.ebuild b/sci-biology/dargcc_bidsdata/dargcc_bidsdata-1.0.ebuild
index df7ba43bb..0312eda29 100644
--- a/sci-biology/dargcc_bidsdata/dargcc_bidsdata-1.0.ebuild
+++ b/sci-biology/dargcc_bidsdata/dargcc_bidsdata-1.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
@@ -7,7 +7,6 @@ DESCRIPTION="BIDS data selection of wildtype animals from DARGCC article"
HOMEPAGE="https://academic.oup.com/cercor/article/28/7/2495/4975475"
SRC_URI="
https://zenodo.org/record/3885733/files/${P}.tar.xz
- http://chymera.eu/distfiles/${P}.tar.xz
"
LICENSE="GPL-3"
diff --git a/sci-biology/drlfom_bidsdata/drlfom_bidsdata-1.1.ebuild b/sci-biology/drlfom_bidsdata/drlfom_bidsdata-1.1.ebuild
index 6385db093..227aafd54 100644
--- a/sci-biology/drlfom_bidsdata/drlfom_bidsdata-1.1.ebuild
+++ b/sci-biology/drlfom_bidsdata/drlfom_bidsdata-1.1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
@@ -9,7 +9,6 @@ DESCRIPTION="BIDS data files released with the DRLFOM publication"
HOMEPAGE="http://www.aic-fmi.ethz.ch/"
SRC_URI="
https://zenodo.org/record/3598424/files/${P}.tar.xz
- http://chymera.eu/distfiles/${P}.tar.xz
"
LICENSE="CC-BY-SA-4.0"
diff --git a/sci-biology/fsl/files/fsl-6.0.2-fsldir_redux-p1.patch b/sci-biology/fsl/files/fsl-6.0.2-fsldir_redux-p1.patch
deleted file mode 100644
index ca3945442..000000000
--- a/sci-biology/fsl/files/fsl-6.0.2-fsldir_redux-p1.patch
+++ /dev/null
@@ -1,240 +0,0 @@
-From 2bc4be1f55b27a733e1e624b34bc570187ba95e1 Mon Sep 17 00:00:00 2001
-From: François Bissey <frp.bissey@gmail.com>
-Date: Mon, 20 Jan 2020 11:40:53 +1300
-Subject: [PATCH] Making sure fsl code and executable can find other executable
- and data in standard location.
-
----
- src/fast4/fast_two.cc | 8 ++++----
- src/feat5/feat_model.cc | 8 +++-----
- src/feat5/tsplot.cc | 7 +++----
- src/first/first_utils.cc | 4 ++--
- src/fnirt/fnirtfns.cpp | 11 ++++-------
- src/fslsurface/fslsurface_first.cc | 6 ++----
- src/fslsurface/fslsurfacemaths.cpp | 12 ------------
- src/libvis/miscpic.h | 7 +------
- src/melodic/meldata.cc | 4 ++--
- src/melodic/meloptions.cc | 8 --------
- src/melodic/meloptions.h | 1 -
- src/melodic/melreport.cc | 12 ++++++------
- src/melodic/melreport.h | 20 ++++++++++----------
- src/mm/mixture_model.cc | 4 ++--
- src/siena/siena_diff.cc | 28 +++++++++++++---------------
- src/topup/topupfns.cpp | 3 +--
- 16 files changed, 53 insertions(+), 90 deletions(-)
-
-diff --git a/src/fast4/fast_two.cc b/src/fast4/fast_two.cc
-index 592b5df..b525444 100644
---- a/src/fast4/fast_two.cc
-+++ b/src/fast4/fast_two.cc
-@@ -166,7 +166,7 @@ int prior_registration(string inname, string main_prior_vol, NEWIMAGE::volume<fl
- string csfPriorName, grayPriorName, whitePriorName;
- if(alternatePriors.unset())
- {
-- string priorRootName=string(getenv("FSLDIR")) + "/data/standard/tissuepriors/avg152T1_";
-+ string priorRootName="@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/tissuepriors/avg152T1_";
- csfPriorName = priorRootName+"csf";
- grayPriorName = priorRootName+"gray";
- whitePriorName = priorRootName+"white";
-@@ -215,15 +215,15 @@ string csfPriorName, grayPriorName, whitePriorName;
- if(bapused>0)
- {
- char reg[1024];
-- sprintf(reg, "%s/bin/flirt -ref %s -in %s -out %s -applyxfm -init %s", getenv("FSLDIR"), inname.c_str(), csfPriorName.c_str(), (main_prior_vol+"_csf_stdspace").c_str(), bapriori.value().c_str());
-+ sprintf(reg, "flirt -ref %s -in %s -out %s -applyxfm -init %s", inname.c_str(), csfPriorName.c_str(), (main_prior_vol+"_csf_stdspace").c_str(), bapriori.value().c_str());
- if(verbose.value())
- cout<<reg<<endl;
- system(reg);
-- sprintf(reg, "%s/bin/flirt -ref %s -in %s -out %s -applyxfm -init %s", getenv("FSLDIR"), inname.c_str(), grayPriorName.c_str(), (main_prior_vol+"_gm_stdspace").c_str(), bapriori.value().c_str());
-+ sprintf(reg, "flirt -ref %s -in %s -out %s -applyxfm -init %s", inname.c_str(), grayPriorName.c_str(), (main_prior_vol+"_gm_stdspace").c_str(), bapriori.value().c_str());
- if(verbose.value())
- cout<<reg<<endl;
- system(reg);
-- sprintf(reg, "%s/bin/flirt -ref %s -in %s -out %s -applyxfm -init %s", getenv("FSLDIR"), inname.c_str(), whitePriorName.c_str(), (main_prior_vol+"_wm_stdspace").c_str(), bapriori.value().c_str());
-+ sprintf(reg, "flirt -ref %s -in %s -out %s -applyxfm -init %s", inname.c_str(), whitePriorName.c_str(), (main_prior_vol+"_wm_stdspace").c_str(), bapriori.value().c_str());
- if(verbose.value())
- cout << reg << endl;
- system(reg);
-diff --git a/src/feat5/feat_model.cc b/src/feat5/feat_model.cc
-index 399a13e..e15e43c 100644
---- a/src/feat5/feat_model.cc
-+++ b/src/feat5/feat_model.cc
-@@ -744,7 +744,7 @@ int main(int argc, char **argv)
- vector<int> G;
- vector<string> titles;
- float tr, mult, trmult, nltffwhm=0, maxconvwin=0;
-- char fl[10000], *FSLDIR;
-+ char fl[10000];
- string fn, filename;
- FONT_DATA *font_data = new FONT_DATA[1];
-
-@@ -763,8 +763,6 @@ int main(int argc, char **argv)
- if (argc==3)
- motionparams=remmean(read_ascii_matrix(argv[2]));
-
-- FSLDIR=getenv("FSLDIR");
--
- fn = string(argv[1])+".fsf";
-
- level = atoi(find_line(fn, "fmri(level)", fl));
-@@ -1510,7 +1508,7 @@ int main(int argc, char **argv)
- writeCovarianceImage(string(argv[1])+"_cov.ppm", contrasts, F, nftests, realDesign, level, evs.eigenvals, font_data, contrasts.RE);
- writeImagePreview(string(argv[1])+".ppm", contrasts, F, nftests, realDesign, level, evs, font_data, titles, tr, nltffwhm, nTimepoints, G);
-
-- filename=string(getenv("FSLDIR"))+"/bin/wpng -q -overwrite "+string(argv[1])+".ppm ";
-+ filename="wpng -q -overwrite "+string(argv[1])+".ppm ";
- system(filename.c_str());
-
- return(0);
-@@ -2161,6 +2159,6 @@ char the_string[10000];
-
- fclose(outputfile);
-
-- filename=string(getenv("FSLDIR")) + "/bin/wpng -q -overwrite " + filename;
-+ filename="wpng -q -overwrite " + filename;
- system(filename.c_str());
- }
-diff --git a/src/feat5/tsplot.cc b/src/feat5/tsplot.cc
-index ae191fd..3a02b55 100644
---- a/src/feat5/tsplot.cc
-+++ b/src/feat5/tsplot.cc
-@@ -293,7 +293,7 @@ int main(int argc, char **argv)
- ofstream outputFile;
- int numEVs, npts, numContrasts=1, nftests=0, GRPHSIZE(600), PSSIZE(600);
- vector<double> normalisedContrasts, model, triggers;
-- string fmriFileName, fslPath, featdir, vType, indexText;
-+ string fmriFileName, featdir, vType, indexText;
- ColumnVector NewimageVoxCoord(4),NiftiVoxCoord(4);
- bool outputText(true), useCoordinate(false), prewhiten(false), useTriggers(false), customMask(false), modelFree(false), isHigherLevel(false), outputDataOnly(false);
- bool zWeightClusters(true);
-@@ -307,7 +307,6 @@ volume<float> immask;
- if (argc<2) usage("");
- featdir=string(argv[1]);
- fmriFileName=featdir+"/filtered_func_data";
-- fslPath=string(getenv("FSLDIR"));
-
- string outputName(featdir);
-
-@@ -753,7 +752,7 @@ volume4D<float> acs;
- cerr << "Can't open output report file " << outputName << endl;
- exit(1);
- }
-- outputFile << "<HTML>\n<TITLE>"<< statType << num2str(i) <<"</TITLE>\n<BODY BACKGROUND=\"file:"<< fslPath <<"/doc/images/fsl-bg.jpg\">\n<hr><CENTER>\n<H1>FEAT Time Series Report - "<< statType << num2str(i) <<"</H1>\n</CENTER>\n<hr><b>Full plots</b><p>\n"<< graphText;
-+ outputFile << "<HTML>\n<TITLE>"<< statType << num2str(i) <<"</TITLE>\n<BODY BACKGROUND=\"file:"<< "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-bg.jpg\">\n<hr><CENTER>\n<H1>FEAT Time Series Report - "<< statType << num2str(i) <<"</H1>\n</CENTER>\n<hr><b>Full plots</b><p>\n"<< graphText;
- if (useTriggers) outputFile << "\n<hr><b>Peristimulus plots</b><p>\n"<< peristimulusText <<"\n<HR></BODY></HTML>\n\n";
- else outputFile << "\n</BODY></HTML>\n\n";
- outputFile.close();
-@@ -768,7 +767,7 @@ volume4D<float> acs;
- cerr << "Can't open output report file " << outputName << endl;
- exit(1);
- }
-- outputFile << "<HTML>\n<TITLE>FEAT Time Series Report</TITLE>\n<BODY BACKGROUND=\"file:" << fslPath << "/doc/images/fsl-bg.jpg\">\n<hr><CENTER>\n<H1>FEAT Time Series Report</H1>\n</CENTER>\n<hr>" << indexText << "<HR></BODY></HTML>" << endl << endl;
-+ outputFile << "<HTML>\n<TITLE>FEAT Time Series Report</TITLE>\n<BODY BACKGROUND=\"file:" << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-bg.jpg\">\n<hr><CENTER>\n<H1>FEAT Time Series Report</H1>\n</CENTER>\n<hr>" << indexText << "<HR></BODY></HTML>" << endl << endl;
- outputFile.close();
-
- /* now output same thing without start and end, for inclusion in feat report */
-diff --git a/src/first/first_utils.cc b/src/first/first_utils.cc
-index 68be44b..85960f4 100644
---- a/src/first/first_utils.cc
-+++ b/src/first/first_utils.cc
-@@ -1954,8 +1954,8 @@ void do_work_bvars(){
- if (!surfaceVAout.value()) {
- // do not output on the surface, instead do the new default of outputting a volume with the scalar normal dot product values (for use with randomise)
- volume<float> refim;
-- if (useReconMNI.value()) { read_volume(refim,string(getenv("FSLDIR")) + "/data/standard/MNI152_T1_1mm"); }
-- else { read_volume(refim,string(getenv("FSLDIR")) + "/data/standard/MNI152_T1_1mm"); }
-+ if (useReconMNI.value()) { read_volume(refim,"@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/MNI152_T1_1mm"); }
-+ else { read_volume(refim,"@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/MNI152_T1_1mm"); }
- volume<float> maskvol(refim);
- maskvol=0.0f;
- volume4D<float> volnormals;
-diff --git a/src/fnirt/fnirtfns.cpp b/src/fnirt/fnirtfns.cpp
-index 24e26fd..77899e7 100644
---- a/src/fnirt/fnirtfns.cpp
-+++ b/src/fnirt/fnirtfns.cpp
-@@ -1203,8 +1203,7 @@ string existing_ref_fname(const string& ref_fname)
- return(string(ref_fname));
- }
- else {
-- const char *fsldir_ptr = getenv("FSLDIR");
-- string eref_fname = string(fsldir_ptr) + string("/data/standard/") + ref_fname;
-+ string eref_fname = string("@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/") + ref_fname;
- if (NEWIMAGE::FslFileExists(eref_fname)) return(eref_fname);
- else return(string(""));
- }
-@@ -1230,9 +1229,8 @@ string existing_ref_fname(const string& ref_fname)
- NEWIMAGE::read_volume_hdr_only(vref,ref_fname); // Throws if file dont exist
- eref_fname = ref_fname;
- }
-- catch(...) { // Didn't exist in current directory, try in ${FSLDIR}/data/standard
-- const char *fsldir_ptr = getenv("FSLDIR");
-- eref_fname = string(fsldir_ptr) + string("/data/standard/") + ref_fname;
-+ catch(...) { // Didn't exist in current directory, try in .../data/standard
-+ eref_fname = string("@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/") + ref_fname;
- try {
- cout << "Could not find " << ref_fname << ", now checking " << eref_fname << endl;
- NEWIMAGE::read_volume_hdr_only(vref,eref_fname); // Throws if file dont exist
-@@ -1267,8 +1265,7 @@ string existing_conf_file(const string& cfname)
- if (check_exist(ecfname)) return(ecfname);
- }
- if (!FNIRT::path(cfname).length()) { // If no path explicitly given
-- const char *fsldir_ptr = getenv("FSLDIR");
-- ecfname = string(fsldir_ptr) + string("/etc/flirtsch/") + cfname;
-+ ecfname = string("@GENTOO_PORTAGE_EPREFIX@/etc/flirtsch/") + cfname;
- if (check_exist(ecfname)) return(ecfname);
- else if (!FNIRT::extension(ecfname).length()) { // If no path _and_ no extension given
- ecfname += string(".cnf");
-diff --git a/src/fslsurface/fslsurface_first.cc b/src/fslsurface/fslsurface_first.cc
-index faec642..b2ef794 100644
---- a/src/fslsurface/fslsurface_first.cc
-+++ b/src/fslsurface/fslsurface_first.cc
-@@ -500,8 +500,7 @@ namespace fslsurface_name {
-
- volume<float>* immni = new volume<float>();
-
-- char* fsldir = getenv("FSLDIR");
-- read_volume_hdr_only(*immni, string(fsldir) + "/data/standard/MNI152_T1_1mm");
-+ read_volume_hdr_only(*immni, "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/MNI152_T1_1mm");
-
- //read_volume_hdr_only(*immni, template_name);
-
-@@ -699,8 +698,7 @@ namespace fslsurface_name {
-
- volume<float>* immni = new volume<float>();
-
-- char* fsldir = getenv("FSLDIR");
-- read_volume_hdr_only(*immni, string(fsldir) + "/data/standard/MNI152_T1_1mm");
-+ read_volume_hdr_only(*immni, "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/MNI152_T1_1mm");
-
- //read_volume_hdr_only(*immni, template_name);
-
-diff --git a/src/fslsurface/fslsurfacemaths.cpp b/src/fslsurface/fslsurfacemaths.cpp
-index eaf55eb..3dc184d 100644
---- a/src/fslsurface/fslsurfacemaths.cpp
-+++ b/src/fslsurface/fslsurfacemaths.cpp
-@@ -598,12 +598,6 @@ int main (int argc, char * argv[])
-
- }else if (command == "-reconFromBvars"){
- cout<<"do recon "<<endl;
-- char* fsldir = getenv("FSLDIR");
-- if (fsldir == NULL)
-- {
-- cerr<<"FSLDIR has not been set. "<<endl;
-- exit(EXIT_FAILURE);
-- }
- //file.bvars,mni_template.nii.gz
- // string mni = string(fsldir)+"/data/standard/MNI152_T1_1mm";
- reconSurface_from_bvars( surf, string(argv[i_arg+1]));
-@@ -612,12 +606,6 @@ int main (int argc, char * argv[])
-
- }else if (command == "-reconAllFromBvarsAndSave"){
- cout<<"do recon+save "<<argc<<" "<<i_arg<<endl;
-- char* fsldir = getenv("FSLDIR");
-- if (fsldir == NULL)
-- {
-- cerr<<"FSLDIR has not been set. "<<endl;
-- exit(EXIT_FAILURE);
-- }
- //file.bvars,mni_template.nii.gz
- // string mni = string(fsldir)+"/data/standard/MNI152_T1_1mm";
- cout<<"recon "<< string(argv[i_arg+1])<<endl;
diff --git a/sci-biology/fsl/files/fsl-6.0.2-fsldir_redux-p2.patch b/sci-biology/fsl/files/fsl-6.0.2-fsldir_redux-p2.patch
deleted file mode 100644
index 74bf19169..000000000
--- a/sci-biology/fsl/files/fsl-6.0.2-fsldir_redux-p2.patch
+++ /dev/null
@@ -1,255 +0,0 @@
-diff --git a/src/libvis/miscpic.h b/src/libvis/miscpic.h
-index a2f3855..5f440f2 100644
---- a/src/libvis/miscpic.h
-+++ b/src/libvis/miscpic.h
-@@ -90,12 +90,7 @@ namespace MISCPIC{
- markRight=false;
- trans= -10;
- edgethresh = 0.0;
-- if(getenv("FSLDIR")!=0){
-- lutbase = string(getenv("FSLDIR")) + "/etc/luts/";
-- }
-- else{
-- lutbase = string("/");
-- }
-+ lutbase = "@GENTOO_PORTAGE_EPREFIX@/etc/luts/";
- title = string("");
- cbartype = string("");
- cbarptr = NULL;
-diff --git a/src/melodic/meldata.cc b/src/melodic/meldata.cc
-index 1749a45..c4ad234 100644
---- a/src/melodic/meldata.cc
-+++ b/src/melodic/meldata.cc
-@@ -992,7 +992,7 @@ namespace Melodic{
- void MelodicData::est_smoothness()
- {
- if(Resels == 0){
-- string SM_path = opts.binpath + "smoothest";
-+ string SM_path = "smoothest";
- string Mask_fname = logger.appendDir("mask");
-
- if(opts.segment.value().length()>0){
-@@ -1157,7 +1157,7 @@ namespace Melodic{
- // set up all strings
- string BET_outputfname = string(Mean_fname)+"_brain";
-
-- string BET_path = opts.binpath + "bet";
-+ string BET_path = "bet";
- string BET_optarg = "-m -f 0.4"; // see man bet
- string Mask_fname = BET_outputfname+"_mask";
-
-diff --git a/src/melodic/meloptions.cc b/src/melodic/meloptions.cc
-index 08170c7..252e72b 100644
---- a/src/melodic/meloptions.cc
-+++ b/src/melodic/meloptions.cc
-@@ -93,14 +93,6 @@ MelodicOptions* MelodicOptions::gopt = NULL;
- explicitnums = false;
- logfname = string("log.txt");
-
-- // work out the path to the $FSLDIR/bin directory
-- if(getenv("FSLDIR")!=0){
-- binpath = (string) getenv("FSLDIR") + "/bin/";
-- } else{
-- binpath = argv[0];
-- binpath = binpath.substr(0,binpath.length()-7);
-- }
--
- // parse once to establish log directory name
- for(int a = options.parse_command_line(argc, argv); a < argc; a++);
-
-diff --git a/src/melodic/meloptions.h b/src/melodic/meloptions.h
-index f546125..b964b7d 100644
---- a/src/melodic/meloptions.h
-+++ b/src/melodic/meloptions.h
-@@ -93,7 +93,6 @@ class MelodicOptions {
- ~MelodicOptions() { delete gopt; }
-
- string version;
-- string binpath;
- string logfname;
- bool filtermode;
- bool explicitnums;
-diff --git a/src/melodic/melreport.cc b/src/melodic/melreport.cc
-index 141b6c2..2625059 100644
---- a/src/melodic/melreport.cc
-+++ b/src/melodic/melreport.cc
-@@ -84,8 +84,8 @@ namespace Melodic{
- IChtml.setDir(report.getDir(),mmodel.get_prefix()+".html");
-
- {//start IC page
-- IChtml << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" +
-- (string) getenv("FSLDIR") +"/doc/fsl.css>" << endl
-+ IChtml << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:"
-+ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" << endl
- << "<style type=\"text/css\">OBJECT { width: 100% }</style>"
- << "<TITLE>FSL</TITLE></HEAD>" << endl
- << "<IFRAME height=" << int(melodat.get_numfiles()/30 + 1)*50
-@@ -486,8 +486,8 @@ namespace Melodic{
-
- {//start IC2 page
- IChtml2.setDir(report.getDir(),mmodel.get_prefix()+"_MM.html");
-- IChtml2 << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" +
-- (string) getenv("FSLDIR") +"/doc/fsl.css>" << endl
-+ IChtml2 << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:"
-+ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" << endl
- << "<style type=\"text/css\">OBJECT { width: 100% }</style>"
- << "<TITLE>FSL</TITLE></HEAD>" << endl
- << "<IFRAME height="<< int(melodat.get_numfiles()/30 + 1)*50
-@@ -665,8 +665,8 @@ namespace Melodic{
- IChtml << "<HTML> " << endl
- << "<TITLE>MELODIC Component " << num2str(cnum)
- << "</TITLE>" << endl
-- << "<BODY BACKGROUND=\"file:" << getenv("FSLDIR")
-- << "/doc/images/fsl-bg.jpg\">" << endl
-+ << "<BODY BACKGROUND=\"file:"
-+ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-bg.jpg\">" << endl
- << "<hr><CENTER><H1>MELODIC Component " << num2str(cnum)
- << "</H1>"<< endl;
-
-diff --git a/src/melodic/melreport.h b/src/melodic/melreport.h
-index 574fc4c..e444681 100644
---- a/src/melodic/melreport.h
-+++ b/src/melodic/melreport.h
-@@ -104,21 +104,21 @@ namespace Melodic{
- const time_t tmptime = time(NULL);
- system(("mkdir "+ logger.appendDir("report") + " 2>/dev/null").c_str());
- report.setDir(logger.appendDir("report"),"00index.html",true,false,ios::out);
-- report << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" +
-- (string) getenv("FSLDIR") +"/doc/fsl.css>"
-+ report << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:"
-+ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>"
- << "<TITLE>MELODIC report</TITLE></HEAD><BODY>"
- << endl <<endl;
- loghtml.setDir(report.getDir(),"log.html");
-- loghtml << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" +
-- (string) getenv("FSLDIR") +"/doc/fsl.css>"
-+ loghtml << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:"
-+ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>"
- << "<TITLE>MELODIC report</TITLE></HEAD><BODY>"
- << endl <<endl;
- navigator.setDir(report.getDir(),"nav.html");
- head.setDir(report.getDir(),"head.html");
-- navigator << "<link REL=stylesheet TYPE=text/css href=file:"+
-- (string) getenv("FSLDIR") +"/doc/fsl.css>" << endl;
-- head << "<link REL=stylesheet TYPE=text/css href=file:"+
-- (string) getenv("FSLDIR") +"/doc/fsl.css>" << endl;
-+ navigator << "<link REL=stylesheet TYPE=text/css href=file:"
-+ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" << endl;
-+ head << "<link REL=stylesheet TYPE=text/css href=file:"
-+ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" << endl;
- head <<"<TABLE BORDER=0><TR>" << endl
- <<" <TD ALIGN=CENTER WIDTH=100%>"<< endl
- <<"<TABLE BORDER=0>"<< endl
-@@ -130,8 +130,8 @@ namespace Melodic{
- << "</tr></table>" << endl
- << "<TD ALIGN=RIGHT>" << endl
- << "<a href=http://www.fmrib.ox.ac.uk/fsl target=_top>" << endl
