diff options
Diffstat (limited to 'sci-biology')
31 files changed, 252 insertions, 437 deletions
diff --git a/sci-biology/HTSeq/HTSeq-2.0.2.ebuild b/sci-biology/HTSeq/HTSeq-2.0.2.ebuild index 25620147ddb8..b4b7974e60d0 100644 --- a/sci-biology/HTSeq/HTSeq-2.0.2.ebuild +++ b/sci-biology/HTSeq/HTSeq-2.0.2.ebuild @@ -4,7 +4,7 @@ EAPI=8 DISTUTILS_IN_SOURCE_BUILD=1 -PYTHON_COMPAT=( python3_{9..10} ) +PYTHON_COMPAT=( python3_{9..11} ) inherit distutils-r1 flag-o-matic @@ -23,8 +23,6 @@ fi LICENSE="GPL-3+" SLOT="0" -IUSE="test" -RESTRICT="!test? ( test )" RDEPEND=" dev-python/numpy[${PYTHON_USEDEP}] diff --git a/sci-biology/HTSeq/HTSeq-9999.ebuild b/sci-biology/HTSeq/HTSeq-9999.ebuild index 25620147ddb8..b4b7974e60d0 100644 --- a/sci-biology/HTSeq/HTSeq-9999.ebuild +++ b/sci-biology/HTSeq/HTSeq-9999.ebuild @@ -4,7 +4,7 @@ EAPI=8 DISTUTILS_IN_SOURCE_BUILD=1 -PYTHON_COMPAT=( python3_{9..10} ) +PYTHON_COMPAT=( python3_{9..11} ) inherit distutils-r1 flag-o-matic @@ -23,8 +23,6 @@ fi LICENSE="GPL-3+" SLOT="0" -IUSE="test" -RESTRICT="!test? ( test )" RDEPEND=" dev-python/numpy[${PYTHON_USEDEP}] diff --git a/sci-biology/HTSeq/metadata.xml b/sci-biology/HTSeq/metadata.xml index 649077f8337e..6ada1a530737 100644 --- a/sci-biology/HTSeq/metadata.xml +++ b/sci-biology/HTSeq/metadata.xml @@ -7,5 +7,6 @@ </maintainer> <upstream> <remote-id type="pypi">HTSeq</remote-id> + <remote-id type="github">htseq/htseq</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/bcftools/Manifest b/sci-biology/bcftools/Manifest index af5f3f40dd8b..0f3c24a476a9 100644 --- a/sci-biology/bcftools/Manifest +++ b/sci-biology/bcftools/Manifest @@ -1,2 +1 @@ -DIST bcftools-1.15.1.tar.bz2 6917252 BLAKE2B d2389df8d2a1bbc48fcaccad47d77ff99d700e82e04330189e7d93acdac97a13506c2b799fbba31bdc0988977c7df7c699e7b156f3530dd35e5f052c6f977731 SHA512 60fedacc41051675d372e68146ac8fa0dc019a7fb694fda487d89e62f34edaf5ac11cca38779e9bcfcf8b3148802fadabed12f7e46ad534ad5087b8d6383f97b -DIST bcftools-1.16.tar.bz2 7325862 BLAKE2B 0e1240448d4efb352d3d0cd83decd286f7544fff3676f0a5cca51dec9c445c47c37ac24a3317aa7b41182c576e7e57dba460fc98aca069dc2f8fe0625c0b0f06 SHA512 998d5ac941f73798c35dd1db7ac7aba9067f275bd3055728aabfd8edd9f40484130df1fb57621d1a762a57b28ffcac358570915c341d420ae6f12bd17f7651a3 +DIST bcftools-1.17.tar.bz2 7538043 BLAKE2B 82f65d53ebea0527ff000329f158ebdb1d603e04841a096cf8ca0434e7a5694ab43da7959ee10e9cb29328bf82301c03200e1203578a74e2e1118856b2641502 SHA512 39ae44a682e626a5261900e9412170a269e460b559d6607db697e6a12b1e512ffb3bdeb3486413e19b8adca26a8ccbb2bd4af24459decb74592c54473d2c6a68 diff --git a/sci-biology/bcftools/bcftools-1.15.1.ebuild b/sci-biology/bcftools/bcftools-1.15.1.ebuild deleted file mode 100644 index 9032b97e11d0..000000000000 --- a/sci-biology/bcftools/bcftools-1.15.1.ebuild +++ /dev/null @@ -1,42 +0,0 @@ -# Copyright 1999-2023 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{9..10} ) - -inherit python-single-r1 - -DESCRIPTION="Utilities for variant calling and manipulating VCF and BCF files" -HOMEPAGE="http://www.htslib.org" -SRC_URI="https://github.com/samtools/${PN}/releases/download/${PV}/${P}.tar.bz2" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -RDEPEND=" - dev-lang/perl - $(python_gen_cond_dep 'dev-python/matplotlib[${PYTHON_USEDEP}]') - =sci-libs/htslib-${PV}*:= - sys-libs/zlib - ${PYTHON_DEPS}" -DEPEND="${RDEPEND}" -BDEPEND="${PYTHON_DEPS}" - -src_prepare() { - default - - python_fix_shebang misc/{gff2gff,guess-ploidy,plot-roh}.py - - # remove bundled htslib - rm -r htslib-* || die -} - -src_configure() { - econf \ - --disable-bcftools-plugins \ - --disable-libgsl \ - --with-htslib=system -} diff --git a/sci-biology/bcftools/bcftools-1.16.ebuild b/sci-biology/bcftools/bcftools-1.17.ebuild index 6adee705bb46..6adee705bb46 100644 --- a/sci-biology/bcftools/bcftools-1.16.ebuild +++ b/sci-biology/bcftools/bcftools-1.17.ebuild diff --git a/sci-biology/bedtools/bedtools-2.30.0.ebuild