-- << "<IMG BORDER=0 SRC=file:"<< getenv("FSLDIR")
-- << "/doc/images/fsl-logo-big.jpg WIDTH=165></a>" << endl
-+ << "<IMG BORDER=0 SRC=file:"
-+ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-logo-big.jpg WIDTH=165></a>" << endl
- << "</TD>"<<endl<<"</TR></TABLE> <hr>"<<endl;
- if(opts.guireport.value()==""){
- report <<"<OBJECT data=head.html></OBJECT>" << endl;
-diff --git a/src/mm/mixture_model.cc b/src/mm/mixture_model.cc
-index b8e6167..5f00693 100644
---- a/src/mm/mixture_model.cc
-+++ b/src/mm/mixture_model.cc
-@@ -2224,8 +2224,8 @@ namespace Mm {
-
- htmllog << "<HTML> " << endl
- << "<TITLE>Mixture Model fit for" << data_name << "</TITLE>" << endl
-- << "<BODY BACKGROUND=\"file:" << getenv("FSLDIR")
-- << "/doc/images/fsl-bg.jpg\">" << endl
-+ << "<BODY BACKGROUND=\"file:"
-+ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-bg.jpg\">" << endl
- << "<hr><CENTER><H1>Mixture Model fit for<br>" << data_name << " </H1>"<< endl;
-
- htmllog << "<hr><p>" << endl;
-diff --git a/src/siena/siena_diff.cc b/src/siena/siena_diff.cc
-index e19193a..17d8701 100644
---- a/src/siena/siena_diff.cc
-+++ b/src/siena/siena_diff.cc
-@@ -107,7 +107,7 @@ int main(int argc,char *argv[])
- {
- // {{{ vars
-
--char thestring[10000], segoptions[10000], fsldir[10000];
-+char thestring[10000], segoptions[10000];
- int x_size, y_size, z_size, size, x, y, z, i, count,
- seg2=0, ignore_z=0, ignore_top_slices=0, //erode_mask=0,
- ignore_bottom_slices=0, debug=0, flow_output=1, edge_masking=0;
-@@ -124,8 +124,6 @@ if (argc<3)
-
- string argv1(argv[1]), argv2(argv[2]);
-
--sprintf(fsldir,"%s",getenv("FSLDIR"));
--
- for (i = 3; i < argc; i++) {
- if (!strcmp(argv[i], "-i"))
- ignore_z=1;
-@@ -209,26 +207,26 @@ for (i = 3; i < argc; i++) {
- // }}}
- // {{{ transform images and masks
-
--sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s",
-- fsldir,argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]);
-+sprintf(thestring,"flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s",
-+ argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]);
- printf("%s\n",thestring); system(thestring);
-
--sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s",
-- fsldir,argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
-+sprintf(thestring,"flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s",
-+ argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
- printf("%s\n",thestring); system(thestring);
-
--sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask",
-- fsldir,argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]);
-+sprintf(thestring,"flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask",
-+ argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]);
- printf("%s\n",thestring); system(thestring);
-
--sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask",
-- fsldir,argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
-+sprintf(thestring,"flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask",
-+ argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
- printf("%s\n",thestring); system(thestring);
-
- if (edge_masking)
- {
-- sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s_valid_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_valid_mask_with_%s",
-- fsldir,argv[1],argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
-+ sprintf(thestring,"flirt -o %s_halfwayto_%s_valid_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_valid_mask_with_%s",
-+ argv[1],argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
- printf("%s\n",thestring); system(thestring);
- }
-
-@@ -287,8 +285,8 @@ if(1) // always done unless the above uncommented and used instead of this test
- cout << "saving image 1 to disk prior to segmentation" << endl;
- save_volume(in1,argv1+"_halfwayto_"+argv2+"_brain");
- in1.destroy();
-- sprintf(thestring,"%s/bin/fast %s %s %s_halfwayto_%s_brain > %s_halfwayto_%s_brain.vol 2>&1",
-- fsldir,segtype,segoptions,argv[1],argv[2],argv[1],argv[2]);
-+ sprintf(thestring,"fast %s %s %s_halfwayto_%s_brain > %s_halfwayto_%s_brain.vol 2>&1",
-+ segtype,segoptions,argv[1],argv[2],argv[1],argv[2]);
- cout << thestring << endl;
- system(thestring);
- }
-diff --git a/src/topup/topupfns.cpp b/src/topup/topupfns.cpp
-index 6873758..9e8b956 100644
---- a/src/topup/topupfns.cpp
-+++ b/src/topup/topupfns.cpp
-@@ -463,8 +463,7 @@ string existing_conf_file(const string& cfname)
- if (TOPUP::check_exist(ecfname)) return(ecfname);
- }
- if (!TOPUP::path(cfname).length()) { // If no path explicitly given
-- const char *fsldir_ptr = getenv("FSLDIR");
-- ecfname = string(fsldir_ptr) + string("/etc/flirtsch/") + cfname;
-+ ecfname = string("@GENTOO_PORTAGE_EPREFIX@/etc/flirtsch/") + cfname;
- if (TOPUP::check_exist(ecfname)) return(ecfname);
- else if (!TOPUP::extension(ecfname).length()) { // If no path _and_ no extension given
- ecfname += string(".cnf");
---
-2.24.1
-
diff --git a/sci-biology/fsl/fsl-6.0.4.ebuild b/sci-biology/fsl/fsl-6.0.4.ebuild
index 4797c1298..cd91cf192 100644
--- a/sci-biology/fsl/fsl-6.0.4.ebuild
+++ b/sci-biology/fsl/fsl-6.0.4.ebuild
@@ -28,12 +28,8 @@ DEPEND="
dev-lang/tk:0=
>=virtual/lapack-3.8
>=virtual/blas-3.8
-
cuda? (
- || (
- ( =dev-util/nvidia-cuda-toolkit-10* =sys-devel/gcc-8*:* )
- ( =dev-util/nvidia-cuda-toolkit-11* =sys-devel/gcc-9*:* )
- )
+ =dev-util/nvidia-cuda-toolkit-11* =sys-devel/gcc-9*:*
)
"
RDEPEND="${DEPEND}"
diff --git a/sci-biology/fsl/fsl-6.0.5.ebuild b/sci-biology/fsl/fsl-6.0.5.ebuild
index c51a9d30e..d3ec1de1d 100644
--- a/sci-biology/fsl/fsl-6.0.5.ebuild
+++ b/sci-biology/fsl/fsl-6.0.5.ebuild
@@ -39,9 +39,7 @@ DEPEND="
>=virtual/lapack-3.8
>=virtual/blas-3.8
cuda? (
- || (
- ( =dev-util/nvidia-cuda-toolkit-11* =sys-devel/gcc-9*:* )
- )
+ =dev-util/nvidia-cuda-toolkit-11* =sys-devel/gcc-9*:*
)
"
RDEPEND="${DEPEND}"
diff --git a/sci-biology/gffread/Manifest b/sci-biology/gffread/Manifest
index ea0f27b53..999049e10 100644
--- a/sci-biology/gffread/Manifest
+++ b/sci-biology/gffread/Manifest
@@ -1,2 +1,2 @@
-DIST gclib-0.11.0.tar.gz 184895 BLAKE2B ea8434c8a68fc7d032341271ed55eab3dcc8618da0ea823f7e1588598275a775369d1b7e7ce38eba02437272c28b56543ac50a50f5b0a03d01f37e24e85bb53e SHA512 ec773a805141e8f0f98774760e0608aac6c66c7541d4777c8cb0edcf2172a4bc86a0f0c1f6f7459858b408f47d8b1f6eeb35c871668991424f74d55a9c19bce2
-DIST gffread-0.11.0.tar.gz 28887 BLAKE2B 0d9e89666770c64713d0edb256aa9f18b8d33cba941afbb14a82e26359bfa96044a1655678095a8468e1d1d651406fb0250b20696b4026c4a47892cc45785935 SHA512 79d8a376c892c1567c80a045b08b8f4c97d8778a46b89bcce0372e2e3d6b4bcfe746b64b2101fd8411d02a2d157585eb39d0e067a2aaeb5e8c1e1f7da21bc834
+DIST gclib-0.12.7.tar.gz 259314 BLAKE2B 9e3d4b535a7bbeb4b03360801a4ce4c81055d49525857cce306009e18f78709808732e24cb3dc3efa050b293c863d6f045f5fc3a5d3c14f3c6a2566acbc1f6f4 SHA512 2ff7be21f8ae002afdd7e34b6200e308f87077331c174dbea863972a01a0b6758062accda431bb73ef45ae91db44871f9eb0f5ae4bd564252599236282e57f90
+DIST gffread-0.12.7.tar.gz 403734 BLAKE2B e925518fad8e1047d7e4a785338e51cd0317d8e26545587024ee2617a2e432426e80172c62b9d4103ec9da0d33d758105d8803cc82b4f74cf5dba07009aab477 SHA512 33a2308caecd3e891788a76c6b68b79569afd8d0d749bf57a8c528550d26f7a7b61b8ca77e8a37e05a7dfaeac600470c255a22314ea94f63e2b2cac45674f97b
diff --git a/sci-biology/gffread/gffread-0.11.0.ebuild b/sci-biology/gffread/gffread-0.12.7.ebuild
index 871d38d03..9758ccef0 100644
--- a/sci-biology/gffread/gffread-0.11.0.ebuild
+++ b/sci-biology/gffread/gffread-0.12.7.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
DESCRIPTION="GFF/GTF utility providing format conversions, filter/extract regions from FASTA"
HOMEPAGE="http://ccb.jhu.edu/software/stringtie/gff.shtml
@@ -12,13 +12,8 @@ SRC_URI="https://github.com/gpertea/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz
LICENSE="MIT"
SLOT="0"
KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}"
src_prepare(){
- src_unpack "${DISTDIR}"/gclib-${PV}.tar.gz
default
sed -e "s/-g -O3/${CXXFLAGS}/" -i Makefile || die
cd .. && ln -s gclib-"${PV}" gclib || die
@@ -30,4 +25,5 @@ src_compile(){
src_install(){
dobin gffread
+ einstalldocs
}
diff --git a/sci-biology/irsabi_bidsdata/irsabi_bidsdata-1.4.ebuild b/sci-biology/irsabi_bidsdata/irsabi_bidsdata-1.4.ebuild
index b8cc73c5a..d50ebf927 100644
--- a/sci-biology/irsabi_bidsdata/irsabi_bidsdata-1.4.ebuild
+++ b/sci-biology/irsabi_bidsdata/irsabi_bidsdata-1.4.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
@@ -8,7 +8,6 @@ inherit check-reqs
DESCRIPTION="BIDS data files released with the IRSABI publication"
HOMEPAGE="http://www.aic-fmi.ethz.ch/"
SRC_URI="
- http://chymera.eu/distfiles/${P}.tar.xz
https://zenodo.org/record/3601531/files/${P}.tar.xz
"
diff --git a/sci-biology/jigsaw/Manifest b/sci-biology/jigsaw/Manifest
deleted file mode 100644
index 1fcded0c0..000000000
--- a/sci-biology/jigsaw/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST jigsaw-3.2.10m.tar.gz 1024885 BLAKE2B 59b98b3e8469b84fcb8bdceadc0cef3a628bf5b1e059af905a07b89de29a686aa66c20c451308bd980b8daba4e9c1ff0ec953b56a58d926ef626e1f4ee8b1a48 SHA512 5d19e933b5c9f2c57cb73a56a9017e5c088ce0135c2899caf21f2b9c0f092c35673b96be918e73f5fdb1c641dce853123e8f9d5592a64ac8704c28314b2d7877
diff --git a/sci-biology/jigsaw/jigsaw-3.2.10m.ebuild b/sci-biology/jigsaw/jigsaw-3.2.10m.ebuild
deleted file mode 100644
index 1a78ae08e..000000000
--- a/sci-biology/jigsaw/jigsaw-3.2.10m.ebuild
+++ /dev/null
@@ -1,28 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DESCRIPTION="Combine results from external gene predictors into final gene models"
-HOMEPAGE="https://www.cbcb.umd.edu/software/jigsaw"
-SRC_URI="https://www.cbcb.umd.edu/software/jigsaw/${P}.tar.gz"
-
-LICENSE="Artistic"
-SLOT="0"
-KEYWORDS=""
-
-S="${WORKDIR}/${PN}-${PV//m}"
-
-src_compile() {
- cd src/main || die
- emake
- cd ../../lib/oc1
- emake
-}
-
-src_install() {
- cd src/main || die
- emake DESTDIR="${ED}" install
- cd ../../lib/oc1
- emake DESTDIR="${ED}" install
-}
diff --git a/sci-biology/jigsaw/metadata.xml b/sci-biology/jigsaw/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/jigsaw/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/jtreeview-bin/jtreeview-bin-1.2.0.ebuild b/sci-biology/jtreeview-bin/jtreeview-bin-1.2.0.ebuild
index fe8fef44a..d146efd5a 100644
--- a/sci-biology/jtreeview-bin/jtreeview-bin-1.2.0.ebuild
+++ b/sci-biology/jtreeview-bin/jtreeview-bin-1.2.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
@@ -13,6 +13,7 @@ SRC_URI="
https://sourceforge.net/projects/jtreeview/files/jtreeview/${PV}/TreeView-${PV}-bin.tar.gz
https://sourceforge.net/projects/jtreeview/files/helper-scripts/0.0.2/helper-scripts-0.0.2.tar.gz
"
+S="${WORKDIR}/TreeView-${PV}-bin"
LICENSE="GPL-2"
SLOT="0"
@@ -20,11 +21,10 @@ KEYWORDS="~amd64"
DEPEND="
>virtual/jdk-1.5:*
- !sci-biology/jtreeview"
+"
RDEPEND="${DEPEND}
- >=virtual/jre-1.5:*"
-
-S="${WORKDIR}/TreeView-${PV}-bin"
+ >=virtual/jre-1.5:*
+"
# TODO: use xltproc to create docs following TreeView-1.1.6r4-src/doc/README
diff --git a/sci-biology/jtreeview/Manifest b/sci-biology/jtreeview/Manifest
deleted file mode 100644
index db64018f4..000000000
--- a/sci-biology/jtreeview/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST TreeView-1.2.0-src.tar.gz 3176518 BLAKE2B 0e80c2298236fa064d8a36f5cea71d962f1a1b38bf9128bcc964ad44f5c0502d92008e1f5c70a290522763fff356beb01584b02eea0834392df14196f4313c93 SHA512 b2c2d8c2d2e9201fb9877c7014607bd21a946a57159ebda0fb834563e9a8751298e964bd32474bc6f53303727c2a3d03c72869d1485d9656150591c44c26a9b1
-DIST helper-scripts-0.0.2.tar.gz 18260 BLAKE2B 2f794063fa2f9263b92465b48a891efc5ae65ab3a64ade7250aa3a9f166873d9a6f9c5ad69387caa6d9f15affb907cd2b3587e7c261b862337319c0e7d7be9d6 SHA512 6d335ffa4da7db2d5b2d0009e8db87145cc9b3b85772059f6afde55f544de1ee1348a8450e69393ea59313268549204be3d26931dc43085d843ff3c6c3c27d88
diff --git a/sci-biology/jtreeview/jtreeview-1.2.0.ebuild b/sci-biology/jtreeview/jtreeview-1.2.0.ebuild
deleted file mode 100644
index 8f0e777c9..000000000
--- a/sci-biology/jtreeview/jtreeview-1.2.0.ebuild
+++ /dev/null
@@ -1,39 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit perl-module java-pkg-2 java-ant-2
-
-DESCRIPTION="Viewer for Microarray Data in PCL or CDT formats"
-HOMEPAGE="http://jtreeview.sourceforge.net/" # no https
-SRC_URI="
- https://sourceforge.net/projects/jtreeview/files/jtreeview/${PV}/TreeView-${PV}-src.tar.gz
- https://sourceforge.net/projects/jtreeview/files/helper-scripts/0.0.2/helper-scripts-0.0.2.tar.gz
-"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64"
-
-DEPEND=">virtual/jdk-1.7:*
- dev-java/nanoxml"
-RDEPEND="${DEPEND}
- >=virtual/jre-1.7:*"
-
-S="${WORKDIR}/TreeView-${PV}-src"
-JAVA_PKG_BSFIX_NAME="${S}"
-
-# TODO: use xltproc to create docs following TreeView-1.1.6r4-src/doc/README
-
-src_install(){
- java-pkg_dojar TreeView.jar
- java-pkg_dolauncher ${PN} TreeView.jar
- cd ../helper-scripts-0.0.2 || die
- perl_set_version
- perl_domodule *.pm
- perl_domodule *.pl
- insinto /usr/share/"${PN}"/examples
- doins blues.color
- newdoc README README.helper-scripts
-}
diff --git a/sci-biology/jtreeview/jtreeview-9999.ebuild b/sci-biology/jtreeview/jtreeview-9999.ebuild
deleted file mode 100644
index 316368b4e..000000000
--- a/sci-biology/jtreeview/jtreeview-9999.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
-
-inherit perl-module java-pkg-2 java-ant-2 git-r3
-
-DESCRIPTION="Viewer for Microarray Data in PCL or CDT formats"
-HOMEPAGE="http://jtreeview.sourceforge.net/" # no https
-EGIT_REPO_URI="https://bitbucket.org/TreeView3Dev/treeview3.git"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS=""
-
-DEPEND=">virtual/jdk-1.7:*"
-RDEPEND="${DEPEND}
- >=virtual/jre-1.7:*"
-
-src_install(){
- java-pkg_dojar TreeView.jar
- java-pkg_dolauncher ${PN} TreeView.jar
- cd ../helper-scripts-0.0.2 || die
- perl_set_version
- perl_domodule *.pm
- perl_domodule *.pl
- insinto /usr/share/"${PN}"/examples
- doins blues.color
- newdoc README README.helper-scripts
-}
diff --git a/sci-biology/jtreeview/metadata.xml b/sci-biology/jtreeview/metadata.xml
deleted file mode 100644
index 5139daeeb..000000000
--- a/sci-biology/jtreeview/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="bitbucket">TreeView3Dev/treeview3</remote-id>
- <remote-id type="sourceforge">jtreeview</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/sci-biology/libblasr/Manifest b/sci-biology/libblasr/Manifest
new file mode 100644
index 000000000..c575f4081
--- /dev/null
+++ b/sci-biology/libblasr/Manifest
@@ -0,0 +1 @@
+DIST libblasr-5.3.5.tar.gz 3950694 BLAKE2B 879910dbbfc60592528fab4de0e3bd975f8d12b7e68ca80e031577c9b18a6959a95c76186455fbdecbe3d8455320ba5b83db2c88318467d50a2470569860c514 SHA512 45997fce4fba12ff40c4624bc152990a683e4298d898b404f82e645493557a0565476ead2420fd9c28790e1985cdf3a88401c30181fdc57f84bbd61a707a8b5e
diff --git a/sci-biology/libblasr/libblasr-9999.ebuild b/sci-biology/libblasr/libblasr-5.3.5.ebuild
index 5f5ba504c..a12dc25ac 100644
--- a/sci-biology/libblasr/libblasr-9999.ebuild
+++ b/sci-biology/libblasr/libblasr-5.3.5.ebuild
@@ -1,26 +1,25 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
-inherit meson git-r3
+inherit meson
DESCRIPTION="Library for blasr"
HOMEPAGE="http://www.smrtcommunity.com/SMRT-Analysis/Algorithms/BLASR"
-EGIT_REPO_URI="https://github.com/PacificBiosciences/blasr_libcpp.git"
-#SRC_URI="https://github.com/PacificBiosciences/blasr_libcpp/archive/${PV}.tar.gz -> ${P}.tar.gz"
+SRC_URI="https://github.com/PacificBiosciences/blasr_libcpp/archive/${PV}.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}/blasr_libcpp-${PV}"
LICENSE="blasr"
SLOT="0"
-KEYWORDS=""
+KEYWORDS="~amd64"
BDEPEND="
dev-util/cmake
virtual/pkgconfig
"
DEPEND="
+ sci-biology/pbbam
sci-libs/hdf5[cxx]
"
RDEPEND="${DEPEND}"
-
-S="${WORKDIR}/blasr_libcpp-${PV}"
diff --git a/sci-biology/longstitch/longstitch-1.0.1.ebuild b/sci-biology/longstitch/longstitch-1.0.1.ebuild
index 6cd035d86..b14bdee87 100644
--- a/sci-biology/longstitch/longstitch-1.0.1.ebuild
+++ b/sci-biology/longstitch/longstitch-1.0.1.ebuild
@@ -1,15 +1,16 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
DESCRIPTION="Scaffold genome assemblies by Chromium/PacBio/Nanopore reads"
HOMEPAGE="https://github.com/bcgsc/LongStitch"
SRC_URI="https://github.com/bcgsc/LongStitch/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}/LongStitch-${PV}"
LICENSE="GPL-3"
SLOT="0"
-KEYWORDS=""
+KEYWORDS="~amd64"
RESTRICT="test"
@@ -20,8 +21,6 @@ RDEPEND="
sci-biology/samtools
"
-S="${WORKDIR}"/LongStitch-"${PV}"
-
src_install(){
dobin longstitch
dodoc README.md LongStitch_overview.pdf
diff --git a/sci-biology/manatee-igs/Manifest b/sci-biology/manatee-igs/Manifest
deleted file mode 100644
index 89599e152..000000000
--- a/sci-biology/manatee-igs/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST manatee-2.23.1_linux.tgz 19879146 BLAKE2B bd69d0d701c92ad4e4c8bbfdf8c9cb23184fa2778a924f71dd83e01901a8054296fb32adb58c5bb66d442b29c564c31c8690398479d214e020697726fc413a59 SHA512 50a76d36f69e3b8b80bcdf7fe28e1c9eb7c15bd8889bd8d130bc65f879ec99aa0caec6d0df495d7ab5804e6414599fc316073c9c55ecd1d370c5dd72aadd65ba
diff --git a/sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild b/sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild
deleted file mode 100644
index 8a21f8f36..000000000
--- a/sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild
+++ /dev/null
@@ -1,65 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DESCRIPTION="IGS-modified version of the genome annotation tool using Chado database schema"
-HOMEPAGE="http://manatee.sourceforge.net/igs" # no https
-SRC_URI="https://downloads.sourceforge.net/project/manatee/igs_manatee/${PV}/manatee-${PV}_linux.tgz"
-
-LICENSE="Artistic-Manatee"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-DEPEND="
- >=dev-libs/expat-1.95.8
- >=media-libs/gd-2.0.34
- dev-perl/CGI
- dev-perl/Bio-DB-Das-Chado
- dev-perl/DBI
- dev-perl/DBD-mysql
- dev-perl/XML-Parser
- dev-perl/XML-Twig
- dev-perl/XML-Simple
- dev-perl/XML-Writer
- dev-perl/HTML-Template
- dev-perl/Tree-DAG_Node
- virtual/perl-File-Spec
- virtual/perl-Data-Dumper
- dev-perl/GD
- dev-perl/GDTextUtil
- dev-perl/GDGraph
- virtual/perl-Storable
- dev-perl/Log-Log4perl
- dev-perl/Log-Cabin
- dev-perl/Date-Manip
- dev-perl/IO-Tee
- dev-perl/MLDBM
- dev-perl/JSON
- dev-perl/JSON-Any
- sci-biology/bioperl"
-RDEPEND="${DEPEND}
- >=virtual/mysql-5:*
- >=www-servers/apache-2.2"
-
-S="${WORKDIR}/manatee-${PV}_linux"
-
-src_prepare(){
- default
- find "${S}" -name \*.cgi | while read f; do sed -e 's|#!/usr/local/bin/perl|#!/usr/bin/perl|' -i $f; done
- find "${S}" -name \*.pl | while read f; do sed -e 's|#!/usr/local/bin/perl|#!/usr/bin/perl|' -i $f; done
- find "${S}" -name \*.pm | while read f; do sed -e 's|#!/usr/local/bin/perl|#!/usr/bin/perl|' -i $f; done
-}
-
-src_install(){
- dodir /var/www/localhost/cgi-bin
- cp -r src/cgi-bin/chado_prok_manatee "${D}"/var/www/localhost/cgi-bin
- dodir /var/www/localhost/htdocs/manatee
- cp -r src/htdocs/tdb "${D}"/var/www/localhost/htdocs/manatee
-
- einfo "Please read the "${S}"/databases/Makefile.PL and import the databases into your MySQL database"
-
- einfo "You have to fetch the 1.1 GB large file from https://sourceforge.net/projects/manatee/files/igs_manatee/"${PV}"/lookups-"${PV}"_linux.tgz"
- einfo "You need to update it regularly."
- einfo "Also fetch https://sourceforge.net/projects/manatee/files/igs_manatee/"${PV}"/blastdb-"${PV}".tgz (about 2MB in size)"
-}
diff --git a/sci-biology/manatee-igs/metadata.xml b/sci-biology/manatee-igs/metadata.xml
deleted file mode 100644
index 8a3d26043..000000000
--- a/sci-biology/manatee-igs/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>mmokrejs@fold.natur.cuni.cz</email>
- <name>Martin Mokrejs</name>
- </maintainer>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
- <upstream>
- <remote-id type="sourceforge">manatee</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/sci-biology/manatee-jcvi/Manifest b/sci-biology/manatee-jcvi/Manifest
deleted file mode 100644
index 9efd473f9..000000000
--- a/sci-biology/manatee-jcvi/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST manatee-2.4.3.tgz 1840410 BLAKE2B e80b499e4a9a6fddc60851e1da126dc48356d675df36938f1ed1a920f19a5f76708fc4be295164ae69330d1978cebbf6e6b9c1f7c098e8049710a3e48eeee0d3 SHA512 0bfb9dff8bdaec1e602fdaa1ec6e2939cba1813ac639b95b9e2679e3473719ad74bb383ba54c56cf4dc0553eac002ea3955ae05a1bc87215c7553b9edb9f9fcf
diff --git a/sci-biology/manatee-jcvi/manatee-jcvi-2.4.3.ebuild b/sci-biology/manatee-jcvi/manatee-jcvi-2.4.3.ebuild
deleted file mode 100644
index 7bc28decf..000000000
--- a/sci-biology/manatee-jcvi/manatee-jcvi-2.4.3.ebuild
+++ /dev/null
@@ -1,54 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DESCRIPTION="Genome annotation tool"
-HOMEPAGE="http://manatee.sourceforge.net/jcvi/downloads.shtml"
-SRC_URI="http://downloads.sourceforge.net/project/manatee/manatee/manatee-${PV}/manatee-2.4.3.tgz"
-
-LICENSE="Artistic-Manatee"
-SLOT="0"
-KEYWORDS=""
-
-DEPEND=">=dev-libs/expat-1.95.8
- >=media-libs/gd-2.0.34
- dev-perl/DBI
- dev-perl/DBD-mysql
- dev-perl/XML-Parser
- dev-perl/XML-Twig
- dev-perl/XML-Simple
- dev-perl/XML-Writer
- dev-perl/HTML-Template
- dev-perl/Tree-DAG_Node
- virtual/perl-File-Spec
- virtual/perl-Data-Dumper
- dev-perl/GD
- virtual/perl-Storable
- dev-perl/Log-Log4perl
- dev-perl/Log-Cabin
- dev-perl/IO-Tee
- dev-perl/MLDBM
- dev-perl/CGI
- dev-perl/DBI
- dev-perl/Apache-DBI
- dev-perl/Date-Manip
-"
-# dev-perl/CGI-Carp
-# dev-perl/CGI-Cookie
-# dev-perl/GD-Text
-# dev-perl/GD-Graph
-#
-RDEPEND="${DEPEND}
- >=virtual/mysql-5:*
- >=www-servers/apache-2.2"
-
-S="${WORKDIR}"/manatee-"${PV}"
-
-src_configure(){
- econf HTTPD=/usr/sbin/httpd HTTPD_SCRIPT_HOME=/var/www/cgi-bin HTTPD_DOC_HOME=/var/www/htdocs MYSQLD=/usr/sbin/mysqld
-}
-
-src_compile(){
- default
-}
diff --git a/sci-biology/manatee-jcvi/metadata.xml b/sci-biology/manatee-jcvi/metadata.xml
deleted file mode 100644
index 0f267b755..000000000
--- a/sci-biology/manatee-jcvi/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>mmokrejs@fold.natur.cuni.cz</email>
- <name>Martin Mokrejs</name>
- </maintainer>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
- <upstream>
- <remote-id type="sourceforge">downloads</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/sci-biology/mappy/Manifest b/sci-biology/mappy/Manifest
index 511c8e3d0..c39d0ea60 100644
--- a/sci-biology/mappy/Manifest
+++ b/sci-biology/mappy/Manifest
@@ -1 +1 @@
-DIST mappy-2.17.tar.gz 199280 BLAKE2B b79175016f26ed7f33bdff65cc5187c4c777849e5d89c44d0acb94d95189ccce7d89839cfc81c681d3bda6b29ae4ba1934205bd72472f7f228dbedc40dd78602 SHA512 399ceeb710f496c3d9bc409dcafb11122c5b93453dcfdf41c2f6d7d3a052d3600baff29ff08ed1322fcf10f1fc060434f9b0e79cb627c155d559f579b43dd267
+DIST mappy-2.24.tar.gz 140859 BLAKE2B af8ecf8f00c33951b2c7e81bec1e45fe39b7b41da1692fc8c4804b3ad5465320f453e2d53f771c09ce88fa681ad60c0c3706334ace8a682eee8b6f4ebccb02fc SHA512 5500b76ffb0f530aa8f1433c01f1805f5b95e329445ab103847e6ec6e0977a54e5c0dabe405869c7dd8d9103646db0b3cff0ef13b79d7021752ed266002a1dd4
diff --git a/sci-biology/mappy/mappy-2.17.ebuild b/sci-biology/mappy/mappy-2.24.ebuild
index 15399c913..3e25ed1eb 100644
--- a/sci-biology/mappy/mappy-2.17.ebuild
+++ b/sci-biology/mappy/mappy-2.24.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
-PYTHON_COMPAT=( python3_{7,8} ) # compile failure with py3.9
+PYTHON_COMPAT=( python3_{8..10} )
inherit distutils-r1
diff --git a/sci-biology/mmseqs2/Manifest b/sci-biology/mmseqs2/Manifest
new file mode 100644
index 000000000..dbfe85988
--- /dev/null
+++ b/sci-biology/mmseqs2/Manifest
@@ -0,0 +1 @@
+DIST mmseqs2-13.0.tar.gz 10199551 BLAKE2B 282d270c2b63a186d7534add93f6c23d625c5011392dc2cdff3cf11572ff23cb527726c19f5e9b092830216fa70a788faa46b1a4a2daafee05a513bff37a8a14 SHA512 90904392edd8a619577f79d75b44461b1bb647133850cc384caddb39bcfa3de0793392521edef0e86436ea0f76c9626298bd7975aba961ac7e846786eaf2e919
diff --git a/sci-biology/mmseqs2/files/mmseqs2-13.0-properly-handle-cpuflags.patch b/sci-biology/mmseqs2/files/mmseqs2-13.0-properly-handle-cpuflags.patch
new file mode 100644
index 000000000..10884765c
--- /dev/null
+++ b/sci-biology/mmseqs2/files/mmseqs2-13.0-properly-handle-cpuflags.patch
@@ -0,0 +1,40 @@
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 1a677e3..df1d765 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -56,23 +56,29 @@ if (HAVE_AVX2)
+ set(MMSEQS_ARCH "${MMSEQS_ARCH} -mavx2 -mcx16 -Wa,-q")
+ endif ()
+ set(X64 1)
+-elseif (HAVE_SSE4_1)
++endif ()
++if (HAVE_SSE4_1)
+ set(MMSEQS_ARCH "${MMSEQS_ARCH} -msse4.1 -mcx16")
+ set(X64 1)
+-elseif (HAVE_SSE2)
++endif ()
++if (HAVE_SSE2)
+ set(MMSEQS_ARCH "${MMSEQS_ARCH} -msse2")
+ set(DISABLE_IPS4O 1)
+ set(X64 1)
+-elseif (HAVE_POWER9)
++endif ()
++if (HAVE_POWER9)
+ set(MMSEQS_ARCH "${MMSEQS_ARCH} -mcpu=power9 -mvsx")
+ set(PPC64 1)
+-elseif (HAVE_POWER8)
++endif ()
++if (HAVE_POWER8)
+ set(MMSEQS_ARCH "${MMSEQS_ARCH} -mcpu=power8 -mvsx")
+ set(PPC64 1)
+-elseif (HAVE_ARM8)
++endif ()
++if (HAVE_ARM8)
+ set(MMSEQS_ARCH "${MMSEQS_ARCH} -march=armv8-a+simd")
+ set(ARM 1)
+-elseif (HAVE_S390X)
++endif ()
++if (HAVE_S390X)
+ set(MMSEQS_ARCH "${MMSEQS_ARCH} -mzarch -march=z14")
+ set(ZARCH 1)
+ endif ()
diff --git a/sci-biology/mmseqs2/metadata.xml b/sci-biology/mmseqs2/metadata.xml
new file mode 100644
index 000000000..c957d777e
--- /dev/null
+++ b/sci-biology/mmseqs2/metadata.xml
@@ -0,0 +1,22 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <upstream>
+ <remote-id type="github">soedinglab/mmseqs2</remote-id>
+ <doc>https://github.com/soedinglab/mmseqs2/wiki</doc>
+ </upstream>
+ <maintainer type="person">
+ <email>joel@generisbio.com</email>
+ <name>Joel Berendzen</name>
+ </maintainer>
+ <longdescription>
+ MMseqs2 (Many-against-Many sequence searching) is a software suite toi
+ search and cluster huge protein and nucleotide sequence sets.
+ MMseqs2 is open source GPL-licensed software implemented in C++.
+ The software is designed to run on multiple cores and servers
+ and exhibits very good scalability. MMseqs2 can run 10000 times
+ faster than BLAST. At 100 times its speed it achieves almost the
+ same sensitivity. It can perform profile searches with the same
+ sensitivity as PSI-BLAST at over 400 times its speed.
+ </longdescription>
+</pkgmetadata>
diff --git a/sci-biology/mmseqs2/mmseqs2-13.0-r1.ebuild b/sci-biology/mmseqs2/mmseqs2-13.0-r1.ebuild
new file mode 100644
index 000000000..6cbd139d8
--- /dev/null
+++ b/sci-biology/mmseqs2/mmseqs2-13.0-r1.ebuild
@@ -0,0 +1,55 @@
+# Copyright 2021-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit bash-completion-r1 cmake
+
+MY_PN="MMseqs2"
+
+# Must be manually updated with each release
+COMMIT="45111b641859ed0ddd875b94d6fd1aef1a675b7e"
+
+DESCRIPTION="Fast and sensitive sequence search and clustering"
+HOMEPAGE="https://github.com/soedinglab/MMseqs2"
+SRC_URI="https://github.com/soedinglab/${MY_PN}/archive/${COMMIT}.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}/${MY_PN}-${COMMIT}"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE="cpu_flags_x86_sse4_1 cpu_flags_x86_sse2 cpu_flags_x86_avx2"
+
+RDEPEND="
+ app-arch/zstd[static-libs]
+ sys-libs/zlib
+ app-arch/bzip2
+"
+DEPEND="${RDEPEND}"
+
+PATCHES=(
+ "${FILESDIR}/${P}-properly-handle-cpuflags.patch"
+)
+
+src_configure() {
+ local mycmakeargs=(
+ # Need static libs: https://github.com/soedinglab/MMseqs2/issues/411
+ -DBUILD_SHARED_LIBS=OFF
+ -DUSE_SYSTEM_ZSTD=ON
+ # Disable auto detection, build respecting cpu flags instead
+ -DNATIVE_ARCH=OFF
+ -DHAVE_AVX2="$(usex cpu_flags_x86_avx2)"
+ -DHAVE_SSE4_1="$(usex cpu_flags_x86_sse4_1)"
+ -DHAVE_SSE2="$(usex cpu_flags_x86_sse2)"
+ # We also have cpu flags for ppc/arm/s390x
+ -DVERSION_OVERRIDE=${PV}
+ )
+ cmake_src_configure
+}
+
+src_install(){
+ cmake_src_install
+ # move the bashcomp to correct dir
+ newbashcomp "${ED}/usr/util/bash-completion.sh" "${PN}"
+ rm -r "${ED}/usr/util/" || die
+}
diff --git a/sci-biology/mouse-brain-atlases/mouse-brain-atlases-0.5.3.ebuild b/sci-biology/mouse-brain-atlases/mouse-brain-atlases-0.5.3.ebuild
index 65963d55a..0709fb65d 100644
--- 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
@@ -8,8 +8,8 @@ inherit check-reqs
DESCRIPTION="A collection of mouse brain atlases in NIfTI format"
HOMEPAGE="https://github.com/IBT-FMI/mouse-brain-atlases"
SRC_URI="
- http://chymera.eu/distfiles/${P}.tar.xz
- hires? ( http://chymera.eu/distfiles/${PN}HD-${PV}.tar.xz )
+ http://resources.chymera.eu/distfiles/${P}.tar.xz
+ hires? ( http://resources.chymera.eu/distfiles/${PN}HD-${PV}.tar.xz )
"
LICENSE="fairuse"
diff --git a/sci-biology/mouse-brain-templates/mouse-brain-templates-0.5.3.ebuild b/sci-biology/mouse-brain-templates/mouse-brain-templates-0.5.3.ebuild
index 1ba2221aa..79c042a2a 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
@@ -8,8 +8,8 @@ inherit check-reqs
DESCRIPTION="A collection of mouse brain templates in NIfTI format"
HOMEPAGE="https://github.com/IBT-FMI/mouse-brain-atlases"
SRC_URI="
- http://chymera.eu/distfiles/${P}.tar.xz
- hires? ( http://chymera.eu/distfiles/${PN}HD-${PV}.tar.xz )
+ http://resources.chymera.eu/distfiles/${P}.tar.xz
+ hires? ( http://resources.chymera.eu/distfiles/${PN}HD-${PV}.tar.xz )
"
LICENSE="fairuse"
diff --git a/sci-biology/mrsfast/Manifest b/sci-biology/mrsfast/Manifest
deleted file mode 100644
index b6da5c3dd..000000000
--- a/sci-biology/mrsfast/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST mrsfast-3.4.2.tar.gz 47451 BLAKE2B e8dc3d06ec53d036ef2b556fc536b5430c6bc392846341e86afcd3131f38cc2ac2a642e8f4cf97e2bb56039604b18e839f0bc3803665a713cdb13374eee0fb46 SHA512 3ca0e166a165b338a3949fea1f80c6e3f228e36663af3cd6de57eb22ac05fa0d8a4c5fa8c2ca5ee5ce8cfe17d7df05362f26a9ae77f9d117ea256461a3c3e9a0
diff --git a/sci-biology/mrsfast/metadata.xml b/sci-biology/mrsfast/metadata.xml
deleted file mode 100644
index 309390097..000000000
--- a/sci-biology/mrsfast/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
- <upstream>
- <remote-id type="sourceforge">mrsfast</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/sci-biology/mrsfast/mrsfast-3.4.2.ebuild b/sci-biology/mrsfast/mrsfast-3.4.2.ebuild
deleted file mode 100644
index 91f7d771c..000000000
--- a/sci-biology/mrsfast/mrsfast-3.4.2.ebuild
+++ /dev/null
@@ -1,28 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit toolchain-funcs
-
-DESCRIPTION="Micro Read Fast Alignment Search Tool"
-HOMEPAGE="https://sfu-compbio.github.io/mrsfast/"
-SRC_URI="https://github.com/sfu-compbio/mrsfast/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS=""
-
-src_prepare() {
- default
- sed \
- -e "s:gcc:$(tc-getCC) ${LDFLAGS}:g" \
- -e '/^CFLAGS/d' \
- -e '/^LDFLAGS/d' \
- -i Makefile || die
- tc-export CC
-}
-
-src_install() {
- dobin ${PN}
-}
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.11.0.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.11.0.ebuild
index 623759901..527acfadf 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.11.0.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.11.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
@@ -37,7 +37,6 @@ REQUIRED_USE="${PYTHON_REQUIRED_USE}"
DEPEND="
<sys-devel/gcc-10:=
!sci-biology/ncbi-tools++
- !sci-biology/sra_sdk
berkdb? ( sys-libs/db:=[cxx(-)] )
boost? ( dev-libs/boost )
curl? ( net-misc/curl )
@@ -61,7 +60,7 @@ DEPEND="
muparser? ( dev-cpp/muParser )
hdf5? ( sci-libs/hdf5[cxx] )
gif? ( media-libs/giflib )
- jpeg? ( virtual/jpeg:0= )
+ jpeg? ( media-libs/libjpeg-turbo:0= )
png? ( media-libs/libpng:0= )
tiff? ( media-libs/tiff:0= )
xpm? ( x11-libs/libXpm )
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild
index d4ae93742..e90652f38 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
@@ -32,7 +32,6 @@ RESTRICT="!test? ( test )"
DEPEND="
<sys-devel/gcc-10:=
!sci-biology/ncbi-tools++
- !sci-biology/sra_sdk
berkdb? ( sys-libs/db:=[cxx(-)] )
boost? ( dev-libs/boost )
curl? ( net-misc/curl )
@@ -55,7 +54,7 @@ DEPEND="
muparser? ( dev-cpp/muParser )
hdf5? ( sci-libs/hdf5[cxx] )
gif? ( media-libs/giflib )
- jpeg? ( virtual/jpeg:0= )
+ jpeg? ( media-libs/libjpeg-turbo:0= )
png? ( media-libs/libpng:0= )
tiff? ( media-libs/tiff:0= )
xpm? ( x11-libs/libXpm )
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild
index f0269f0b5..ddeeac07d 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
@@ -32,7 +32,6 @@ RESTRICT="!test? ( test )"
DEPEND="
<sys-devel/gcc-10:=
!sci-biology/ncbi-tools++
- !sci-biology/sra_sdk
berkdb? ( sys-libs/db:=[cxx(-)] )
boost? ( dev-libs/boost )
curl? ( net-misc/curl )
@@ -55,7 +54,7 @@ DEPEND="
muparser? ( dev-cpp/muParser )
hdf5? ( sci-libs/hdf5[cxx] )
gif? ( media-libs/giflib )
- jpeg? ( virtual/jpeg:0= )
+ jpeg? ( media-libs/libjpeg-turbo:0= )
png? ( media-libs/libpng:0= )
tiff? ( media-libs/tiff:0= )
xpm? ( x11-libs/libXpm )
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild
index b232894b4..976ea3804 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
@@ -33,7 +33,6 @@ RESTRICT="!test? ( test )"
DEPEND="
<sys-devel/gcc-10:=
!sci-biology/ncbi-tools++
- !sci-biology/sra_sdk
berkdb? ( sys-libs/db:=[cxx(-)] )
boost? ( dev-libs/boost )
curl? ( net-misc/curl )
@@ -56,7 +55,7 @@ DEPEND="
muparser? ( dev-cpp/muParser )
hdf5? ( sci-libs/hdf5[cxx] )
gif? ( media-libs/giflib )
- jpeg? ( virtual/jpeg:0= )
+ jpeg? ( media-libs/libjpeg-turbo:0= )
png? ( media-libs/libpng:0= )
tiff? ( media-libs/tiff:0= )
xpm? ( x11-libs/libXpm )
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild
index 623759901..527acfadf 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
@@ -37,7 +37,6 @@ REQUIRED_USE="${PYTHON_REQUIRED_USE}"
DEPEND="
<sys-devel/gcc-10:=
!sci-biology/ncbi-tools++
- !sci-biology/sra_sdk
berkdb? ( sys-libs/db:=[cxx(-)] )
boost? ( dev-libs/boost )
curl? ( net-misc/curl )
@@ -61,7 +60,7 @@ DEPEND="
muparser? ( dev-cpp/muParser )
hdf5? ( sci-libs/hdf5[cxx] )
gif? ( media-libs/giflib )
- jpeg? ( virtual/jpeg:0= )
+ jpeg? ( media-libs/libjpeg-turbo:0= )
png? ( media-libs/libpng:0= )
tiff? ( media-libs/tiff:0= )
xpm? ( x11-libs/libXpm )
diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
index 6daf7b3f0..009085d15 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
@@ -36,7 +36,6 @@ RESTRICT="!test? ( test )"
# dev-libs/boost must have Boost.Test suite, probably dev-libs/boost[test] then?
DEPEND="
<sys-devel/gcc-10:=
- !sci-biology/sra_sdk
app-arch/cpio
berkdb? ( sys-libs/db:=[cxx(-)] )
boost? ( dev-libs/boost[tools] )
@@ -60,7 +59,7 @@ DEPEND="
muparser? ( dev-cpp/muParser )
hdf5? ( sci-libs/hdf5[cxx] )
gif? ( media-libs/giflib )
- jpeg? ( virtual/jpeg:0= )
+ jpeg? ( media-libs/libjpeg-turbo:0= )
png? ( media-libs/libpng:0= )
tiff? ( media-libs/tiff:0= )
xpm? ( x11-libs/libXpm )
diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
index e2db30639..604c9c638 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
@@ -39,7 +39,6 @@ REQUIRED_USE="${PYTHON_REQUIRED_USE}"
# dev-libs/boost must have Boost.Test suite, probably dev-libs/boost[test] then?
DEPEND="
<sys-devel/gcc-10:=
- !sci-biology/sra_sdk
app-arch/cpio
berkdb? ( sys-libs/db:=[cxx(-)] )
boost? ( dev-libs/boost[tools] )
@@ -64,7 +63,7 @@ DEPEND="
muparser? ( dev-cpp/muParser )
hdf5? ( sci-libs/hdf5[cxx] )
gif? ( media-libs/giflib )
- jpeg? ( virtual/jpeg:0= )
+ jpeg? ( media-libs/libjpeg-turbo:0= )
png? ( media-libs/libpng:0= )
tiff? ( media-libs/tiff:0= )
xpm? ( x11-libs/libXpm )
diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild
index 7df161c99..4d0d6363e 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
@@ -39,7 +39,6 @@ REQUIRED_USE="${PYTHON_REQUIRED_USE}"
# dev-libs/boost must have Boost.Test suite, probably dev-libs/boost[test] then?
DEPEND="
<sys-devel/gcc-10:=
- !sci-biology/sra_sdk
app-arch/cpio
berkdb? ( sys-libs/db:=[cxx(-)] )
boost? ( dev-libs/boost[tools] )
@@ -64,7 +63,7 @@ DEPEND="
muparser? ( dev-cpp/muParser )
hdf5? ( sci-libs/hdf5[cxx] )
gif? ( media-libs/giflib )
- jpeg? ( virtual/jpeg:0= )
+ jpeg? ( media-libs/libjpeg-turbo:0= )
png? ( media-libs/libpng:0= )
tiff? ( media-libs/tiff:0= )
xpm? ( x11-libs/libXpm )
diff --git a/sci-biology/nilearn/Manifest b/sci-biology/nilearn/Manifest
index 580b087b0..5dd197214 100644
--- a/sci-biology/nilearn/Manifest
+++ b/sci-biology/nilearn/Manifest
@@ -1 +1,2 @@
-DIST nilearn-0.8.0.tar.gz 6603264 BLAKE2B f96621b68255722f89ac18cfc8b44e2dc5fc6d4bda2d867d5f83ba669f1c3369318e8458360071245398362122b501c70849741068f7bfa567e49a7f8cdeefa1 SHA512 6e7da3963cd29282ab77bbf1dbb5c1879897dae3d3296a8e0c57edc11a272d9e386914fc3af81d13b57199d64880f534806dca6851b5d8ddecae9083ec5df18e
+DIST nilearn-0.8.1.tar.gz 11305317 BLAKE2B adefde80f5bce5ef115299326d212a7771a6ca1fc1ed7afc20fdd5b099882cfe37cc2d163807677450328916704d44e8f4044229b1470f764c75ee12d2e72b63 SHA512 4de95caa5c2080665e827310de28efb48a8b2e8161ac62f9e799984dbcd364f45ce486fcd21e9f30ef1fc41f48d2e41e477846acec5f89caf3cc1489373293d4
+DIST nilearn-0.9.1.tar.gz 11660100 BLAKE2B f2031b531faf2b7f77a6128ce2c41d4d8c4c9d5fab79df453ca127228f7ec4784b319107a9e9988b3d3a9ce87358d251e500a88dfb8226a6d4510ae5fe9f3a0c SHA512 f824fc563fd56b25508ee5803963fc98c2048fbab8823a6a6bde39e4b428a871588211649b4ce939f65173f6d4afd019e9fe1445b5cfdd00fba7823d9e23a571
diff --git a/sci-biology/nilearn/files/nilearn-0.9.1-tests.patch b/sci-biology/nilearn/files/nilearn-0.9.1-tests.patch
new file mode 100644
index 000000000..6d13b76b1
--- /dev/null
+++ b/sci-biology/nilearn/files/nilearn-0.9.1-tests.patch
@@ -0,0 +1,10 @@
+--- a/setup.cfg
++++ b/setup.cfg
+@@ -78,7 +78,6 @@
+ doctest_optionflags = NORMALIZE_WHITESPACE ELLIPSIS
+ junit_family = xunit2
+ addopts =
+- --doctest-modules
+ -s
+ -vv
+ --durations=0
diff --git a/sci-biology/nilearn/nilearn-0.8.0.ebuild b/sci-biology/nilearn/nilearn-0.8.1.ebuild
index a70e8d0fc..c73c9f519 100644
--- a/sci-biology/nilearn/nilearn-0.8.0.ebuild
+++ b/sci-biology/nilearn/nilearn-0.8.1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
@@ -38,5 +38,5 @@ distutils_enable_tests pytest
python_test() {
echo "backend: Agg" > matplotlibrc
- MPLCONFIGDIR=. pytest -vv || die
+ MPLCONFIGDIR=. epytest
}
diff --git a/sci-biology/nilearn/nilearn-0.9.1.ebuild b/sci-biology/nilearn/nilearn-0.9.1.ebuild
new file mode 100644
index 000000000..7e3716791
--- /dev/null
+++ b/sci-biology/nilearn/nilearn-0.9.1.ebuild
@@ -0,0 +1,52 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..9} )
+
+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 -> ${P}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="test"
+
+RDEPEND="
+ >=dev-python/joblib-0.15[${PYTHON_USEDEP}]
+ dev-python/lxml[${PYTHON_USEDEP}]
+ >=dev-python/matplotlib-3[${PYTHON_USEDEP}]
+ >=dev-python/numpy-1.18[${PYTHON_USEDEP}]
+ >=dev-python/pandas-1[${PYTHON_USEDEP}]
+ >=dev-python/requests-2[${PYTHON_USEDEP}]
+ >=dev-python/scipy-1.5[${PYTHON_USEDEP}]
+ >=sci-libs/nibabel-3[${PYTHON_USEDEP}]
+ >=sci-libs/scikit-learn-0.22[${PYTHON_USEDEP}]
+"
+
+PATCHES=( "${FILESDIR}/${P}-tests.patch" )
+
+distutils_enable_tests pytest
+
+EPYTEST_IGNORE=(
+ "examples/05_glm_second_level/plot_second_level_association_test.py"
+ "examples/05_glm_second_level/plot_second_level_one_sample_test.py"
+ "examples/05_glm_second_level/plot_second_level_two_sample_test.py"
+)
+# Reported upstream:
+# https://github.com/nilearn/nilearn/issues/3232
+EPYTEST_DESELECT=(
+ "nilearn/interfaces/fmriprep/tests/test_load_confounds.py::test_nilearn_standardize[False-True-zscore]"
+ "nilearn/interfaces/fmriprep/tests/test_load_confounds.py::test_nilearn_standardize[False-True-psc]"
+ "nilearn/interfaces/fmriprep/tests/test_load_confounds.py::test_nilearn_standardize[True-True-zscore]"
+ "nilearn/interfaces/fmriprep/tests/test_load_confounds.py::test_nilearn_standardize[True-True-psc]"
+)
+
+python_test() {
+ echo "backend: Agg" > matplotlibrc
+ MPLCONFIGDIR=. epytest
+}
diff --git a/sci-biology/nilearn/nilearn-9999.ebuild b/sci-biology/nilearn/nilearn-9999.ebuild
deleted file mode 100644
index a9478fc8e..000000000
--- a/sci-biology/nilearn/nilearn-9999.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{8..9} )
-
-inherit distutils-r1 git-r3
-
-DESCRIPTION="Fast and easy statistical learning on NeuroImaging data"
-HOMEPAGE="http://nilearn.github.io/"
-EGIT_REPO_URI="https://github.com/nilearn/nilearn"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-# Tests attempt to download external data.
-RESTRICT="test"
-
-BDEPEND="
- test? (
- dev-python/matplotlib[${PYTHON_USEDEP}]
- )
-"
-
-RDEPEND="
- >=dev-python/joblib-0.12[${PYTHON_USEDEP}]
- >=dev-python/numpy-1.16[${PYTHON_USEDEP}]
- >=sci-libs/scikit-learn-0.21[${PYTHON_USEDEP}]
- >=dev-python/scipy-1.2[${PYTHON_USEDEP}]
- >=sci-libs/nibabel-2.5[${PYTHON_USEDEP}]
- >=dev-python/pandas-0.24.0[${PYTHON_USEDEP}]
- >=dev-python/requests-2[${PYTHON_USEDEP}]
-"
-
-distutils_enable_tests pytest
-
-python_test() {
- echo "backend: Agg" > matplotlibrc
- MPLCONFIGDIR=. pytest -vv || die
-}
diff --git a/sci-biology/oases/Manifest b/sci-biology/oases/Manifest
deleted file mode 100644
index 031a5ff34..000000000
--- a/sci-biology/oases/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST OasesManual.pdf 113886 BLAKE2B aa8492887cea64e67966238e620b24aa5f90a8622a6de9bc4d4e1f56554f624c9ae7a19e0c46d83478849ec5d2ecb758fd8e253d8327d4d2bdcdda9db2e114a7 SHA512 c710a62cd1982060f723918f5f4de91adff12870d1682d0729035a3588ed37d26898c399c07b1b81b4b399c7ea1a14509784a6dbb9de6004bcadf6677cd5859f
-DIST oases_0.2.08.tgz 92037 BLAKE2B ff9762264d18c42e20b2208a057b073a2a960dab1ca17372db2fbf6f09094d3446ccd29a6038e17ee59b5adee9afe23cd59bbc4b640f57ce04141d2990b32b90 SHA512 e9a73a9227ce13995fcac7f456534a650099d8160d48d2d9831f3f05e482353c29dd76bbc74b0b451154eb5061ddb473649d21442941360f0e8c7623f6fe586c
diff --git a/sci-biology/oases/files/Makefile.patch b/sci-biology/oases/files/Makefile.patch
deleted file mode 100644
index fcd0842ff..000000000
--- a/sci-biology/oases/files/Makefile.patch
+++ /dev/null
@@ -1,15 +0,0 @@
---- a/Makefile 2016-04-10 22:34:31.976222662 +0200
-+++ b/Makefile 2016-04-10 22:37:49.636225327 +0200
-@@ -1,8 +1,8 @@
--CC = gcc
--CFLAGS = -Wall
--DEBUG = -g
-+CC ?= gcc
-+CFLAGS ?= -Wall
-+DEBUG ?= -g
- LIBS = -lm
--OPT = -O3
-+#OPT = -O3
- export MAXKMERLENGTH = 64
- export CATEGORIES = 2
- DEF = -D MAXKMERLENGTH=$(MAXKMERLENGTH) -D CATEGORIES=$(CATEGORIES)
diff --git a/sci-biology/oases/metadata.xml b/sci-biology/oases/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/oases/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>mmokrejs@fold.natur.cuni.cz</email>
- <name>Martin Mokrejs</name>
- </maintainer>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
-</pkgmetadata>
diff --git a/sci-biology/oases/oases-0.2.08.ebuild b/sci-biology/oases/oases-0.2.08.ebuild
deleted file mode 100644
index 74ad30f59..000000000
--- a/sci-biology/oases/oases-0.2.08.ebuild
+++ /dev/null
@@ -1,40 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DESCRIPTION="De novo transcriptome assembler"
-HOMEPAGE="http://www.ebi.ac.uk/~zerbino/oases"
-if [ "$PV" == "9999" ]; then
- inherit git-r3
- EGIT_REPO_URI="https://github.com/dzerbino/oases.git"
- SRC_URI="http://www.ebi.ac.uk/~zerbino/oases/OasesManual.pdf"
-else
- SRC_URI="http://www.ebi.ac.uk/~zerbino/oases/oases_0.2.08.tgz
- http://www.ebi.ac.uk/~zerbino/oases/OasesManual.pdf"
- S="${WORKDIR}/oases_0.2.8"
- KEYWORDS=""
- # fails to find globals.h, but which globals.h does it want?
-fi
-
-LICENSE="GPL-3"
-SLOT="0"
-
-DEPEND=""
-RDEPEND="${DEPEND}
- >=sci-biology/velvet-1.2.08"
-
-PATCHES=(
- "${FILESDIR}/Makefile.patch"
-)
-
-src_prepare(){
- default
- sed -e 's#cleanobj velvet oases doc#oases#' -i Makefile || die
-}
-
-src_install(){
- dobin oases
- dodoc README.md
- dodoc "${DISTDIR}"/OasesManual.pdf
-}
diff --git a/sci-biology/oases/oases-9999.ebuild b/sci-biology/oases/oases-9999.ebuild
deleted file mode 100644
index 74ad30f59..000000000
--- a/sci-biology/oases/oases-9999.ebuild
+++ /dev/null
@@ -1,40 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DESCRIPTION="De novo transcriptome assembler"
-HOMEPAGE="http://www.ebi.ac.uk/~zerbino/oases"
-if [ "$PV" == "9999" ]; then
- inherit git-r3
- EGIT_REPO_URI="https://github.com/dzerbino/oases.git"
- SRC_URI="http://www.ebi.ac.uk/~zerbino/oases/OasesManual.pdf"
-else
- SRC_URI="http://www.ebi.ac.uk/~zerbino/oases/oases_0.2.08.tgz
- http://www.ebi.ac.uk/~zerbino/oases/OasesManual.pdf"
- S="${WORKDIR}/oases_0.2.8"
- KEYWORDS=""
- # fails to find globals.h, but which globals.h does it want?
-fi
-
-LICENSE="GPL-3"
-SLOT="0"
-
-DEPEND=""
-RDEPEND="${DEPEND}
- >=sci-biology/velvet-1.2.08"
-
-PATCHES=(
- "${FILESDIR}/Makefile.patch"
-)
-
-src_prepare(){
- default
- sed -e 's#cleanobj velvet oases doc#oases#' -i Makefile || die
-}
-
-src_install(){
- dobin oases
- dodoc README.md
- dodoc "${DISTDIR}"/OasesManual.pdf
-}
diff --git a/sci-biology/open-ephys-gui/Manifest b/sci-biology/open-ephys-gui/Manifest
index 9f8d8eeac..a2611bd74 100644
--- a/sci-biology/open-ephys-gui/Manifest
+++ b/sci-biology/open-ephys-gui/Manifest
@@ -1,2 +1 @@
-DIST open-ephys-gui-0.5.2.2.tar.gz 64533170 BLAKE2B dc70c3eca6a8fbc7c4f6e84580fa6d5b31b837fedbdff20f532e3c01c764cbc3c51637e4fd678d048c78b6f79b4b4a5cd4d437125beeaf712f6f322e82579c85 SHA512 b6369bb0abd8ca18ff225cffab04a24915865647ee1ab5b6d83d5d6fbda3bc64d1b7db04c23deb8d29b8ff378e703b88cfa9d409f4cde62a3af34a7984427219
DIST open-ephys-gui-0.5.5.tar.gz 63347783 BLAKE2B 8f3ab3c20e23dd4f613e2ed47dca1827ddbcc5e95be5ca12dfeefdc84611653d531d629b78049397fd4951d558f63531ea2265d13e629c8da793fc20090d1075 SHA512 b835a7f8bb3eeb08ec77f6d14f988d6278b2f5b1966fbf8bec55d429c9cee36050cf574dd78a2ebad4adc5c681bcec5b64dcfb1ec87e548c55e2bf1bff2eb2dc
diff --git a/sci-biology/open-ephys-gui/files/open-ephys-gui-0.5.2.2.patch b/sci-biology/open-ephys-gui/files/open-ephys-gui-0.5.2.2.patch
deleted file mode 100644
index 77e401639..000000000
--- a/sci-biology/open-ephys-gui/files/open-ephys-gui-0.5.2.2.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-# Add 'Gentoo' build type
-
---- ../CMakeLists.txt 2019-12-02 22:29:24.021065669 -0300
-+++ ../CMakeLists.txt 2019-12-02 22:29:11.251065418 -0300
-@@ -123,6 +123,7 @@
- if(${CMAKE_BUILD_TYPE} STREQUAL "Debug")
-
- elseif (${CMAKE_BUILD_TYPE} STREQUAL "Release")
-+ elseif (${CMAKE_BUILD_TYPE} STREQUAL "Gentoo")
- else()
- message(FATAL_ERROR "Invalid build type")
- endif()
diff --git a/sci-biology/open-ephys-gui/open-ephys-gui-0.5.2.2.ebuild b/sci-biology/open-ephys-gui/open-ephys-gui-0.5.2.2.ebuild
deleted file mode 100644
index b4cbc6d8f..000000000
--- a/sci-biology/open-ephys-gui/open-ephys-gui-0.5.2.2.ebuild
+++ /dev/null
@@ -1,82 +0,0 @@
-# Copyright 2019-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-inherit cmake
-
-DESCRIPTION="Processing, recording, and visualizing multichannel ephys data"
-HOMEPAGE="https://open-ephys.org/gui/"
-LICENSE="GPL-3"
-
-if [[ ${PV} == "9999" ]] ; then
- inherit git-r3
- EGIT_REPO_URI="https://github.com/open-ephys/plugin-GUI"
- EGIT_BRANCH="master"
- Suffix=$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"
-
-BDEPEND="
- <sys-devel/gcc-9
-"
-DEPEND="
- media-libs/alsa-lib
- media-libs/freeglut
- media-libs/freetype
- x11-libs/libXrandr
- x11-libs/libXcursor
- x11-libs/libXinerama
- jack? ( media-sound/jack-audio-connection-kit )
-"
-RDEPEND="${DEPEND}"
-
-BUILD_DIR="$S/Build"
-PATCHES=( "${FILESDIR}"/${P}.patch )
-
-QA_PREBUILT="opt/open-ephys-0.5.2.2/shared/*.so"
-QA_PRESTRIPPED="
- opt/open-ephys-0.5.2.2/plugins/*.so
- opt/open-ephys-0.5.2.2/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}"/Gentoo/* "${ED}"/opt/open-ephys-"$Suffix"/
- cp -R "${WORKDIR}"/"${SubDir}"/Resources/Scripts/40-open-ephys.rules "${ED}"/lib/udev/rules.d/
- dosym ../../opt/open-ephys-"$Suffix"/open-ephys usr/bin/open-ephys-"$Suffix"
-}
-
-pkg_postinst() {
- ewarn " "
- ewarn "You must restart the udev service in order to allow your computer to"
- ewarn "communicate with the Open Ephys acquisition board."
- ewarn " "
-}
diff --git a/sci-biology/opfvta_bidsdata/opfvta_bidsdata-2.0.ebuild b/sci-biology/opfvta_bidsdata/opfvta_bidsdata-2.0.ebuild
index 988f6ba6f..c43c10257 100644
--- a/sci-biology/opfvta_bidsdata/opfvta_bidsdata-2.0.ebuild
+++ b/sci-biology/opfvta_bidsdata/opfvta_bidsdata-2.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
@@ -8,7 +8,6 @@ inherit check-reqs
DESCRIPTION="BIDS data files released with the OPFVTA publication"
HOMEPAGE="http://www.aic-fmi.ethz.ch/"
SRC_URI="
- http://chymera.eu/distfiles/${P}.tar.xz
https://zenodo.org/record/3575149/files/${P}.tar.xz
"
diff --git a/sci-biology/pbbam/Manifest b/sci-biology/pbbam/Manifest
index 28d1a1423..c35432703 100644
--- a/sci-biology/pbbam/Manifest
+++ b/sci-biology/pbbam/Manifest
@@ -1 +1 @@
-DIST pbbam-1.6.0.tar.gz 11037740 BLAKE2B 72bd0b7b427dd9704095c0a5b1763aaf320438b4cbb394cc85fe13b8c2a678191dc55112869fa87a87426e44ce02c492b49f6ef9226331ac2ca379b4f4968c96 SHA512 5d07184aba0dd3873a769376174b5558071c1dbcd8ad140c7c9a9f58cd3825763d3050b971358be0e4916aa8b2b41ee51dc0bf063a78976a92c520b2d40f633f
+DIST pbbam-1.8.1.tar.gz 11069936 BLAKE2B 6ef23c81f4cfbdb060bfc8355ca628024038466482a6cacb3dd162fa58ab1052702e482ab797a60160264fd2cc70fe116dd5385c6094560060adf6fe2cf74d10 SHA512 ea28b4683c72fafb2e459ac1f37a9be258ddc82e059ba9d8b094e8dd6e3a40d3f25d5edcc790c5bd274805190caf1123311199e30166bd4f3e815dcc77929387
diff --git a/sci-biology/pbbam/pbbam-1.6.0.ebuild b/sci-biology/pbbam/pbbam-1.8.1.ebuild
index 076b04e81..a114da0fc 100644
--- a/sci-biology/pbbam/pbbam-1.6.0.ebuild
+++ b/sci-biology/pbbam/pbbam-1.8.1.ebuild
@@ -1,7 +1,7 @@
# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
inherit meson
@@ -20,6 +20,7 @@ BDEPEND="
"
DEPEND="
sci-biology/pbcopper
+ sci-biology/samtools:0
>=sci-libs/htslib-1.3.1:=
>=dev-libs/boost-1.55:=
"
diff --git a/sci-biology/pbbam/pbbam-9999.ebuild b/sci-biology/pbbam/pbbam-9999.ebuild
deleted file mode 100644
index 1f03ab1a9..000000000
--- a/sci-biology/pbbam/pbbam-9999.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
-
-inherit git-r3 meson
-
-DESCRIPTION="PacBio modified BAM file format"
-HOMEPAGE="https://pbbam.readthedocs.io/en/latest/index.html"
-EGIT_REPO_URI="https://github.com/PacificBiosciences/pbbam.git"
-
-LICENSE="blasr"
-SLOT="0"
-KEYWORDS=""
-
-BDEPEND="
- virtual/pkgconfig
- >=dev-cpp/gtest-1.8.1
- >=dev-lang/swig-3.0.5
-"
-DEPEND="
- sci-biology/pbcopper
- >=sci-libs/htslib-1.3.1:=
- >=dev-libs/boost-1.55:=[threads]
-"
-RDEPEND="${DEPEND}"
diff --git a/sci-biology/pbcopper/Manifest b/sci-biology/pbcopper/Manifest
index 6c1e6f430..93e0659d5 100644
--- a/sci-biology/pbcopper/Manifest
+++ b/sci-biology/pbcopper/Manifest
@@ -1 +1 @@
-DIST pbcopper-1.9.0.tar.gz 3325390 BLAKE2B be25b28e23bb24d44ea2f42e6efef123ab2e9922987afbb4028a7c401897a8489bc304d9cb742f6606ee1e63ef3244dff0ee2147e955f1c1bfb49d15a2465009 SHA512 20649185f1f85cefad78e984a4e07ace4657fa3ca848049f59b803c32d4d1f90e40580878cfe245496448c3749bcb01edacf30aa397d43008431d2defe05e92e
+DIST pbcopper-1.9.5.tar.gz 3386984 BLAKE2B d38b6dfa7c5f0a9ed7fc9b89f9ee71bcd0e2248a36e593cea82ce214411b0e16bac6aff289805bcafb38ad69abe38805fbd4d7c5c0bdb7b197691ee0514c397b SHA512 006470f318341c311f600e12495b9e72a47a0fb1795dcd4d13b06c02e4872f7cde077d98bebc32ac29bb41d410d0bc7b73eead4da4ac6cf3c110e896c15df8c6
diff --git a/sci-biology/pbcopper/pbcopper-1.9.0.ebuild b/sci-biology/pbcopper/pbcopper-1.9.5.ebuild
index 9e065dbcc..79307d839 100644
--- a/sci-biology/pbcopper/pbcopper-1.9.0.ebuild
+++ b/sci-biology/pbcopper/pbcopper-1.9.5.ebuild
@@ -1,7 +1,7 @@
# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
inherit meson
diff --git a/sci-biology/pilon-bin/Manifest b/sci-biology/pilon-bin/Manifest
deleted file mode 100644
index 3f3de6bcc..000000000
--- a/sci-biology/pilon-bin/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST pilon-1.24.jar 11034933 BLAKE2B 7c97c8e30a05ad56c8d2830e414c285eb086bc3ccb51ab10af33fe53771287b4c99880930484fe7574dd1f57df5c003af3ceb98b9026d842ee447aecaacb78f8 SHA512 48d3688059f0bcb2055fd9291cd36d282733724f68832633ffc08adb883af4b3146759bb2b13d99f0695b11f283d3bb89a2f8ff18102b1a125e38fb2de0f5461
diff --git a/sci-biology/pilon-bin/metadata.xml b/sci-biology/pilon-bin/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/pilon-bin/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/pilon-bin/pilon-bin-1.24.ebuild b/sci-biology/pilon-bin/pilon-bin-1.24.ebuild
deleted file mode 100644
index 49d15366f..000000000
--- a/sci-biology/pilon-bin/pilon-bin-1.24.ebuild
+++ /dev/null
@@ -1,29 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit java-pkg-2
-
-DESCRIPTION="Fix assembled reference using BAM-aligned reads, call SNPs"
-HOMEPAGE="
- https://github.com/broadinstitute/pilon
- https://github.com/broadinstitute/pilon/wiki"
-SRC_URI="https://github.com/broadinstitute/pilon/releases/download/v${PV}/pilon-${PV}.jar"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64"
-
-# contains bundled sbt-assembly module
-DEPEND=">=virtual/jdk-1.7:*"
-RDEPEND="${DEPEND}
- >=virtual/jre-1.7:*
- >=dev-java/htsjdk-1.130"
-
-S="${WORKDIR}"
-
-src_install(){
- cp -p "${DISTDIR}"/pilon-${PV}.jar . || die
- java-pkg_dojar pilon-${PV}.jar
-}
diff --git a/sci-biology/primerD/Manifest b/sci-biology/primerD/Manifest
deleted file mode 100644
index 063af78cf..000000000
--- a/sci-biology/primerD/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST primerD.tar.gz 58132 BLAKE2B 4fdf1126649ba3bddb92852dacd14a4e4bf652715166f7c6d9ba23aa3ebe8ab7419cf939131e6bde09190c65e5ed04222172757ff642d7af9eb34bfadd9875eb SHA512 9f70ccb2a8304fe9e3a3885f2607969ca00483c1f3bb70ea3b5da709db0c43979cdd6bbf2b9ef805c13d215000afab2053fdeda66dc48006cb50f536886b86b2
diff --git a/sci-biology/primerD/metadata.xml b/sci-biology/primerD/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/primerD/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>mmokrejs@fold.natur.cuni.cz</email>
- <name>Martin Mokrejs</name>
- </maintainer>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
-</pkgmetadata>
diff --git a/sci-biology/primerD/primerD-1.0.0.ebuild b/sci-biology/primerD/primerD-1.0.0.ebuild
deleted file mode 100644
index 6d46832a9..000000000
--- a/sci-biology/primerD/primerD-1.0.0.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit toolchain-funcs
-
-DESCRIPTION="Design degenerate primers"
-HOMEPAGE="https://mblab.wustl.edu/software.html"
-SRC_URI="primerD.tar.gz"
-#SRC_URI="https://mblab.wustl.edu/software/download/primerD.tar.gz -> primerD-1.0.tar.gz"
-# ERROR: cannot verify mblab.wustl.edu's certificate, issued by ‘CN=InCommon RSA Server CA,OU=InCommon,O=Internet2,L=Ann Arbor,ST=MI,C=US’:
-# Unable to locally verify the issuer's authority.
-# To connect to mblab.wustl.edu insecurely, use `--no-check-certificate'.
-RESTRICT="fetch"
-
-LICENSE="LGPL-2.1"
-SLOT="0"
-# make: *** No rule to make target '/usr/include/linux/new.h', needed by 'Main.o'. Stop.
-KEYWORDS=""
-
-S="${WORKDIR}"/primerD
-
-src_prepare(){
- default
- sed -i -e "s:CC=g++:CC=$(tc-getCXX):; s:-Wall -g:${CFLAGS}:" \
- -e "s:/usr/include/g++-3/stl_algobase.h:/usr/lib/gcc/${CHOST}/$(gcc-fullversion)/include/g++-v$(gcc-major-version )/bits/stl_algobase.h:g" \
- -e "s:/usr/include/g++-3/stl_relops.h:/usr/lib/gcc/${CHOST}/$(gcc-fullversion)/include/g++-v$(gcc-major-version )/bits/stl_relops.h:g" \
- -e "s:/usr/include/g++-3/stl_pair.h:/usr/lib/gcc/${CHOST}/$(gcc-fullversion)/include/g++-v$(gcc-major-version )/bits/stl_pair.h:g" \
- -e "s:/usr/include/g++-3/type_traits.h:/usr/lib/gcc/${CHOST}/$(gcc-fullversion)/include/g++-v$(gcc-major-version )/ext/type_traits.h:g" \
- -e "s:/usr/include/g++-3/stl_config.h:/usr/lib/gcc/${CHOST}/$(gcc-fullversion)/include/g++-v$(gcc-major-version )/pstl/pstl_config.h:g" \
- -e "s:/usr/include/g++-3/:/usr/lib/gcc/${CHOST}/$(gcc-fullversion)/include/g++-v$(gcc-major-version )/:g" \
- -e "s:/usr/include/_G_config.h:/usr/include/stdio.h:g" \
- -e "s:/usr/lib/gcc-lib/i386-redhat-linux/2.96/include/:/usr/include/linux/:g" \
- Makefile || die
-
-}
-
-src_install(){
- dodoc README
- dobin primerD
-}
diff --git a/sci-biology/pufferfish/Manifest b/sci-biology/pufferfish/Manifest
deleted file mode 100644
index 4ca8429dc..000000000
--- a/sci-biology/pufferfish/Manifest
+++ /dev/null
@@ -1,4 +0,0 @@
-DIST htslib-pufferfish-1.4.0.tar.gz 1262620 BLAKE2B 7fff233fadd4737e416058a24d9dc916e5ecf1fa10c456cfb15001df7c664daedecdbcef49469dffb6516c47e00937cbe399a68032fcf18ab9070768d40d3091 SHA512 52ae9099ddadb1d0136f1a62825ff0539baf754302c735ea81b8748a1c349107766b2022cc59814728d366b6df2c9f1b93edf926c1a6a7af78a4f40c4e821c4c
-DIST pufferfish-1.4.0.tar.gz 3099274 BLAKE2B 65c26b02513840b3f7b6f381af674b59a21960fe56559b8d87dd22051fa02e7e5c06ab1ba1b9f81516f9831ea1b79492a9cc0e2d0b9258d9c21ddfb7ea162d69 SHA512 683bad5a5e3512c56c211af1270ea1e627d2483d601d20ef70f92087b37327463b36224eda38699231f8daa8c318d745757eed2a4190351ebb8b4a252fca6474
-DIST seqlib-pufferfish-1.4.0.tar.gz 315441 BLAKE2B b402f94837aeb43e4d443044c65d1c193ce7b24a8507b9a79da6cbfc5d7093d286ccd8573eca64c78bd3c65830dc11a18ec26dc619e7ab95d04a472c15ec70d7 SHA512 b3efa0511df9c39ed8021c1bf316f88fb6b51ebd745b7f799bc92edebf31ff7dbd466b83ba30a3381e411d36455f4074163267d4331c5fe16f2934762865d22f
-DIST setcover-pufferfish-1.4.0.tar.gz 33911 BLAKE2B 690cfca7e271490ef8b7119fe9fb7df3e7c06897eab52346b485c22a8a7b8e75d344a07f24dbf44aa68919793f942c8f5d1bd1932d2ce1a21a18631e3e64aecf SHA512 8954b38a183f81fff36663c6cbbef25fbf003045d93462933d09f0384f6e17fa726d48e9d94daa5195052e6ff9650aba4a2c8a6f0691f50c360462f02760e2a1
diff --git a/sci-biology/pufferfish/files/pufferfish-do-not-fetch.patch b/sci-biology/pufferfish/files/pufferfish-do-not-fetch.patch
deleted file mode 100644
index c86fe847f..000000000
--- a/sci-biology/pufferfish/files/pufferfish-do-not-fetch.patch
+++ /dev/null
@@ -1,31 +0,0 @@
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index 7f1516a..90f7cdd 100644
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -282,12 +282,9 @@ message("TBB_LIBRARIES = ${TBB_LIBRARIES}")
-
-
- ExternalProject_Add(libseqlib
--GIT_REPOSITORY https://github.com/COMBINE-lab/SeqLib.git
--GIT_TAG master
- UPDATE_COMMAND ""
- UPDATE_DISCONNECTED 1
- BUILD_IN_SOURCE TRUE
--DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/seqlib
- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/seqlib
- INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
- CONFIGURE_COMMAND ./configure
-@@ -300,13 +297,10 @@ INSTALL_COMMAND mkdir -p <INSTALL_DIR>/lib && mkdir -p <INSTALL_DIR>/include &
- )
-
- ExternalProject_Add(libSetCover
-- GIT_REPOSITORY https://github.com/martin-steinegger/setcover.git
-- GIT_TAG master
- UPDATE_COMMAND ""
- CONFIGURE_COMMAND ""
- UPDATE_DISCONNECTED 1
- BUILD_IN_SOURCE TRUE
-- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/setcover
- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/setcover
- INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
- BUILD_COMMAND make -j8
diff --git a/sci-biology/pufferfish/metadata.xml b/sci-biology/pufferfish/metadata.xml
deleted file mode 100644
index 7b582e896..000000000
--- a/sci-biology/pufferfish/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
- <upstream>
- <remote-id type="github">COMBINE-lab/pufferfish</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/sci-biology/pufferfish/pufferfish-1.4.0.ebuild b/sci-biology/pufferfish/pufferfish-1.4.0.ebuild
deleted file mode 100644
index 588970e06..000000000
--- a/sci-biology/pufferfish/pufferfish-1.4.0.ebuild
+++ /dev/null
@@ -1,35 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit cmake
-
-SC_COMMIT="b1de7919c0a4d0e65c5cd0b6d78963516e44be25"
-SL_COMMIT="340dad36dff67ca96815bd412fe65587d4d64479"
-HL_COMMIT="be22a2a1082f6e570718439b9ace2db17a609eae"
-
-DESCRIPTION="Index for the colored, compacted, de Bruijn graph"
-HOMEPAGE="https://github.com/COMBINE-lab/pufferfish"
-SRC_URI="https://github.com/COMBINE-lab/pufferfish/archive/salmon-v${PV}.tar.gz -> ${P}.tar.gz
- https://github.com/martin-steinegger/setcover/archive/${SC_COMMIT}.tar.gz -> setcover-${P}.tar.gz
- https://github.com/COMBINE-lab/SeqLib/archive/${SL_COMMIT}.tar.gz -> seqlib-${P}.tar.gz
- https://github.com/samtools/htslib/archive/${HL_COMMIT}.tar.gz -> htslib-${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS=""
-
-DEPEND="dev-cpp/tbb"
-
-S="${WORKDIR}/${PN}-salmon-v${PV}"
-
-PATCHES=( "${FILESDIR}/${PN}-do-not-fetch.patch" )
-
-src_prepare() {
- mkdir -p external/{setcover,seqlib}
- mv "../setcover-${SC_COMMIT}"/* external/setcover || die
- mv "../SeqLib-${SL_COMMIT}"/* external/seqlib || die
- mv "../htslib-${HL_COMMIT}"/* external/seqlib/htslib || die
- cmake_src_prepare
-}
diff --git a/sci-biology/quorum/Manifest b/sci-biology/quorum/Manifest
deleted file mode 100644
index 68b3dd9c6..000000000
--- a/sci-biology/quorum/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST quorum-1.1.1.tar.gz 659218 BLAKE2B 26710674e12115b3d218c113eaa6b36d9694f85c65bb5e1a8b8e2b4405b585115b2e3ded34c84bdb24d680ae5a1d6e4c387689bdde8bc63824d8eb254d0894da SHA512 12d7a03ffa45dd358f52c55226e6888fc92bff8e361e1c5eca7b4f8545d70243793dd963602932b895702284f89cd77361b2b5636c062d86b467b538df0b9f16
diff --git a/sci-biology/quorum/files/quorum-0.2.1-use-jellyfish1.patch b/sci-biology/quorum/files/quorum-0.2.1-use-jellyfish1.patch
deleted file mode 100644
index b5b68a8fb..000000000
--- a/sci-biology/quorum/files/quorum-0.2.1-use-jellyfish1.patch
+++ /dev/null
@@ -1,74 +0,0 @@
---- src/error_correct_reads.cc 2018-04-21 14:25:41.310473159 +0200
-+++ src/error_correct_reads.cc 2018-04-21 14:26:58.262493179 +0200
-@@ -25,9 +25,9 @@
- #endif
-
- //#define DEBUG 1
--#include <jellyfish/dbg.hpp>
--#include <jellyfish/atomic_gcc.hpp>
--#include <jellyfish/mer_counting.hpp>
-+#include <jellyfish1/dbg.hpp>
-+#include <jellyfish1/atomic_gcc.hpp>
-+#include <jellyfish1/mer_counting.hpp>
-
- #include <jflib/multiplexed_io.hpp>
- #include <gzip_stream.hpp>
---- src/combine_jf_dbs.cc 2018-04-21 14:25:50.220707057 +0200
-+++ src/combine_jf_dbs.cc 2018-04-21 14:27:04.652660923 +0200
-@@ -1,9 +1,9 @@
--#include <jellyfish/err.hpp>
--#include <jellyfish/misc.hpp>
--#include <jellyfish/mer_counting.hpp>
--#include <jellyfish/compacted_hash.hpp>
--#include <jellyfish/thread_exec.hpp>
--#include <jellyfish/misc.hpp>
-+#include <jellyfish1/err.hpp>
-+#include <jellyfish1/misc.hpp>
-+#include <jellyfish1/mer_counting.hpp>
-+#include <jellyfish1/compacted_hash.hpp>
-+#include <jellyfish1/thread_exec.hpp>
-+#include <jellyfish1/misc.hpp>
- #include <src/combine_jf_dbs.hpp>
-
- int main(int argc, char *argv[])
---- src/error_correct_reads.hpp 2018-04-21 14:26:10.091228666 +0200
-+++ src/error_correct_reads.hpp 2018-04-21 14:27:09.792795853 +0200
-@@ -2,12 +2,12 @@
- #define __ERROR_CORRECT_READS_HPP__
-
- #include <config.h>
--#include <jellyfish/err.hpp>
--#include <jellyfish/mapped_file.hpp>
--#include <jellyfish/invertible_hash_array.hpp>
--#include <jellyfish/allocators_mmap.hpp>
--#include <jellyfish/parse_read.hpp>
--#include <jellyfish/thread_exec.hpp>
-+#include <jellyfish1/err.hpp>
-+#include <jellyfish1/mapped_file.hpp>
-+#include <jellyfish1/invertible_hash_array.hpp>
-+#include <jellyfish1/allocators_mmap.hpp>
-+#include <jellyfish1/parse_read.hpp>
-+#include <jellyfish1/thread_exec.hpp>
- #include <iostream>
- #include <fstream>
- #include <assert.h>
---- configure.ac.ori 2018-04-21 15:00:35.225439196 +0200
-+++ configure.ac 2018-04-21 15:01:37.977086449 +0200
-@@ -28,7 +28,7 @@
- JELLYFISH_VERSION=$(pkg-config --modversion jellyfish-1.1)
- AC_SUBST([JELLYFISH_VERSION])
- AC_ARG_VAR([JELLYFISH], [Jellyfish executable absolute path (default to looking in PATH)])
--AS_IF([test "x$JELLYFISH" = "x"], [AC_PATH_PROG([JELLYFISH], [jellyfish], [false])])
-+AS_IF([test "x$JELLYFISH" = "x"], [AC_PATH_PROG([JELLYFISH], [jellyfish1], [false])])
-
- AC_ARG_VAR([JF_LIB_PATH], [Append this path to LD_LIBRARY_PATH in quorum])
-
-@@ -47,7 +47,7 @@
- # --with-relative-jf-path
- AC_ARG_WITH([relative-jf-path],
- [AC_HELP_STRING([--with-relative-jf-path], [relative path from quorum to jellyfish (use an absolute path if not given. default to "." if given with no argument)])],
-- [case "$withval" in (yes) with_relative_jf_path="jellyfish" ;; (no) with_relative_jf_path= ;; (*) with_relative_jf_path=$withval/jellyfish ;; esac],
-+ [case "$withval" in (yes) with_relative_jf_path="jellyfish1" ;; (no) with_relative_jf_path= ;; (*) with_relative_jf_path=$withval/jellyfish1 ;; esac],
- [with_relative_jf_path= ])
- AC_SUBST([RELATIVE_JF_PATH], $with_relative_jf_path)
- AM_CONDITIONAL([HAVE_RELATIVE_JF_PATH], [test x$with_relative_jf_path != x])
diff --git a/sci-biology/quorum/metadata.xml b/sci-biology/quorum/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/quorum/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/quorum/quorum-1.1.1.ebuild b/sci-biology/quorum/quorum-1.1.1.ebuild
deleted file mode 100644
index 4af286fcb..000000000
--- a/sci-biology/quorum/quorum-1.1.1.ebuild
+++ /dev/null
@@ -1,28 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DESCRIPTION="Correct substitution errors in Illumina reads"
-HOMEPAGE="http://www.genome.umd.edu/quorum.html
- https://github.com/gmarcais/Quorum"
-SRC_URI="https://github.com/gmarcais/Quorum/releases/download/v${PV}/${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-DEPEND=">=sci-biology/jellyfish-2.1.4:2"
-RDEPEND="${DEPEND}"
-
-src_prepare() {
- default
- # fix jellyfish include path
- find -type f -name "*.cc" -exec sed -i -e 's/<jellyfish\//<jellyfish2\//g' {} + || die
- find -type f -name "*.hpp" -exec sed -i -e 's/<jellyfish\//<jellyfish2\//g' {} + || die
-}
-
-src_configure(){
- econf --enable-relative-paths --with-relative-jf-path
- default
-}
diff --git a/sci-biology/rat-brain-templates/rat-brain-templates-0.2.ebuild b/sci-biology/rat-brain-templates/rat-brain-templates-0.2.ebuild
index 20c923eb0..d41c14a11 100644
--- a/sci-biology/rat-brain-templates/rat-brain-templates-0.2.ebuild
+++ b/sci-biology/rat-brain-templates/rat-brain-templates-0.2.ebuild
@@ -7,7 +7,7 @@ inherit check-reqs
DESCRIPTION="A collection of rat brain templates in NIfTI format"
HOMEPAGE="https://gitlab.com/FOS-FMI/rat-brain-templates_generator"
-SRC_URI="http://chymera.eu/distfiles/${P}.tar.xz"
+SRC_URI="http://resources.chymera.eu/distfiles/${P}.tar.xz"
LICENSE="fairuse"
SLOT="0"
diff --git a/sci-biology/sailfish/Manifest b/sci-biology/sailfish/Manifest
deleted file mode 100644
index 025cfe9ea..000000000
--- a/sci-biology/sailfish/Manifest
+++ /dev/null
@@ -1,5 +0,0 @@
-DIST jellyfish-2.2.5.tar.gz 1083486 BLAKE2B 545c110199cb2661656ddd558f5ee2b9715a78f6d33275f53aa5a9719247dff4421ef5dd37c3683a3423c8b79ff33395bf4e0ac86cade7480bc604a2b197e214 SHA512 7747030628f82562669c5021aeaca03d8dfc559dc9c3a407e2e4e8de633673f7cf9c60989c16f73deb8e88e7204a3fe84993209a2ebffcb34fd35eac7784e9ab
-DIST quasi-mph.zip 414036 BLAKE2B 414ccd806fc11fdc949ecf107db079e4ab0dec8f443f4ba27df9c4273bc3e01f9d4e7c377651a930cf28c77198526a7ed52eb65419a9c29d6cf12a6ecf268b6c SHA512 65d420af549ce138e6d240438919cbfb76a6f137d2767ba45c099c9a946ca04686fedca609a5ebe4c9d371d2587379f35d9e5dd591abe1afc4b7d433bb4f61c9
-DIST sailfish-0.10.0.tar.gz 1621862 BLAKE2B d04d8db99e1d191ad1bea690bf43f31d23d6505bc3e80399cfafbbf4e1404edf8a4bbe0532e2c47ec59a5a26f50509342a7143bc0b0c41c3a8723ec0f6e53bd4 SHA512 ec66cff89dac037b84deaf997b7769802f594e69820d42915fb830bfcd527786c9c466a9476bdf2b29b9f7481e98905acf580f4a766765bccaa1b0ced22c4bb2
-DIST sparsehash-2.0.2.tar.gz 321951 BLAKE2B 057776f89fe3ca4b826eec7a142a18106561e4a20eaf907b3996f4dc52f484b84196c3bf9cf6d8bc31bd09aec34fc68b5992560c5fbe8c279c94d18062a96855 SHA512 e086b8beb45f2aa395b5ae49aed8ebaed1cafc9a59ece862f64f067098e2b9c28efc5cfac6b26eea46e5fe6b3db1bfa1afc0b9656c48adc01c3c3d05a5b327e8
-DIST v1.0.tar.gz 86404 BLAKE2B ce59ff034cbd70a504ed8c2e42e552489cc07a80a7130149234294aa2c75329f15ff5c4da4709a40712e18762e160355de67f4f68810856f8bc8218ceffb671d SHA512 ba4b395374da16f9ac22dd3cbf96ab5a67ab4d64a312f382ace883633199bbbd5f7602abe768ac84f6ddf2611eaf2db3d402893bd5dad135d598b4b9853ccd6b
diff --git a/sci-biology/sailfish/files/sailfish-0.9.2-no-boost-static.patch b/sci-biology/sailfish/files/sailfish-0.9.2-no-boost-static.patch
deleted file mode 100644
index 7ac3d0882..000000000
--- a/sci-biology/sailfish/files/sailfish-0.9.2-no-boost-static.patch
+++ /dev/null
@@ -1,20 +0,0 @@
-Do not force static and multithreaded boost libs, use what is available
-
-Patch by Michael Schubert
-
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -162,13 +162,6 @@ if ( DEFINED CUSTOM_BOOST_PATH )
- set (CMAKE_LIBRARY_PATH ${CUSTOM_BOOST_PATH}/lib ${CMAKE_LIBRARY_PATH})
- endif ( DEFINED CUSTOM_BOOST_PATH )
-
--##
--# We want static, multithreaded boost libraries
--##
--set (Boost_USE_STATIC_LIBS ON)
--set (Boost_USE_MULTITHREADED ON)
--#set (Boost_USE_STATIC_RUNTIME OFF)
--
- find_package (ZLIB)
- if (NOT ZLIB_FOUND)
- message (FATAL_ERROR "zlib must be installed before configuration & building can proceed")
diff --git a/sci-biology/sailfish/files/sailfish-allow-newer-boost.patch b/sci-biology/sailfish/files/sailfish-allow-newer-boost.patch
deleted file mode 100644
index 985f83f4a..000000000
--- a/sci-biology/sailfish/files/sailfish-allow-newer-boost.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index ee4b34c..3c58830 100755
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -176,7 +176,7 @@ endif()
- ##
- # Set the latest version and look for what we need
- ##
--set(Boost_ADDITIONAL_VERSIONS "1.53" "1.53.0" "1.54" "1.55" "1.56" "1.57.0" "1.58" "1.59")
-+set(Boost_ADDITIONAL_VERSIONS "1.72.0" "1.74.0" "1.75.0")
- find_package(Boost 1.53.0 COMPONENTS iostreams filesystem system thread timer chrono program_options serialization)
- message("BOOST_INCLUDEDIR = ${BOOST_INCLUDEDIR}")
- message("BOOST_LIBRARYDIR = ${BOOST_LIBRARYDIR}")
diff --git a/sci-biology/sailfish/files/sailfish-no-curl.patch b/sci-biology/sailfish/files/sailfish-no-curl.patch
deleted file mode 100644
index 2ec97808e..000000000
--- a/sci-biology/sailfish/files/sailfish-no-curl.patch
+++ /dev/null
@@ -1,121 +0,0 @@
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index 1be4117..ee4b34c 100755
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -230,9 +230,6 @@ elseif(FETCH_BOOST)
- message("Build system will fetch and build Boost")
- message("==================================================================")
- ExternalProject_Add(libboost
-- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
-- DOWNLOAD_COMMAND curl -k -L http://downloads.sourceforge.net/project/boost/boost/1.59.0/boost_1_59_0.tar.gz -o boost_1_59_0.tar.gz &&
-- tar xzf boost_1_59_0.tar.gz
- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/boost_1_59_0
- INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
- #PATCH_COMMAND patch -p2 < ${CMAKE_CURRENT_SOURCE_DIR}/external/boost156.patch
-@@ -292,10 +289,6 @@ if (NOT JELLYFISH_FOUND)
- message("Build system will fetch and build Jellyfish")
- message("==================================================================")
- ExternalProject_Add(libjellyfish
-- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
-- DOWNLOAD_COMMAND curl -k -L https://github.com/gmarcais/Jellyfish/releases/download/v2.2.5/jellyfish-2.2.5.tar.gz -o jellyfish-2.2.5.tgz &&
-- rm -fr jellyfish-2.2.5 &&
-- tar -xzvf jellyfish-2.2.5.tgz
- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/jellyfish-2.2.5
- INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
- CONFIGURE_COMMAND ${CMAKE_CURRENT_SOURCE_DIR}/external/jellyfish-2.2.5/configure --prefix=<INSTALL_DIR> CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} CXXFLAGS=${JELLYFISH_CXX_FLAGS}
-@@ -335,11 +328,7 @@ if ("${TBB_COMPILER}" STREQUAL "gcc")
- endif()
-
- ExternalProject_Add(libtbb
-- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
-- URL http://www.threadingbuildingblocks.org/sites/default/files/software_releases/source/tbb43_20140724oss_src.tgz
-- DOWNLOAD_COMMAND curl -k -L http://www.threadingbuildingblocks.org/sites/default/files/software_releases/source/tbb43_20140724oss_src.tgz -o tbb_20140724oss_src.tgz &&
-- tar -xzvf tbb_20140724oss_src.tgz
-- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/tbb43_20140724oss
-+ SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/tbb43_20140724oss
- INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
- PATCH_COMMAND "${TBB_PATCH_STEP}"
- CONFIGURE_COMMAND ""
-@@ -407,11 +396,6 @@ message("TBB_LIBRARIES = ${TBB_LIBRARIES}")
- message("Build system will compile libgff")
- message("==================================================================")
- ExternalProject_Add(libgff
-- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
-- DOWNLOAD_COMMAND curl -k -L https://github.com/Kingsford-Group/libgff/archive/v1.0.tar.gz -o libgff.tgz &&
-- tar -xzvf libgff.tgz &&
-- rm -fr libgff &&
-- mv libgff-1.0 libgff
- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/libgff
- UPDATE_COMMAND sh -c "mkdir -p <SOURCE_DIR>/build"
- INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
-@@ -445,9 +429,6 @@ if (NOT HAVE_FAST_MALLOC)
- message("Build system will fetch and use JEMalloc")
- message("==================================================================")
- ExternalProject_Add(libjemalloc
-- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
-- DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/jemalloc/archive/3.6.0.tar.gz -o jemalloc-3.6.0.tar.gz &&
-- tar -xzf jemalloc-3.6.0.tar.gz
- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/jemalloc-3.6.0
- BUILD_IN_SOURCE TRUE
- INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
-@@ -465,9 +446,6 @@ endif ()
- message("Build system will fetch and build SparseHash")
- message("==================================================================")
- ExternalProject_Add(libsparsehash
-- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
-- DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/sparsehash/archive/sparsehash-2.0.2.tar.gz -o sparsehash-2.0.2.tar.gz &&
-- tar -xzf sparsehash-2.0.2.tar.gz
- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/sparsehash-sparsehash-2.0.2
- BUILD_IN_SOURCE TRUE
- INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
-@@ -487,7 +465,6 @@ ExternalProject_Add(libsparsehash
- #
- ####
- if(NOT FETCHED_RAPMAP)
-- exec_program(${CMAKE_CURRENT_SOURCE_DIR}/scripts/fetchRapMap.sh)
- set(FETCHED_RAPMAP TRUE CACHE BOOL "Has RapMap been fetched?" FORCE)
- endif()
-
-diff --git a/scripts/fetchRapMap.sh b/scripts/fetchRapMap.sh
-deleted file mode 100755
-index cab05a1..0000000
---- a/scripts/fetchRapMap.sh
-+++ /dev/null
-@@ -1,37 +0,0 @@
--#!/bin/bash
--
--CURR_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )
--EXTERNAL_DIR=${CURR_DIR}/../external
--INSTALL_DIR=${CURR_DIR}/../external/install
--
--if [ -d ${EXTERNAL_DIR}/RapMap ] ; then
-- rm -fr ${EXTERNAL_DIR}/RapMap
--fi
--
--if [ -d ${INSTALL_DIR}/include/rapmap ] ; then
-- rm -fr ${INSTALL_DIR}/include/rapmap
--fi
--
--if [ -d ${INSTALL_DIR}/src/rapmap ] ; then
-- rm -fr ${INSTALL_DIR}/src/rapmap
--fi
--
--mkdir -p ${EXTERNAL_DIR}
--curl -k -L https://github.com/COMBINE-lab/RapMap/archive/quasi-mph.zip -o ${EXTERNAL_DIR}/rapmap.zip
--rm -fr ${EXTERNAL_DIR}/RapMap
--unzip ${EXTERNAL_DIR}/rapmap.zip -d ${EXTERNAL_DIR}
--mv ${EXTERNAL_DIR}/RapMap-quasi-mph ${EXTERNAL_DIR}/RapMap
--
--mkdir -p ${INSTALL_DIR}/include/rapmap
--mkdir -p ${INSTALL_DIR}/src/rapmap
--
--rm ${EXTERNAL_DIR}/RapMap/src/xxhash.c
--rm ${EXTERNAL_DIR}/RapMap/include/xxhash.h
--
--cp -r ${EXTERNAL_DIR}/RapMap/external/libdivsufsort.zip ${EXTERNAL_DIR}
--cp -r ${EXTERNAL_DIR}/RapMap/src/*.c ${INSTALL_DIR}/src/rapmap
--cp -r ${EXTERNAL_DIR}/RapMap/src/*.cpp ${INSTALL_DIR}/src/rapmap
--cp -r ${EXTERNAL_DIR}/RapMap/include/tclap ${INSTALL_DIR}/include/rapmap
--cp -r ${EXTERNAL_DIR}/RapMap/include/*.h ${INSTALL_DIR}/include/rapmap
--cp -r ${EXTERNAL_DIR}/RapMap/include/*.hpp ${INSTALL_DIR}/include/rapmap
--cp -r ${EXTERNAL_DIR}/RapMap/include/emphf ${INSTALL_DIR}/include/rapmap
diff --git a/sci-biology/sailfish/metadata.xml b/sci-biology/sailfish/metadata.xml
deleted file mode 100644
index 530333987..000000000
--- a/sci-biology/sailfish/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
- <maintainer type="person">
- <email>mschu.dev@gmail.com</email>
- <name>Michael Schubert</name>
- </maintainer>
- <upstream>
- <remote-id type="github">kingsfordgroup/sailfish</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/sci-biology/sailfish/sailfish-0.10.0.ebuild b/sci-biology/sailfish/sailfish-0.10.0.ebuild
deleted file mode 100644
index 9fa4060ca..000000000
--- a/sci-biology/sailfish/sailfish-0.10.0.ebuild
+++ /dev/null
@@ -1,83 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit cmake
-
-DESCRIPTION="Rapid Mapping-based Isoform Quantification from RNA-Seq Reads"
-HOMEPAGE="https://www.cs.cmu.edu/~ckingsf/software/sailfish/"
-SRC_URI="https://github.com/kingsfordgroup/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz
- https://github.com/COMBINE-lab/RapMap/archive/quasi-mph.zip
- https://github.com/gmarcais/Jellyfish/releases/download/v2.2.5/jellyfish-2.2.5.tar.gz
- https://github.com/COMBINE-lab/sparsehash/archive/sparsehash-2.0.2.tar.gz
- https://github.com/Kingsford-Group/libgff/archive/v1.0.tar.gz
-"
-
-LICENSE="GPL-3+"
-SLOT="0"
-KEYWORDS=""
-
-DEPEND="
- dev-libs/boost:0
- dev-libs/jemalloc
- dev-libs/libdivsufsort
- dev-cpp/tbb
- dev-cpp/sparsehash
- sci-biology/jellyfish:2
-"
-RDEPEND="${DEPEND}"
-BDEPEND="app-arch/unzip"
-# a C++-11 compliant compiler is needs, aka >=gcc-4.7
-
-# TODO: disable running wget/curl during src_compile
-# https://github.com/kingsfordgroup/sailfish/issues/80
-# contains bundled RapMap https://github.com/COMBINE-lab/RapMap
-# contains bundled libdivsufsort
-# contains bundled libgff https://github.com/COMBINE-lab/libgff
-# contains bundled jellyfish-2.2.5
-# contains bundled sparsehash-2.0.2
-
-PATCHES=(
- "${FILESDIR}/${PN}-0.9.2-no-boost-static.patch"
- "${FILESDIR}/${PN}-no-curl.patch"
- "${FILESDIR}/${PN}-allow-newer-boost.patch"
-)
-
-src_unpack() {
- default
- mkdir -p "${S}/external"
- cp "${DISTDIR}/quasi-mph.zip" "${S}/external/rapmap.zip" || die
- mv "${WORKDIR}/RapMap-quasi-mph" "${S}/external/RapMap" || die
- mv "${WORKDIR}/jellyfish-2.2.5" "${S}/external/jellyfish-2.2.5" || die
- mv "${WORKDIR}/sparsehash-sparsehash-2.0.2" "${S}/external/sparsehash-sparsehash-2.0.2" || die
- mv "${WORKDIR}/libgff-1.0" "${S}/external/libgff" || die
- mkdir -p "${S}/external/install/lib"
- cp "${EPREFIX}/usr/$(get_libdir)/libdivsufsort.so" "${S}/external/install/lib/" || die
- cp "${EPREFIX}/usr/$(get_libdir)/libdivsufsort64.so" "${S}/external/install/lib/" || die
- cp "${EPREFIX}/usr/$(get_libdir)/libjellyfish-2.0.so" "${S}/external/install/lib/" || die
- mkdir -p "${S}/external/install/src/rapmap"
- cp "${S}/external/RapMap/src/"* "${S}/external/install/src/rapmap" || die
-}
-
-src_prepare() {
- cmake_src_prepare
- # use the dynamic library
- sed -i -e 's/libdivsufsort.a/libdivsufsort.so/g' \
- -e 's/libdivsufsort64.a/libdivsufsort64.so/g' \
- -e 's/libjellyfish-2.0.a/libjellyfish-2.0.so/g' \
- src/CMakeLists.txt || die
-}
-
-src_configure() {
- JELLYFISH_INCLUDE_DIR="/usr/include/jellyfish2" cmake_src_configure
- # jellyfish2 instead of jellyfish
- find -type f -name "*.hpp" -exec sed -i -e 's/#include \"jellyfish\//#include \"jellyfish2\//g' {} + || die
- find -type f -name "*.hpp" -exec sed -i -e 's/#include <jellyfish\//#include <jellyfish2\//g' {} + || die
-}
-
-src_install() {
- cmake_src_install
- rm -r "${ED}"/usr/tests || die
- rm -f "${ED}"/usr/bin/jellyfish "${ED}"/usr/$(get_libdir)/libjellyfish || die
-}
diff --git a/sci-biology/sailfish/sailfish-9999.ebuild b/sci-biology/sailfish/sailfish-9999.ebuild
deleted file mode 100644
index a76e8ee89..000000000
--- a/sci-biology/sailfish/sailfish-9999.ebuild
+++ /dev/null
@@ -1,62 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit cmake git-r3
-
-DESCRIPTION="Rapid Mapping-based Isoform Quantification from RNA-Seq Reads"
-HOMEPAGE="https://www.cs.cmu.edu/~ckingsf/software/sailfish/"
-EGIT_REPO_URI="https://github.com/kingsfordgroup/sailfish.git"
-
-LICENSE="GPL-3"
-SLOT="0"
-
-PATCHES=( "${FILESDIR}/${PN}-0.9.2-no-boost-static.patch" )
-
-DEPEND="
- dev-libs/boost:0
- dev-libs/jemalloc
- dev-libs/libdivsufsort
- dev-cpp/tbb
- sci-biology/jellyfish:2
-"
-RDEPEND="${DEPEND}"
-
-# TODO: disable running wget/curl during src_compile
-# https://github.com/kingsfordgroup/sailfish/issues/80
-# contains bundled RapMap https://github.com/COMBINE-lab/RapMap
-# contains bundled libdivsufsort
-# contains bundled libgff https://github.com/COMBINE-lab/libgff
-# contains bundled jellyfish-2.2.5
-# contains bundled sparsehash-2.0.2
-
-src_unpack() {
- default
- mkdir -p "${S}/external"
- cp "${DISTDIR}/quasi-mph.zip" "${S}/external/rapmap.zip" || die
- mkdir -p "${S}/external/install/lib"
- cp "${EPREFIX}/usr/$(get_libdir)/libdivsufsort.so" "${S}/external/install/lib/" || die
- cp "${EPREFIX}/usr/$(get_libdir)/libdivsufsort64.so" "${S}/external/install/lib/" || die
- cp "${EPREFIX}/usr/$(get_libdir)/libjellyfish-2.0.so" "${S}/external/install/lib/" || die
-}
-
-src_prepare() {
- cmake_src_prepare
- # use the dynamic library
- sed -i -e 's/libdivsufsort.a/libdivsufsort.so/g' \
- -e 's/libdivsufsort64.a/libdivsufsort64.so/g' \
- -e 's/libjellyfish-2.0.a/libjellyfish-2.0.so/g' \
- src/CMakeLists.txt || die
-
- # jellyfish2 instead of jellyfish
- pushd external/install/include/rapmap
- find -type f -name "*.hpp" -exec sed -i -e 's/jellyfish/jellyfish2/g' {} + || die
- popd
-}
-
-src_install() {
- cmake_src_install
- rm -r "${ED}"/usr/tests || die
- rm -f "${ED}"/usr/bin/jellyfish "${ED}"/usr/$(get_libdir)/libjellyfish || die
-}
diff --git a/sci-biology/salmon/Manifest b/sci-biology/salmon/Manifest
index cf8f50df3..37410d297 100644
--- a/sci-biology/salmon/Manifest
+++ b/sci-biology/salmon/Manifest
@@ -1,8 +1,10 @@
DIST bwa-0.7.12.5.tar.gz 224584 BLAKE2B af273aa6751d73e82ce1891acdd42c7cbb0f332312157e1bcaf3f6175417f7358f1d73fd900ede7bddc4071b62f68ea8c79d1e0eb04f02ee618130bd0c33579f SHA512 c56a08c115fd15ca017f5ca5a2e053aef4df9fdf7b3a8f575646b2443cb38853dcd17e72588750dc0c8acdd7accca173d84894220d6cd06959ba0d994851f6c9
DIST cereal-1.2.2.tar.gz 335759 BLAKE2B 6804b9aabb235a546758c70554502208f1b7b6bcab9b602fa075123335331f0522191a83027fdbac4ee947881c6866f24f48223a00b9490fca5ca961f3e4b260 SHA512 9567b2e19add9446b24f8afd122eea09ba6ecd1a090335cf0ab31fdc8f64c6c97daa3d9eaf0801c36a770737488e0eebf81d96d7b7a65deed30da6130f2d47eb
DIST libgff-1.1.tgz 79006 BLAKE2B 626a62614c4c52d823104eae78e4f04e0976eb43cd2ea7b820ac6549535771fb2ecccbcf4476a22f53a66b5d8bea4fd260c6d3cee864a2c1b264c6f223744dac SHA512 af797fdc753c21a61a817f0b57da55c523220a9c831a71b73328a49ec66b667a503f1fcbddab714826f802a4e2becf310265535276973e2978d5ad73525fa0bb
+DIST libgff-salmon-1.6.0.tar.gz 102152 BLAKE2B 56bccaadf82fe51db4f6297177b3c49d7ab4fe858719e3a689834ef10b63dd0ffabba2424771865efab1bd226dccb3a104307ef406e3861e762426cfcc5de543 SHA512 c5e84fad659502134e90c45a0075e79fe1dcf84d08ec4820c337b898fae24c8fe3985cb5fb3e653a13d1756179730ff0cae53bb2c78fe37038f7bd9c7eae85e2
+DIST pufferfish-salmon-1.6.0.tar.gz 3119250 BLAKE2B f3db6506d003418fcaeeb78c114acc0dcd89d745d2433dcbf87dc8ff8dbec15299a799b469f6a07fd07f85afd925c85643c3791819413db3fc14de5686ae112f SHA512 82c1137a14ef7773101b35070b6a943213443d98e218118e6a5c2df1cab860ed9543bcac3b7408e0b7eeb74fe1997d521b4883515a964d03813bcea8b2bfaa8d
DIST salmon-0.10.2.tar.gz 10766806 BLAKE2B f9ba6f208a72a11f37c44a056e9b464f4bf018db88c13e67ce84fcdecee98d878046b2018b144dd48a152300f1ba0a178cf03c5c541b16358e210a5013fdfdce SHA512 828c3d5f3f8f42181bf4b563a49f789bdb82843cbdc9aec4555e7623642e2c663a2552ea7bfd1967cc4f8033e6f0678f8f6f82ce776bc2312bc0b4b8ab7ed19f
DIST salmon-0.10.2_RapMap.zip 1141708 BLAKE2B 397341693e0388093af8ffe620fa91941c584de0887a648d219a3f5662ffd6f9af22179f205bfb83927bc8913756b4d68cbc9179cbfb11f9b329c6aed32220a1 SHA512 8aa593feb61a45d25cc757f39b907e6e0cc108831bad69857268f3ac19614d76cf88de6d8679e52d3eea43bcf5b603bfd55135ececf39acb1700a23408fca573
-DIST salmon-1.4.0.tar.gz 7061272 BLAKE2B d26685c0a1a888d1acc2d3b6789d572f5c3d811e20068fa923197b04c86ccdda3c9ddbe8cb6df99d6855dfdcdb90ac3b69371804c2fdc78b40469c205e1c96ed SHA512 9007899f91cef2589a965d2d039393e0a19b4fcea488b8f256431907323cadf2d182579ffc6203f19feafad4a72ddad1cbeee6a7acd81cd8d5a4fe890996c5ec
+DIST salmon-1.6.0.tar.gz 7145603 BLAKE2B 5ffa9bd8cdd76232caaa736ffb959922b47f934217bd706417431f92c406f407529b5df67b13506df4365ce56676b70cf470466cdf616d097c96a8cd312d34d5 SHA512 580292b48165ba6db48db44d3e57e5020410f29a48b4015445c4c354e81989ff872e8874e2a7aab128362f178819330fbdc2a11089189bfbc8cd3058fc0eb4d6
DIST spdlog-0.16.1.tar.gz 162408 BLAKE2B c90b94bac128f8b143d85522d224223b1361f7d552d9caa8b253e494dd72de56a2149cbd8d568eb4305224d7caf80d8067fbce606a1071bd94f74c43b3245782 SHA512 0ef741f2abcae7c925808b44bba7d2e55aa8bd3b07a77ab6e785068beb505cdbcd7835d7d103e8e96094235e262954969a176d9f4977e9d373f1bee8e2716ff2
DIST staden-io_lib-1.14.8.tar.gz 2506985 BLAKE2B 0d64847d0958e0efc763e87bf0600e3af90d30b67c77908b2effa20b18ce43a0d5ad1b213747c46f9e9000a75c4f1260759b3c90cd632be821e039870a26eb4b SHA512 535c6701e61a1786ceb7b22905afe702d277e0383816fba82f69af553dd22ca497bf00766f9768fd9173621632483a02ea9919437e1786008b2236c1c2c8c69f
diff --git a/sci-biology/salmon/files/salmon-1.6.0-find-boost.patch b/sci-biology/salmon/files/salmon-1.6.0-find-boost.patch
new file mode 100644
index 000000000..76ef25547
--- /dev/null
+++ b/sci-biology/salmon/files/salmon-1.6.0-find-boost.patch
@@ -0,0 +1,116 @@
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 1be02ab..48ffda2 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -428,9 +428,9 @@ endif()
+ ##
+ # Set the latest version and look for what we need
+ ##
+-set(Boost_ADDITIONAL_VERSIONS "1.59.0" "1.60.0" "1.61.0" "1.62.0" "1.63.0" "1.64.0" "1.65.0" "1.66.0" "1.67.0" "1.68.0" "1.69.0" "1.70.0" "1.71.0")
++set(Boost_ADDITIONAL_VERSIONS "1.59.0" "1.60.0" "1.61.0" "1.62.0" "1.63.0" "1.64.0" "1.65.0" "1.66.0" "1.67.0" "1.68.0" "1.69.0" "1.70.0" "1.71.0" "1.77.0" "1.78.0")
+ if (NOT BOOST_RECONFIGURE)
+-find_package(Boost 1.59.0 COMPONENTS iostreams filesystem system timer chrono program_options)
++find_package(Boost 1.59.0 COMPONENTS ALL)
+ message("BOOST_INCLUDEDIR = ${BOOST_INCLUDEDIR}")
+ message("BOOST_LIBRARYDIR = ${BOOST_LIBRARYDIR}")
+ message("Boost_FOUND = ${Boost_FOUND}")
+@@ -610,7 +610,7 @@ if (NOT CEREAL_FOUND)
+ endif()
+
+ ## Try and find TBB first
+-find_package(TBB 2019.0 COMPONENTS tbb tbbmalloc tbbmalloc_proxy)
++find_package(TBB)
+
+ ## NOTE: we actually require at least 2019 U4 or greater
+ ## since we are using tbb::global_control. However, they
+@@ -618,12 +618,8 @@ find_package(TBB 2019.0 COMPONENTS tbb tbbmalloc tbbmalloc_proxy)
+ ## source. Check before release if we can bump to the 2020
+ ## version (requires having tbb 2020 for OSX).
+ if (${TBB_FOUND})
+- if (${TBB_VERSION} VERSION_GREATER_EQUAL 2019.0)
+ message("FOUND SUITABLE TBB VERSION : ${TBB_VERSION}")
+ set(TBB_TARGET_EXISTED TRUE)
+- else()
+- set(TBB_TARGET_EXISTED FALSE)
+- endif()
+ else()
+ set(TBB_TARGET_EXISTED FALSE)
+ endif()
+@@ -750,10 +746,6 @@ if(NOT libgff_FOUND)
+ message("Build system will compile libgff")
+ message("==================================================================")
+ externalproject_add(libgff
+- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
+- DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/libgff/archive/v2.0.0.tar.gz -o libgff.tgz &&
+- ${SHASUM} 7656b19459a7ca7d2fd0fcec4f2e0fd0deec1b4f39c703a114e8f4c22d82a99c libgff.tgz &&
+- tar -xzvf libgff.tgz
+ ##
+ #URL https://github.com/COMBINE-lab/libgff/archive/v1.1.tar.gz
+ #DOWNLOAD_NAME libff.tgz
+diff --git a/cmake/Modules/FindTBB.cmake b/cmake/Modules/FindTBB.cmake
+index c8b3eb5..b4c23da 100644
+--- a/cmake/Modules/FindTBB.cmake
++++ b/cmake/Modules/FindTBB.cmake
+@@ -184,7 +184,6 @@ if(NOT TBB_FOUND)
+ ##################################
+
+ if(TBB_INCLUDE_DIRS)
+- file(READ "${TBB_INCLUDE_DIRS}/tbb/tbb_stddef.h" _tbb_version_file)
+ string(REGEX REPLACE ".*#define TBB_VERSION_MAJOR ([0-9]+).*" "\\1"
+ TBB_VERSION_MAJOR "${_tbb_version_file}")
+ string(REGEX REPLACE ".*#define TBB_VERSION_MINOR ([0-9]+).*" "\\1"
+diff --git a/scripts/fetchPufferfish.sh b/scripts/fetchPufferfish.sh
+index d32e131..1b5cbf2 100755
+--- a/scripts/fetchPufferfish.sh
++++ b/scripts/fetchPufferfish.sh
+@@ -10,18 +10,6 @@ CURR_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )
+ EXTERNAL_DIR=${CURR_DIR}/../external
+ INSTALL_DIR=${CURR_DIR}/../external/install
+
+-if [ -d ${EXTERNAL_DIR}/pufferfish ] ; then
+- rm -fr ${EXTERNAL_DIR}/pufferfish
+-fi
+-
+-if [ -d ${INSTALL_DIR}/include/pufferfish ] ; then
+- rm -fr ${INSTALL_DIR}/include/pufferfish
+-fi
+-
+-if [ -d ${INSTALL_DIR}/src/pufferfish ] ; then
+- rm -fr ${INSTALL_DIR}/src/pufferfish
+-fi
+-
+ SVER=salmon-v1.6.0
+ #SVER=develop
+ #SVER=sketch-mode
+@@ -29,31 +17,6 @@ SVER=salmon-v1.6.0
+ EXPECTED_SHA256=f71b3c08f254200fcdc2eb8fe3dcca8a8e9489e79ef5952a4958d8b9979831dc
+
+ mkdir -p ${EXTERNAL_DIR}
+-curl -k -L https://github.com/COMBINE-lab/pufferfish/archive/${SVER}.zip -o ${EXTERNAL_DIR}/pufferfish.zip
+-
+-hashcheck=""
+-if exists sha256sum; then
+- hashcheck="sha256sum"
+-elif exists shasum; then
+- hashcheck="shasum -a256"
+-else
+- unset hashcheck
+-fi
+-
+-if [ -z "${hashcheck-}" ]; then
+- echo "Couldn't find shasum command; can't verify contents of downloaded pufferfish";
+-else
+- if [[ $SVER != develop ]]; then
+- echo "${EXPECTED_SHA256} ${EXTERNAL_DIR}/pufferfish.zip" | ${hashcheck} -c - || { echo "pufferfish.zip did not match expected SHA1! Exiting."; exit 1; }
+- else
+- echo "not testing sha since pulling from develop"
+- fi
+-fi
+-
+-
+-rm -fr ${EXTERNAL_DIR}/pufferfish
+-unzip ${EXTERNAL_DIR}/pufferfish.zip -d ${EXTERNAL_DIR}
+-mv ${EXTERNAL_DIR}/pufferfish-${SVER} ${EXTERNAL_DIR}/pufferfish
+
+ mkdir -p ${INSTALL_DIR}/include/pufferfish
+
diff --git a/sci-biology/salmon/salmon-1.4.0.ebuild b/sci-biology/salmon/salmon-1.4.0.ebuild
deleted file mode 100644
index 420cb2ae2..000000000
--- a/sci-biology/salmon/salmon-1.4.0.ebuild
+++ /dev/null
@@ -1,38 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit cmake
-
-DESCRIPTION="Transcript-level quantification from RNA-seq reads using lightweight alignments"
-HOMEPAGE="https://github.com/COMBINE-lab/salmon"
-SRC_URI="https://github.com/COMBINE-lab/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS=""
-
-RDEPEND="
- dev-libs/boost:=[threads(-)]
- sys-libs/zlib
-"
-
-DEPEND="${RDEPEND}
- app-arch/bzip2
- app-arch/xz-utils
- >=dev-libs/jemalloc-5.0.1
- >=dev-cpp/tbb-2018.20180312
- sci-biology/pufferfish
- dev-libs/cereal
-"
-
-BDEPEND="
- app-arch/unzip
- net-misc/curl
-"
-
-PATCHES=(
- "${FILESDIR}/${P}-do-not-fetch-pufferfish.patch"
- "${FILESDIR}/${P}-allow-newer-boost.patch"
-)
diff --git a/sci-biology/salmon/salmon-1.6.0.ebuild b/sci-biology/salmon/salmon-1.6.0.ebuild
new file mode 100644
index 000000000..6c19ff58f
--- /dev/null
+++ b/sci-biology/salmon/salmon-1.6.0.ebuild
@@ -0,0 +1,70 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit cmake
+
+DESCRIPTION="Transcript-level quantification from RNA-seq reads using lightweight alignments"
+HOMEPAGE="https://github.com/COMBINE-lab/salmon"
+SRC_URI="
+ https://github.com/COMBINE-lab/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz
+ https://github.com/COMBINE-lab/pufferfish/archive/salmon-v${PV}.tar.gz -> pufferfish-${P}.tar.gz
+ https://github.com/COMBINE-lab/libgff/archive/v2.0.0.tar.gz -> libgff-${P}.tar.gz
+"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+ dev-libs/boost:=
+ sys-libs/zlib
+"
+
+DEPEND="${RDEPEND}
+ app-arch/bzip2
+ app-arch/xz-utils
+ >=dev-libs/jemalloc-5.0.1
+ >=dev-cpp/tbb-2018.20180312
+ dev-libs/cereal
+ sci-libs/io_lib[static-libs]
+"
+
+BDEPEND="
+ app-arch/unzip
+ net-misc/curl
+"
+
+PATCHES=(
+ "${FILESDIR}/${P}-find-boost.patch"
+)
+
+src_unpack() {
+ default
+ mkdir -p "${S}/external/install/lib" || die
+ mv "${WORKDIR}/pufferfish-${PN}-v${PV}" "${S}/external/pufferfish" || die
+ mv "${WORKDIR}/libgff-2.0.0" "${S}/external/libgff-2.0.0" || die
+ ln -s "${EPREFIX}/usr/lib64/libtbb.so" "${S}/external/install/lib/libtbb.so" || die
+ ln -s "${EPREFIX}/usr/lib64/libtbbmalloc.so" "${S}/external/install/lib/libtbbmalloc.so" || die
+ ln -s "${EPREFIX}/usr/lib64/libtbbmalloc_proxy.so" "${S}/external/install/lib/libtbbmalloc_proxy.so" || die
+}
+
+src_prepare() {
+ cmake_src_prepare
+ sed -e 's:tbb/mutex.h:oneapi/tbb/mutex.h:g' \
+ -i external/pufferfish/external/twopaco/graphconstructor/vertexenumerator.h \
+ -i external/pufferfish/external/twopaco/common/streamfastaparser.h || die
+}
+
+src_configure() {
+ local mycmakeargs=(
+ -DFETCH_BOOST=FALSE
+ -DBOOST_INCLUDEDIR="${EPREFIX}/usr/include/boost"
+ -DBOOST_LIBRARYDIR="${EPREFIX}/usr/lib64"
+ -DBoost_ALL_FOUND=TRUE
+ -Dboost_headers_FOUND=TRUE
+ -DBoost_FOUND=TRUE
+ )
+ cmake_src_configure
+}
diff --git a/sci-biology/salmon/salmon-9999.ebuild b/sci-biology/salmon/salmon-9999.ebuild
deleted file mode 100644
index 89ca690c6..000000000
--- a/sci-biology/salmon/salmon-9999.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 cmake git-r3
-
-DESCRIPTION="Transcript-level quantification from RNA-seq reads using lightweight alignments"
-HOMEPAGE="https://github.com/COMBINE-lab/salmon"
-EGIT_REPO_URI="https://github.com/COMBINE-lab/salmon.git"
-
-LICENSE="GPL-3"
-SLOT="0"
-
-RDEPEND="
- dev-libs/boost:=[threads(-)]
- sys-libs/zlib
-"
-
-DEPEND="${RDEPEND}
- app-arch/bzip2
- app-arch/xz-utils
- >=dev-libs/jemalloc-5.0.1
- >=dev-cpp/tbb-2018.20180312
- sci-biology/pufferfish
- dev-libs/cereal
-"
-
-BDEPEND="
- app-arch/unzip
- net-misc/curl
-"
diff --git a/sci-biology/sambamba/Manifest b/sci-biology/sambamba/Manifest
deleted file mode 100644
index 0c4fb09d1..000000000
--- a/sci-biology/sambamba/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST lz4-sambamba-0.8.0.tar.gz 320972 BLAKE2B e9af776d3a867f551e20c2a3c234f2c9a27e729b972a0b40e25eee830f1c2a2975fe939de68459fda6d56a1b3a63e26937cfbf77fcbb2b711ecdbc9385069d91 SHA512 f51c5332fdc5a74bcd4f9597b187721cc2f33bc535c374c0ff47f438f79f6bec382e20462bb90d8be5f6bdf02ff5d7b4f5bf358bba55e03211ee566035ef3fbd
-DIST sambamba-0.8.0.tar.gz 630637 BLAKE2B ea51a86bb546de3792e6d8bc0494aa2afe525d3914d1cc15ad8d52ca1acd2d109f726154273e98ef0e6144266fc34048f8c5008fe5c50be093b4082fb3fac1b5 SHA512 2d74c5ca3188fe0628b4873891eebecb1f514474bb1a2a8aca4ca3f40275acfb0fda0de5e11097754d317cac39b982b6ae45c5dde457cd83d6f684596ca5a5ac
diff --git a/sci-biology/sambamba/metadata.xml b/sci-biology/sambamba/metadata.xml
deleted file mode 100644
index 3c6df6245..000000000
--- a/sci-biology/sambamba/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>mmokrejs@fold.natur.cuni.cz</email>
- <name>Martin Mokrejs</name>
- </maintainer>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
- <upstream>
- <remote-id type="github">lomereiter/sambamba</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/sci-biology/sambamba/sambamba-0.8.0.ebuild b/sci-biology/sambamba/sambamba-0.8.0.ebuild
deleted file mode 100644
index d5f7c1359..000000000
--- a/sci-biology/sambamba/sambamba-0.8.0.ebuild
+++ /dev/null
@@ -1,36 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-LZ4_COMMIT="b3692db46d2b23a7c0af2d5e69988c94f126e10a"
-
-DESCRIPTION="Parallell process SAM/BAM/CRAM files faster than samtools"
-HOMEPAGE="https://lomereiter.github.io/sambamba/"
-SRC_URI="https://github.com/lomereiter/sambamba/archive/v${PV}.tar.gz -> ${P}.tar.gz
- https://github.com/lz4/lz4/archive/${LZ4_COMMIT}.tar.gz -> lz4-${P}.tar.gz"
-
-LICENSE="GPL-2+"
-SLOT="0"
-KEYWORDS=""
-IUSE="debug"
-
-# https://github.com/ldc-developers/gentoo-overlay/tree/master/dev-lang/ldc2
-#
-# contains bundled htslib
-DEPEND=""
-RDEPEND="${DEPEND}"
-
-src_unpack() {
- default
- rm -r "${S}/lz4" || die
- mv "${WORKDIR}/lz4-${LZ4_COMMIT}" "${S}/lz4" || die
-}
-
-src_compile(){
- if use debug ; then
- emake debug all
- else
- emake all
- fi
-}
diff --git a/sci-biology/sambamba/sambamba-9999.ebuild b/sci-biology/sambamba/sambamba-9999.ebuild
deleted file mode 100644
index e655b10b0..000000000
--- a/sci-biology/sambamba/sambamba-9999.ebuild
+++ /dev/null
@@ -1,28 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit git-r3
-
-DESCRIPTION="Parallell process SAM/BAM/CRAM files faster than samtools"
-HOMEPAGE="https://lomereiter.github.io/sambamba/"
-EGIT_REPO_URI="https://github.com/lomereiter/sambamba.git"
-
-LICENSE="GPL-2+"
-SLOT="0"
-KEYWORDS=""
-IUSE="debug"
-
-DEPEND=""
-RDEPEND="${DEPEND}"
-
-# https://github.com/ldc-developers/gentoo-overlay/tree/master/dev-lang/ldc2
-
-src_compile(){
- if use debug ; then
- emake debug all
- else
- emake all
- fi
-}
diff --git a/sci-biology/samri/Manifest b/sci-biology/samri/Manifest
index d8c689507..d683d1d3b 100644
--- a/sci-biology/samri/Manifest
+++ b/sci-biology/samri/Manifest
@@ -1,2 +1 @@
-DIST samri-0.4.1.tar.gz 4115417 BLAKE2B 882b1fbf213f85919a790d669365498c06269a2cb37ba859606e0e4bd696116e954b6683dd636ff34406b2394b4ae3d743c1840a789a828ca3d535b27c0a80da SHA512 c2eef33e725d0d5b87f30ce8da51d9c46ce735a8d82e41f93eba8d225b58eead4777441db4be9078e7f29b3f92d12525d729dddea888fd7e9a66ba5e607d8caf
DIST samri-0.5.tar.gz 4117149 BLAKE2B 1767d6d07726431e43dad5f843eee04bd5111dde3174905b79b938aa94dbb340ca3f3d6316c6720bf01212b87c895df47c965738dff70ec1debbbd542bb77043 SHA512 94fb981adf78b2062e1beac8433bca34e3db90964f720918603e2b89d617b4dfe9f4bc1591b6953e060553ea0014ebca4db62aa0f5b264feb084bc785a48c367
diff --git a/sci-biology/samri/samri-0.4.1.ebuild b/sci-biology/samri/samri-0.4.1.ebuild
deleted file mode 100644
index f94119541..000000000
--- a/sci-biology/samri/samri-0.4.1.ebuild
+++ /dev/null
@@ -1,58 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7..8} )
-
-inherit distutils-r1 prefix
-
-DESCRIPTION="Small Animal Magnetic Resonance Imaging"
-HOMEPAGE="https://github.com/IBT-FMI/SAMRI"
-SRC_URI="https://github.com/IBT-FMI/SAMRI/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-IUSE="labbookdb test"
-KEYWORDS="~amd64"
-RESTRICT="!test? ( test )"
-
-DEPEND="
- test? (
- dev-python/pytest[${PYTHON_USEDEP}]
- sci-biology/samri_bidsdata
- sci-biology/samri_bindata
- )
-"
-RDEPEND="
- dev-python/argh[${PYTHON_USEDEP}]
- dev-python/joblib[${PYTHON_USEDEP}]
- >=dev-python/matplotlib-2.0.2[${PYTHON_USEDEP}]
- >=dev-python/numpy-1.13.3[${PYTHON_USEDEP}]
- dev-python/pandas[${PYTHON_USEDEP}]
- dev-python/seaborn[${PYTHON_USEDEP}]
- dev-python/statsmodels[${PYTHON_USEDEP}]
- media-gfx/blender
- >=sci-biology/fsl-5.0.9
- sci-biology/bru2nii
- sci-biology/mouse-brain-atlases
- labbookdb? ( sci-libs/labbookdb[${PYTHON_USEDEP}] )
- sci-libs/nibabel[${PYTHON_USEDEP}]
- >=sci-libs/nipy-0.4.1[${PYTHON_USEDEP}]
- >=sci-libs/nipype-1.0.0[${PYTHON_USEDEP}]
- <=sci-libs/pybids-0.6.5[${PYTHON_USEDEP}]
- sci-libs/scikit-image[${PYTHON_USEDEP}]
- dev-python/scipy[${PYTHON_USEDEP}]
- sci-biology/ants
- sci-biology/afni
- sci-biology/nilearn[${PYTHON_USEDEP}]
-"
-
-S="${WORKDIR}/SAMRI-${PV}"
-
-src_prepare() {
- distutils-r1_src_prepare
- sed -i -e "s:/usr:@GENTOO_PORTAGE_EPREFIX@/usr:g" `grep -rlI \'/usr/ samri`
- sed -i -e "s:/usr:@GENTOO_PORTAGE_EPREFIX@/usr:g" `grep -rlI /usr/ test_scripts.sh`
- eprefixify $(grep -rl GENTOO_PORTAGE_EPREFIX samri/* test_scripts.sh)
-}
diff --git a/sci-biology/samri/samri-0.5.ebuild b/sci-biology/samri/samri-0.5.ebuild
index 84161f65f..4cc90a0ef 100644
--- a/sci-biology/samri/samri-0.5.ebuild
+++ b/sci-biology/samri/samri-0.5.ebuild
@@ -1,25 +1,25 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
-PYTHON_COMPAT=( python3_{7..8} )
+PYTHON_COMPAT=( python3_{8..9} )
inherit distutils-r1 prefix
DESCRIPTION="Small Animal Magnetic Resonance Imaging"
HOMEPAGE="https://github.com/IBT-FMI/SAMRI"
SRC_URI="https://github.com/IBT-FMI/SAMRI/archive/${PV}.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}/SAMRI-${PV}"
LICENSE="GPL-3"
SLOT="0"
-IUSE="+atlases labbookdb test"
KEYWORDS="~amd64"
-RESTRICT="!test? ( test )"
+IUSE="+atlases labbookdb"
+REQUIRED_USE="test? ( atlases )"
DEPEND="
test? (
- dev-python/pytest[${PYTHON_USEDEP}]
sci-biology/samri_bidsdata
sci-biology/samri_bindata
)
@@ -36,26 +36,25 @@ RDEPEND="
>=media-gfx/blender-2.83.4
>=sci-biology/fsl-5.0.9
sci-biology/bru2nii
- atlases? ( sci-biology/mouse-brain-atlases )
+ atlases? ( sci-biology/mouse-brain-templates )
labbookdb? ( sci-libs/labbookdb[${PYTHON_USEDEP}] )
sci-libs/nibabel[${PYTHON_USEDEP}]
>=sci-libs/nipy-0.4.1[${PYTHON_USEDEP}]
>=sci-libs/nipype-1.0.0[${PYTHON_USEDEP}]
- sci-libs/pybids[${PYTHON_USEDEP}]
+ <sci-libs/pybids-0.10.2[${PYTHON_USEDEP}]
sci-libs/scikit-image[${PYTHON_USEDEP}]
sci-biology/ants
sci-biology/afni
sci-biology/nilearn[${PYTHON_USEDEP}]
"
-REQUIRED_USE="test? ( atlases )"
-
-S="${WORKDIR}/SAMRI-${PV}"
+distutils_enable_tests pytest
+distutils_enable_sphinx doc/source dev-python/sphinxcontrib-napoleon
src_prepare() {
distutils-r1_src_prepare
- sed -i -e "s:/usr:@GENTOO_PORTAGE_EPREFIX@/usr:g" `grep -rlI \'/usr/ samri`
- sed -i -e "s:/usr:@GENTOO_PORTAGE_EPREFIX@/usr:g" `grep -rlI /usr/ test_scripts.sh`
+ sed -i -e "s:/usr:@GENTOO_PORTAGE_EPREFIX@/usr:g" `grep -rlI \'/usr/ samri` || die
+ sed -i -e "s:/usr:@GENTOO_PORTAGE_EPREFIX@/usr:g" `grep -rlI /usr/ test_scripts.sh` || die
eprefixify $(grep -rl GENTOO_PORTAGE_EPREFIX samri/* test_scripts.sh)
}
@@ -68,5 +67,5 @@ python_test() {
sed -i -e \
"/def test_bru2bids():/i@pytest.mark.skip('Removed in full test suite, as this is already tested in `test_scripts.sh`')" \
samri/pipelines/tests/test_repos.py || die
- pytest -vv -k "not longtime" || die
+ epytest -k "not longtime"
}
diff --git a/sci-biology/samri/samri-9999.ebuild b/sci-biology/samri/samri-9999.ebuild
deleted file mode 100644
index 8dba8864c..000000000
--- a/sci-biology/samri/samri-9999.ebuild
+++ /dev/null
@@ -1,71 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7..8} )
-
-inherit distutils-r1 prefix git-r3
-
-DESCRIPTION="Small Animal Magnetic Resonance Imaging"
-HOMEPAGE="https://github.com/IBT-FMI/SAMRI"
-SRC_URI=""
-EGIT_REPO_URI="https://github.com/IBT-FMI/SAMRI"
-
-LICENSE="GPL-3"
-SLOT="0"
-IUSE="+atlases labbookdb test"
-KEYWORDS=""
-RESTRICT="!test? ( test )"
-
-DEPEND="
- test? (
- dev-python/pytest[${PYTHON_USEDEP}]
- sci-biology/samri_bidsdata
- sci-biology/samri_bindata
- )
- "
-RDEPEND="
- dev-python/argh[${PYTHON_USEDEP}]
- dev-python/joblib[${PYTHON_USEDEP}]
- >=dev-python/matplotlib-2.0.2[${PYTHON_USEDEP}]
- >=dev-python/numpy-1.13.3[${PYTHON_USEDEP}]
- dev-python/pandas[${PYTHON_USEDEP}]
- dev-python/scipy[${PYTHON_USEDEP}]
- dev-python/seaborn[${PYTHON_USEDEP}]
- dev-python/statsmodels[${PYTHON_USEDEP}]
- >=media-gfx/blender-2.83.4
- >=sci-biology/fsl-5.0.9
- sci-biology/bru2nii
- atlases? ( sci-biology/mouse-brain-atlases )
- labbookdb? ( sci-libs/labbookdb[${PYTHON_USEDEP}] )
- sci-libs/nibabel[${PYTHON_USEDEP}]
- >=sci-libs/nipy-0.4.1[${PYTHON_USEDEP}]
- >=sci-libs/nipype-1.0.0[${PYTHON_USEDEP}]
- sci-libs/pybids[${PYTHON_USEDEP}]
- sci-libs/scikit-image[${PYTHON_USEDEP}]
- sci-biology/ants
- sci-biology/afni
- sci-biology/nilearn[${PYTHON_USEDEP}]
-"
-
-REQUIRED_USE="test? ( atlases )"
-
-src_prepare() {
- distutils-r1_src_prepare
- sed -i -e "s:/usr:@GENTOO_PORTAGE_EPREFIX@/usr:g" `grep -rlI \'/usr/ samri`
- sed -i -e "s:/usr:@GENTOO_PORTAGE_EPREFIX@/usr:g" `grep -rlI /usr/ test_scripts.sh`
- eprefixify $(grep -rl GENTOO_PORTAGE_EPREFIX samri/* test_scripts.sh)
-}
-
-python_test() {
- distutils_install_for_testing
- export MPLBACKEND="agg"
- export PATH=${TEST_DIR}/scripts:$PATH
- export PYTHONIOENCODING=utf-8
- ./test_scripts.sh || die "Test scripts failed."
- sed -i -e \
- "/def test_bru2bids():/i@pytest.mark.skip('Removed in full test suite, as this is already tested in `test_scripts.sh`')" \
- samri/pipelines/tests/test_repos.py || die
- pytest -vv -k "not longtime" || die
-}
diff --git a/sci-biology/samri_bidsdata/samri_bidsdata-0.3.ebuild b/sci-biology/samri_bidsdata/samri_bidsdata-0.3.ebuild
index 8216eada8..8e47fb775 100644
--- a/sci-biology/samri_bidsdata/samri_bidsdata-0.3.ebuild
+++ b/sci-biology/samri_bidsdata/samri_bidsdata-0.3.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
@@ -7,7 +7,6 @@ DESCRIPTION="BIDS-formatted example mouse brain data for SAMRI"
HOMEPAGE="https://github.com/IBT-FMI/SAMRI"
SRC_URI="
https://zenodo.org/record/3831124/files/${P}.tar.xz
- http://chymera.eu/distfiles/${P}.tar.xz
"
LICENSE="GPL-3"
diff --git a/sci-biology/samri_bindata/samri_bindata-0.4.ebuild b/sci-biology/samri_bindata/samri_bindata-0.4.ebuild
index 17873ce56..9ab92211a 100644
--- a/sci-biology/samri_bindata/samri_bindata-0.4.ebuild
+++ b/sci-biology/samri_bindata/samri_bindata-0.4.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
@@ -7,7 +7,6 @@ DESCRIPTION="ParaVision Mouse, Rat, and Lemur Testing Data for SAMRI"
HOMEPAGE="https://github.com/IBT-FMI/SAMRI"
SRC_URI="
https://zenodo.org/record/3823441/files/${P}.tar.xz
- http://chymera.eu/distfiles/${P}.tar.xz
"
LICENSE="GPL-3"
diff --git a/sci-biology/ssaha2-bin/ssaha2-bin-2.5.5.ebuild b/sci-biology/ssaha2-bin/ssaha2-bin-2.5.5-r1.ebuild
index 3122e2188..2c0d5f63d 100644
--- a/sci-biology/ssaha2-bin/ssaha2-bin-2.5.5.ebuild
+++ b/sci-biology/ssaha2-bin/ssaha2-bin-2.5.5-r1.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
inherit toolchain-funcs
@@ -20,9 +20,10 @@ LICENSE="all-rights-reserved"
SLOT="0"
KEYWORDS="~amd64 ~x86"
-QA_PREBUILT="/opt/.*"
+QA_PREBUILT="*"
-pkg_setup() {
+src_unpack() {
+ default
use x86 && export S="${WORKDIR}"/${MY_P}_i686
use amd64 && export S="${WORKDIR}"/${MY_P}_x86_64
}
@@ -31,8 +32,7 @@ src_compile() {
}
src_install() {
- dobin samflag
- exeinto /opt/bin
- doexe ssaha2 ssaha2Build ssahaSNP
+ dobin samflag ssaha2 ssaha2Build ssahaSNP
dodoc README "${DISTDIR}"/ssaha2-manual.pdf
+ einstalldocs
}
diff --git a/sci-biology/stacks/Manifest b/sci-biology/stacks/Manifest
index 51adfa214..06b5c03ad 100644
--- a/sci-biology/stacks/Manifest
+++ b/sci-biology/stacks/Manifest
@@ -1 +1 @@
-DIST stacks-2.55.tar.gz 11716625 BLAKE2B ab359095a546a6ae946fd4196f7955b1e6f294c5ade94e1474984c435c3f2dd468fe8665afbcf201b567d2dd84b999bfc8f9ff7a6dd2712e6be0d4b0d609f0f6 SHA512 eb517f5d9a677095efe3000d0e88ee3be3a6abb725290a0fb1cdb9113a4f19d929dd8eb0d8ce3fd3f9d8234fc0b936523f06d754d5c428381fd97fcebbe89a0b
+DIST stacks-2.60.tar.gz 12135281 BLAKE2B 8d529ba75af4c78710bc36230ef7c564551cd2f2cb9c2ff2cfdc9372f5721bcb463b959b67b7082cdc95f88c772b4e6146cd0c48c25a7b4a6f21d8cdb3045b8e SHA512 9bb2bf730ab5a35cb732107b989ca5068c1e2a8d7a647423d62195ab2049f61409e5ad5b9f16444c10791196f322d677aa7f0e0e73bcfccb9b7c4c00ec40ad32
diff --git a/sci-biology/stacks/stacks-2.55.ebuild b/sci-biology/stacks/stacks-2.60.ebuild
index becd91a5d..4de3f8da8 100644
--- a/sci-biology/stacks/stacks-2.55.ebuild
+++ b/sci-biology/stacks/stacks-2.60.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
inherit perl-module webapp autotools
@@ -10,10 +10,8 @@ HOMEPAGE="http://creskolab.uoregon.edu/stacks"
SRC_URI="http://creskolab.uoregon.edu/stacks/source/${P}.tar.gz"
LICENSE="GPL-3"
-# SLOT="0" # webapp ebuilds do not set SLOT
-KEYWORDS=""
+KEYWORDS="~amd64"
-# No rule to make target test
RESTRICT="test"
DEPEND="
@@ -21,11 +19,14 @@ DEPEND="
dev-cpp/sparsehash
sci-biology/samtools:*
sci-biology/bamtools
- sci-biology/gmap" # Source code for both GMAP and GSNAP
+ sci-biology/gmap
+"
+
RDEPEND="${DEPEND}
dev-lang/perl
- >=dev-lang/php-5
- dev-perl/DBD-mysql"
+ >=dev-lang/php-5:*
+ dev-perl/DBD-mysql
+"
PATCHES=(
"${FILESDIR}/${PN}-make-install.patch"
@@ -41,17 +42,13 @@ src_prepare(){
src_configure() {
econf
- webapp_src_preinst
sed -e 's#/usr/lib/libbam.a#-lbam#;#./htslib/libhts.a#-lhts#' -i Makefile || die
}
src_install() {
- emake install DESTDIR="${ED}"
- mydoc="Changes README TODO INSTALL"
- perl-module_src_install DESTDIR="${ED}"
- webapp_src_install || die "Failed running webapp_src_install"
-}
-
-pkg_postinst() {
- webapp_pkg_postinst || die "webapp_pkg_postinst failed"
+ webapp_src_preinst
+ DESTDIR="${ED}" default
+ DESTDIR="${ED}" perl-module_src_install
+ dodir /usr/share/webapps/${PN}/${PV}
+ webapp_src_install
}
diff --git a/sci-biology/staden/files/staden-2.0.0_beta10-ldflags.patch b/sci-biology/staden/files/staden-2.0.0_beta10-ldflags.patch
deleted file mode 100644
index 735feb315..000000000
--- a/sci-biology/staden/files/staden-2.0.0_beta10-ldflags.patch
+++ /dev/null
@@ -1,30 +0,0 @@
- abi/Makefile | 2 +-
- alf/Makefile | 2 +-
- 2 files changed, 2 insertions(+), 2 deletions(-)
-
-diff --git a/abi/Makefile b/abi/Makefile
-index 3c1f8fb..58b4353 100644
---- a/abi/Makefile
-+++ b/abi/Makefile
-@@ -23,7 +23,7 @@ getABISampleName: $(OBJSSN)
- $(CLD) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(OBJSSN) $(LIBS) $(LIBSC)
-
- getABIdate: $(OBJSD)
-- $(CLD) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(OBJSD) $(IOUTILS_LIB) $(MISC_LIB) $(LIBSC)
-+ $(CLD) $(LDFLAGS) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(OBJSD) $(IOUTILS_LIB) $(MISC_LIB) $(LIBSC)
-
- getABIcomment: $(OBJSC)
- $(CLD) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(OBJSC) $(LIBS) $(LIBSC)
-diff --git a/alf/Makefile b/alf/Makefile
-index 94b7480..ef41a26 100644
---- a/alf/Makefile
-+++ b/alf/Makefile
-@@ -16,7 +16,7 @@ INCLUDES_E += $(MISC_INC)
- ALFOBJ = alfsplit.o
-
- alfsplit: $(ALFOBJ)
-- $(CLD) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(ALFOBJ) $(LIBSC)
-+ $(CLD) $(LDFLAGS) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(ALFOBJ) $(LIBSC)
-
- RSOBJ = $(ALFBIN)/2rs.o
-
diff --git a/sci-biology/staden/files/staden-2.0.0_beta10-zlib.patch b/sci-biology/staden/files/staden-2.0.0_beta10-zlib.patch
deleted file mode 100644
index 39537604e..000000000
--- a/sci-biology/staden/files/staden-2.0.0_beta10-zlib.patch
+++ /dev/null
@@ -1,16 +0,0 @@
- gap5/zfio.c | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/gap5/zfio.c b/gap5/zfio.c
-index 35da12a..1b628e4 100644
---- a/gap5/zfio.c
-+++ b/gap5/zfio.c
-@@ -51,7 +51,7 @@ int zfpeek(zfp *zf) {
- if (c != EOF)
- ungetc(c, zf->fp);
- } else {
-- c = gzgetc(zf->gz);
-+ c = gzgetc((gzFile)zf->gz);
- if (c != EOF)
- gzungetc(c, zf->gz);
- }
diff --git a/sci-biology/staden/staden-9999.ebuild b/sci-biology/staden/staden-9999.ebuild
deleted file mode 100644
index b2ed35724..000000000
--- a/sci-biology/staden/staden-9999.ebuild
+++ /dev/null
@@ -1,69 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit flag-o-matic fortran-2 subversion
-
-DESCRIPTION="DNA sequence assembly (gap4, gap5), editing and analysis tools (Spin)"
-HOMEPAGE="https://sourceforge.net/projects/staden/"
-ESVN_REPO_URI="https://svn.code.sf.net/p/${PN}/code/${PN}/trunk"
-
-LICENSE="staden"
-SLOT="0"
-KEYWORDS=""
-IUSE="debug doc fortran png tcl tk X zlib"
-
-# either g77 or gfortran must be available
-# edit src/mk/linux.mk accordingly
-#
-# this is a glibc-2.9 issue, see https://sourceforge.net/tracker/index.php?func=detail&aid=2629155&group_id=100316&atid=627058
-#
-#
-#
-DEPEND="
- app-arch/xz-utils
- dev-lang/tk:0=
- dev-tcltk/tklib
- media-libs/libpng:0
- sci-biology/samtools:0
- >=sci-libs/io_lib-1.13.8
- sys-libs/zlib"
-RDEPEND="${DEPEND}
- >=dev-tcltk/iwidgets-4.0
- tcl? ( >=dev-tcltk/itcl-3.2 )
- tk? ( >=dev-tcltk/itk-3.2 )
- net-misc/curl
- doc? ( sci-biology/staden_doc )"
-
-src_prepare() {
- default
- sed \
- -e 's:svnversion:false:' \
- -i configure.in || die
-}
-
-src_configure(){
- use debug && append-cflags "-DCACHE_REF_DEBUG"
- econf \
- $(use_enable X x) \
- $(use_enable amd64 64bit) \
- --with-tklib="/usr/$(get_libdir)/tklib"
-}
-
-src_install() {
- default
- # install the LDPATH so that it appears in /etc/ld.so.conf after env-update
- # subsequently, apps linked against /usr/lib/staden can be run because
- # loader can find the library (I failed to use '-Wl,-rpath,/usr/lib/staden'
- # somehow for gap2caf, for example
- cat >> "${T}"/99staden <<- EOF
- STADENROOT="${EPREFIX}"/usr/share/staden
- LDPATH="${EPREFIX}/usr/$(get_libdir)/staden"
- EOF
- doenvd "${T}"/99staden
-}
-
-pkg_postinst(){
- einfo "There is a tutorial at https://sourceforge.net/projects/staden/files/tutorials/1.1/course-1.1.tar.gz"
-}
diff --git a/sci-biology/subread/Manifest b/sci-biology/subread/Manifest
index 48a9f7ca3..8b4dcee7c 100644
--- a/sci-biology/subread/Manifest
+++ b/sci-biology/subread/Manifest
@@ -1 +1 @@
-DIST subread-2.0.1-source.tar.gz 23260381 BLAKE2B 498f898c9b5f5e0819fb7ae0a1407805fb3dc34cf5a07b4354d1493315a9e9190735916fb5c5587f972a67a7d47880e31dc3cc627e271dd2e452e856f5fd79c1 SHA512 e7548c426f75a5705a7c0538787007c5d3f23e4a4561022f192b3219f333483a02312986936cbbfcc8f9afa24cb4d91a1cc62fbebb6c6aef957568d5d8fa3505
+DIST subread-2.0.3-source.tar.gz 23304665 BLAKE2B 715907360f477a8ef69ba0465d6de1f23224da0c2095a21141f597a9cfe5c787cbafaa5d3c9cb04175f4d73cc4d184e13628541072d164596ee0b9b24175b501 SHA512 085d436d933c317555f36cbfb8e8c200ca15f20e56e48ae5427a673a74017dca7818320143a4841b78946685839931d48ae563b8b8e3ee6074581536cd0ff13b
diff --git a/sci-biology/subread/files/subread-2.0.1-fno-common.patch b/sci-biology/subread/files/subread-2.0.1-fno-common.patch
deleted file mode 100644
index 8f86840c5..000000000
--- a/sci-biology/subread/files/subread-2.0.1-fno-common.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- a/src/gene-algorithms.h
-+++ b/src/gene-algorithms.h
-@@ -60,7 +60,7 @@ void add_allvote_q(gene_allvote_t* allvote,int qid , int pos, gene_vote_number_t
-
- unsigned char get_next_char(FILE * fp);
-
--unsigned char * replica_index;
-+extern unsigned char * replica_index;
-
- extern double begin_ftime;
-
diff --git a/sci-biology/subread/subread-2.0.1.ebuild b/sci-biology/subread/subread-2.0.3.ebuild
index a16d0af5f..624509aa5 100644
--- a/sci-biology/subread/subread-2.0.1.ebuild
+++ b/sci-biology/subread/subread-2.0.3.ebuild
@@ -1,22 +1,20 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
DESCRIPTION="NGS suite for analysis of mapped reads, summary of exon/intron/gene counts"
HOMEPAGE="http://bioinf.wehi.edu.au/featureCounts/" # no https
SRC_URI="https://sourceforge.net/projects/subread/files/${P}/${P}-source.tar.gz"
+S="${S}-source"
LICENSE="GPL-3"
SLOT="0"
+KEYWORDS="~amd64"
DEPEND="sys-libs/zlib"
RDEPEND="${DEPEND}"
-S="${S}-source"
-
-PATCHES=( "${FILESDIR}"/${P}-fno-common.patch )
-
src_prepare(){
default
sed -e "s/-mtune=core2//g" -e "s/-O9//g" -i src/Makefile.Linux || die
diff --git a/sci-biology/symap/Manifest b/sci-biology/symap/Manifest
deleted file mode 100644
index 4e5ac6ea6..000000000
--- a/sci-biology/symap/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST symap-5.0.6.tar.gz 39447370 BLAKE2B 749769c36d7a46c11ab8bc874915b1dc2e4402b881c7f1fbd56353b4c0dc10cb20864c426c8bdb3ab28aa34d5f7d9bfbf8df66a99de34eebc13f3aa66b4a8d27 SHA512 356bebd7e1afeb78d00e748e1ec4488f180f1225aa3ca117b58cc381dc1d910241d54bc84d932ff6de955b6f4150043508fae6bc0f33c4486025aeb7deb010a8
diff --git a/sci-biology/symap/metadata.xml b/sci-biology/symap/metadata.xml
deleted file mode 100644
index ae9640ffb..000000000
--- a/sci-biology/symap/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@gentoo.org</email>
- <name>Gentoo Science Project</name>
- </maintainer>
-</pkgmetadata>
diff --git a/sci-biology/symap/symap-5.0.6.ebuild b/sci-biology/symap/symap-5.0.6.ebuild
deleted file mode 100644
index 58b444b3d..000000000
--- a/sci-biology/symap/symap-5.0.6.ebuild
+++ /dev/null
@@ -1,40 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DESCRIPTION="Synteny Mapping and Analysis Program"
-HOMEPAGE="http://www.agcol.arizona.edu/software/symap/ https://github.com/csoderlund/SyMAP"
-SRC_URI="https://github.com/csoderlund/SyMAP/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-# error: package netscape.javascript does not exist
-KEYWORDS=""
-
-DEPEND="
- sci-biology/blat
- sci-biology/mummer
- sci-biology/muscle"
-RDEPEND="${DEPEND}
- >=virtual/jre-1.7:*"
-
-S="${WORKDIR}/SyMAP-${PV}/java"
-
-src_unpack() {
- default
- cd "${S}"
- tar xvf classes_ext.tar.gz
- cd ../
- tar xvf ext.tar.gz
-}
-
-src_prepare() {
- default
- sed -e 's/#JAVA_PATH=\/usr/JAVA_PATH=\/usr/g' -i Makefile || die
-}
-
-src_compile() {
- emake class_dirs
- emake
-}
diff --git a/sci-biology/tigr-foundation-libs/tigr-foundation-libs-2.0-r1.ebuild b/sci-biology/tigr-foundation-libs/tigr-foundation-libs-2.0-r2.ebuild
index a03a130c2..18eec4e53 100644
--- a/sci-biology/tigr-foundation-libs/tigr-foundation-libs-2.0-r1.ebuild
+++ b/sci-biology/tigr-foundation-libs/tigr-foundation-libs-2.0-r2.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
DESCRIPTION="TIGR Foundation for C++"
HOMEPAGE="https://sourceforge.net/projects/amos/"
@@ -20,11 +20,7 @@ PATCHES=(
"${FILESDIR}/TigrFoundation-all-patches.patch"
)
-src_prepare(){
- sed -i "s:/export/usr/local:${ED}/usr:g" Makefile || die
- default
-}
-
src_install(){
- emake install DESTDIR="${ED}/usr" # Makefile does not respect DESTDIR
+ sed -i "s:/export/usr/local:${ED}/usr:g" Makefile || die
+ DESTDIR="${ED}/usr" emake install # Makefile does not respect DESTDIR
}
diff --git a/sci-biology/trinityrnaseq/Manifest b/sci-biology/trinityrnaseq/Manifest
index 815ffe565..153f208fd 100644
--- a/sci-biology/trinityrnaseq/Manifest
+++ b/sci-biology/trinityrnaseq/Manifest
@@ -1 +1 @@
-DIST trinityrnaseq-2.11.0.tar.gz 320752461 BLAKE2B 53327a49d31f7350e8fe820ac106f1cbe0577097852a63ea2154004d1945079f737f646c09d9907cfd45fb011845ea5e21eedf8fcda09e1db17d563fbdd0fd66 SHA512 9e9af2a16423ff8c063522c7acb6c8fc9386a95a7b58e01c94cd97971f71c3080cd5b2d34133bb501505d35cae05b77ff8423ad948324f49f9d4ddbb16629d20
+DIST trinityrnaseq-2.13.2.tar.gz 310355363 BLAKE2B 63055e11976a8d70b2c10b4859b25c8a27f23c05d1f5196eca137f281812aa54558b7eda343498a61af0c5aaa0e8d255e5d0a81e53c906859b455e0725180f95 SHA512 8399e12516d6d3cfde6803323b3bfb9ae249528fc79c08a6b290f42e7498783e6b300b89f9890570b28b2847ebe0f7894f59a888bf47d51190aad9e7c1ce54b7
diff --git a/sci-biology/trinityrnaseq/trinityrnaseq-2.11.0.ebuild b/sci-biology/trinityrnaseq/trinityrnaseq-2.11.0.ebuild
deleted file mode 100644
index 9ecaf24f2..000000000
--- a/sci-biology/trinityrnaseq/trinityrnaseq-2.11.0.ebuild
+++ /dev/null
@@ -1,70 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit perl-module
-
-# Butterfly should not require any special compilation, as its written in Java and already provided as portable precompiled software ...
-
-DESCRIPTION="Transcriptome assembler for RNA-seq reads"
-HOMEPAGE="https://github.com/Trinotate/Trinotate.github.io/wiki"
-SRC_URI="https://github.com/trinityrnaseq/trinityrnaseq/releases/download/v${PV}/${PN}-v${PV}.FULL_with_extendedTestData.tar.gz -> ${P}.tar.gz"
-
-LICENSE="BSD-BroadInstitute"
-SLOT="0"
-KEYWORDS="" # PERL5INC path is wrong when /usr/bin/Trinity is executed
-
-DEPEND=""
-RDEPEND="${DEPEND}
- sci-biology/parafly
- >=sci-biology/jellyfish-2.2.6:2
- >=sci-libs/htslib-1.2.1
- >=sci-biology/samtools-1.3:0
- >=sci-biology/trimmomatic-0.36
- >=sci-biology/GAL-0.2.1
- dev-perl/IO-All
- sci-biology/seqtools"
-# optionally install https://github.com/HpcGridRunner/HpcGridRunner/releases
-# has the following "plugins" (aka bundled 3rd-party code)
-# slclust
-# DEXseq_util
-# COLLECTL
-# ParaFly-0.1.0
-
-S="${WORKDIR}/${PN}-v${PV}"
-
-PATCHES=(
- "${FILESDIR}/${PN}-2.11.0-fix-compilation.patch"
-)
-
-src_compile(){
- emake all
- emake plugins # bundled copies of TransDecoder, trimmomatic, fastool, parafly
-}
-
-src_install(){
- dodoc Chrysalis/chrysalis.notes
- dodoc Changelog.txt
- perl_set_version
- dobin Trinity
- perl_domodule util/*.pl
- dobin Inchworm/bin/*
- cd Chrysalis/bin || die
- dobin BubbleUpClustering Chrysalis CreateIwormFastaBundle GraphFromFasta QuantifyGraph ReadsToTranscripts
- cd ../../util/R || die
- insinto /usr/share/"${PN}"/R
- doins *.R
- cd ../PBS || die
- insinto /usr/share/"${PN}"/PBS
- doins *
- cd .. || die
- cp -rp support_scripts misc "${ED}"/usr/share/"${PN}"/ || die
- cd "${S}" || die
- perl_domodule util/misc/PerlLib/*.pm PerlLib/*.pm
- perl_domodule PerlLib/KmerGraphLib/*.pm
- perl_domodule PerlLib/CDNA/*.pm
- perl_domodule PerlLib/Simulate/*.pm
- perl_domodule PerlLib/CanvasXpress/*.pm
- chmod a+rx -R "${ED}/${VENDOR_LIB}/${PN}"
-}
diff --git a/sci-biology/trinityrnaseq/trinityrnaseq-2.13.2.ebuild b/sci-biology/trinityrnaseq/trinityrnaseq-2.13.2.ebuild
new file mode 100644
index 000000000..3b94d9713
--- /dev/null
+++ b/sci-biology/trinityrnaseq/trinityrnaseq-2.13.2.ebuild
@@ -0,0 +1,45 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit perl-module
+
+DESCRIPTION="Transcriptome assembler for RNA-seq reads"
+HOMEPAGE="https://github.com/Trinotate/Trinotate.github.io/wiki"
+SRC_URI="https://github.com/${PN}/${PN}/releases/download/Trinity-v${PV}/${PN}-v${PV}.FULL_with_extendedTestData.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}/${PN}-v${PV}"
+
+LICENSE="BSD-BroadInstitute"
+SLOT="0"
+KEYWORDS="~amd64"
+
+DEPEND=""
+RDEPEND="${DEPEND}
+ sci-biology/parafly
+ >=sci-biology/jellyfish-2.2.6:2
+ >=sci-libs/htslib-1.2.1
+ >=sci-biology/samtools-1.3:0
+ >=sci-biology/trimmomatic-0.36
+ >=sci-biology/GAL-0.2.1
+ dev-perl/IO-All
+ sci-biology/seqtools
+"
+
+PATCHES=(
+ "${FILESDIR}/${PN}-2.11.0-fix-compilation.patch"
+)
+
+src_compile(){
+ # missing submodule for bamsifter
+ emake no_bamsifter
+ emake plugins
+}
+
+src_install(){
+ # fix the install path
+ sed -e "s:/usr/local/bin:${ED}/usr/bin:g" \
+ -i util/support_scripts/trinity_installer.py || die
+ dodir /usr/bin
+ default
+}
diff --git a/sci-biology/vcflib/Manifest b/sci-biology/vcflib/Manifest
index 57b3d1f2b..a535ea547 100644
--- a/sci-biology/vcflib/Manifest
+++ b/sci-biology/vcflib/Manifest
@@ -1 +1 @@
-DIST vcflib-1.0.2-src.tar.gz 20881031 BLAKE2B 67e8fd60db3171fa05cac36306852134cc8c37a3e4715d141547773c3252569a01363298297978d89c015b1120ad0f0d05eb2b67b5ee7d01728f27f0049bc748 SHA512 7dadd2398d4054a1d7e7b520f192243f63c98a4fa184f7c6750dce9296356f4b45bdbb50f7de270a6c4c3aa76deec45980c363e19b22bea64590de711fdb7d71
+DIST vcflib-1.0.3.tar.gz 19213097 BLAKE2B 142685d494759d61e7b0ed40e9d91b78d7856038b6fb73f7f26f80152b0a85006bd6f3e9b5e7422e74841eb9a21e3a86efc3f63545e3fea7545fb91a7475b409 SHA512 16c7b3932fd4e6a985adbc1131dd0b48028501be3023d85fd57b4efccaf071a11ba6f49219df723f6eacc2787218e8f3f2b318e016633ce3e829139b698154a2
diff --git a/sci-biology/vcflib/vcflib-1.0.2.ebuild b/sci-biology/vcflib/vcflib-1.0.3.ebuild
index 272e69483..d4cf1e02f 100644
--- a/sci-biology/vcflib/vcflib-1.0.2.ebuild
+++ b/sci-biology/vcflib/vcflib-1.0.3.ebuild
@@ -1,18 +1,17 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
inherit cmake toolchain-funcs
DESCRIPTION="VCF/BED utils, Genotype Phenotype Association Toolkit (GPAT++)"
HOMEPAGE="https://github.com/vcflib/vcflib"
-SRC_URI="https://github.com/vcflib/vcflib/releases/download/v${PV}/${P}-src.tar.gz"
-
-# vcflib is incorporated into several projects, such as freebayes
+SRC_URI="https://github.com/vcflib/vcflib/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz"
LICENSE="MIT-with-advertising"
SLOT="0"
+# No proper release tarball for this release yet
KEYWORDS=""
IUSE="openmp"
@@ -22,10 +21,6 @@ DEPEND="
sci-biology/tabixpp
"
RDEPEND="${DEPEND}"
-# contains bundled sci-biology/htslib ?
-# see also ./include for possible traces of other bundled sw
-
-S="${WORKDIR}/${PN}"
src_prepare(){
cmake_src_prepare
@@ -47,7 +42,7 @@ src_prepare(){
src_compile(){
mycmakeargs=(
-DOPENMP="$(use_enable openmp)"
- -DHTSLIB_LOCAL=NO
+ -DHTSLIB_LOCAL=ON
)
cmake_src_compile
}
diff --git a/sci-biology/wcd/Manifest b/sci-biology/wcd/Manifest
deleted file mode 100644
index 5209a3925..000000000
--- a/sci-biology/wcd/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-DIST wcd-0.6.3_p20180430.tar.gz 368654 BLAKE2B c6936964d4dd2602e9fd735ddf70ed79e625b6dfa58972a1ba95532b36968da4345ef40d7ba68355f8f53308d0989124c1bbdce48e11d0240ccabc91787d3b61 SHA512 7c847607fcbeb20cb5dbf023968a9174a5d2fd876127a6008b878274ec2e1a6498e7c0a610e4f75473128236661848d6403f96fc868eec773be3a8e4e7dd7f4f
-DIST wcd.html 8448 BLAKE2B d1561925a0f299d12c177f499a95fbc314d558c18106642c49852bd96a104bdef5271b5ea1b4312e70936db6726ea3ea54e3a942d9c9c52e806b48137321cf05 SHA512 11156d4811b7716632fbd7b0330d918ae30b6dcc9ebbd59c95d445ba465504aa68d0fa9863b3ad4b5743c929f4558d1698af03c124fd02299ef13479a80555c2
-DIST wcd.pdf 275513 BLAKE2B 049d0d8b9d6db0e2754322f69903c5680a62c007a9abf5466b21a96f778a9f537a8ec91344d729961317ff6a8b484ca870f5ee0a78fa7cec8ae4ba2d7c5f1939 SHA512 ef2e0e8bbe49a5c5b304a305d8948b253ba2bf789790941600c5d5ba74351fe41e54a66dd189a33846304a8f2a8fa4c70025e516f3b73643da71030cbded63a2
diff --git a/sci-biology/wcd/files/wcd-0.6.3-impl-decl.patch b/sci-biology/wcd/files/wcd-0.6.3-impl-decl.patch
deleted file mode 100644
index 15d851577..000000000
--- a/sci-biology/wcd/files/wcd-0.6.3-impl-decl.patch
+++ /dev/null
@@ -1,15 +0,0 @@
- src/auxcluster.c | 1 +
- 1 file changed, 1 insertion(+)
-
-diff --git a/src/auxcluster.c b/src/auxcluster.c
-index ac00a0f..e98f19f 100644
---- a/src/auxcluster.c
-+++ b/src/auxcluster.c
-@@ -2,6 +2,7 @@
-
- #include "common.h"
- #include "strings.h"
-+#include <string.h>
- #include "assert.h"
-
- extern SeqInfoPtr seqInfo;
diff --git a/sci-biology/wcd/files/wcd-0.6.3-ldflags.patch b/sci-biology/wcd/files/wcd-0.6.3-ldflags.patch
deleted file mode 100644
index d697d00b7..000000000
--- a/sci-biology/wcd/files/wcd-0.6.3-ldflags.patch
+++ /dev/null
@@ -1,16 +0,0 @@
- src/Makefile.am | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/src/Makefile.am b/src/Makefile.am
-index e986a91..ff87e29 100644
---- a/src/Makefile.am
-+++ b/src/Makefile.am
-@@ -7,7 +7,7 @@ wcd_CFLAGS += -DMPI
- endif
- if PTHREADS
- wcd_CFLAGS += -DPTHREADS
--wcd_LDFLAGS += -lpthread
-+wcd_LDADD = -lpthread
- endif
- if !COMPILER
- wcd_CFLAGS += -DNOINLINE
diff --git a/sci-biology/wcd/metadata.xml b/sci-biology/wcd/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/wcd/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>mmokrejs@fold.natur.cuni.cz</email>
- <name>Martin Mokrejs</name>
- </maintainer>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
-</pkgmetadata>
diff --git a/sci-biology/wcd/wcd-0.6.3_p20180430.ebuild b/sci-biology/wcd/wcd-0.6.3_p20180430.ebuild
deleted file mode 100644
index 6593d97ed..000000000
--- a/sci-biology/wcd/wcd-0.6.3_p20180430.ebuild
+++ /dev/null
@@ -1,46 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-COMMIT="aee525029bb661b633097e989c6fe2eaa93d2def"
-
-DESCRIPTION="EST sequence clustering: d2 function, edit distance, common word heuristics"
-HOMEPAGE="https://shaze.github.io/wcdest/"
-SRC_URI="https://github.com/shaze/wcdest/archive/${COMMIT}.tar.gz -> ${P}.tar.gz
- http://www.bioinf.wits.ac.za/~scott/wcd.html
- http://www.bioinf.wits.ac.za/~scott/wcd.pdf"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS=""
-
-IUSE="doc mpi threads"
-
-# This code (0.4.1 at least) has been tested using LAMMPI (RedHat, Suse,
-# MacOS X), MPICH (Ubuntu) and MVAPICH (Suse)
-DEPEND="mpi? ( sys-cluster/mpich2 )"
-
-PATCHES=(
- "${FILESDIR}"/${PN}-0.6.3-ldflags.patch
- "${FILESDIR}"/${PN}-0.6.3-impl-decl.patch
-)
-
-S="${WORKDIR}/${PN}est-${COMMIT}/code"
-
-src_configure(){
- econf \
- $(use_enable mpi) \
- $(use_enable threads pthreads)
-}
-
-src_compile() {
- default
- use doc && emake pdf info html
-}
-
-src_install() {
- use doc && HTML_DOCS=( doc/wcd.html doc/wcd.pdf doc/wcd.texi )
- emake install PREFIX=/usr LIBDIR="${D}"/usr/$(get_libdir)
- dodoc "${DISTDIR}"/wcd.*
-}