b/sci-biology/bedtools/bedtools-2.30.0.ebuild index 5a8174fbdfe0..b86b87e72dc4 100644 --- a/sci-biology/bedtools/bedtools-2.30.0.ebuild +++ b/sci-biology/bedtools/bedtools-2.30.0.ebuild @@ -34,6 +34,7 @@ BDEPEND=" PATCHES=( "${FILESDIR}"/${PN}-2.29.2-buildsystem.patch "${FILESDIR}"/${PN}-2.29.2-python.patch + "${FILESDIR}"/${PN}-2.30.0-gcc13.patch ) src_configure() { diff --git a/sci-biology/bedtools/files/bedtools-2.30.0-gcc13.patch b/sci-biology/bedtools/files/bedtools-2.30.0-gcc13.patch new file mode 100644 index 000000000000..c63faf31c851 --- /dev/null +++ b/sci-biology/bedtools/files/bedtools-2.30.0-gcc13.patch @@ -0,0 +1,25 @@ +https://github.com/arq5x/bedtools2/pull/1045 + +From 7d7fb513b9b05b7a0512a83520e9f60036e5ff9a Mon Sep 17 00:00:00 2001 +From: David Seifert <soap@gentoo.org> +Date: Tue, 18 Apr 2023 11:59:58 +0200 +Subject: [PATCH] Add missing <cstdint> include + +* breaks build with GCC 13: + https://bugs.gentoo.org/895860 +--- + src/utils/general/ParseTools.h | 1 + + 1 file changed, 1 insertion(+) + +diff --git a/src/utils/general/ParseTools.h b/src/utils/general/ParseTools.h +index e056c149..3418eff1 100644 +--- a/src/utils/general/ParseTools.h ++++ b/src/utils/general/ParseTools.h +@@ -16,6 +16,7 @@ + #include "string.h" + #include <cstdio> + #include <cstdlib> ++#include <cstdint> + + using namespace std; + diff --git a/sci-biology/biopandas/Manifest b/sci-biology/biopandas/Manifest index 88c904d40ce4..1a153471c26b 100644 --- a/sci-biology/biopandas/Manifest +++ b/sci-biology/biopandas/Manifest @@ -1 +1 @@ -DIST biopandas-0.2.7.tar.gz 255846 BLAKE2B b8c6a66f51a00266bc1a271ecfe00b4cfddd24b9766e63e2ad4187048ddd8f985d70eb8083b1be3887a0fd9b666c97553029ecd90c7b73ae882e5347bbc54d2e SHA512 cf4f12601b7f63ca3d5e9a17c6628e4975968f722c9db72e32c00e80ec335c5bf6a928a5f887b16ecd316c49b298d77634cbe1c4ef1ca505379b1de5335e2569 +DIST biopandas-0.4.1.gh.tar.gz 5330292 BLAKE2B 78b783ed77bbd8e6efd115a108f99c502fd71ef4c231746575599828699dac1de85125273df1af74d0bd51e092751113474ef2baf312a184e23b3057cd21222a SHA512 e08694fad927a5ac096b2cd78f641a2af262ebfc7351fc4dc37e5df39e98a6e984ccab26718109f18eed988a4a4af5b29d19c5cf3e8e2d794246b1410a9b5440 diff --git a/sci-biology/biopandas/biopandas-0.2.7.ebuild b/sci-biology/biopandas/biopandas-0.2.7.ebuild deleted file mode 100644 index 7458dbcb1cb9..000000000000 --- a/sci-biology/biopandas/biopandas-0.2.7.ebuild +++ /dev/null @@ -1,40 +0,0 @@ -# Copyright 1999-2023 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{9..10} ) - -inherit distutils-r1 - -MY_PN="BioPandas" -MY_P="${MY_PN}-${PV}" - -DESCRIPTION="Molecular Structures in Pandas DataFrames" -HOMEPAGE=" - https://rasbt.github.io/biopandas/ - https://github.com/rasbt/biopandas - https://pypi.org/project/BioPandas/" -SRC_URI="mirror://pypi/${MY_P:0:1}/${MY_PN}/${P}.tar.gz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="test" -RESTRICT="!test? ( test )" - -RDEPEND=" - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/pandas[${PYTHON_USEDEP}] - dev-python/scipy[${PYTHON_USEDEP}]" - -distutils_enable_tests nose - -python_test() { - "${EPYTHON}" --version || die - "${EPYTHON}" -c "import numpy; print('numpy %s' % numpy.__version__)" || die - "${EPYTHON}" -c "import scipy; print('scipy %s' % scipy.__version__)" || die - "${EPYTHON}" -c "import pandas; print('pandas %s' % pandas.__version__)" || die - - nosetests -s --verbose ${PN} || die -} diff --git a/sci-biology/biopandas/biopandas-0.4.1.ebuild b/sci-biology/biopandas/biopandas-0.4.1.ebuild new file mode 100644 index 000000000000..50fe601ed514 --- /dev/null +++ b/sci-biology/biopandas/biopandas-0.4.1.ebuild @@ -0,0 +1,28 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{9..11} ) +DISTUTILS_USE_PEP517=setuptools + +inherit distutils-r1 + +DESCRIPTION="Molecular Structures in Pandas DataFrames" +HOMEPAGE=" + https://rasbt.github.io/biopandas/ + https://github.com/BioPandas/biopandas + https://pypi.org/project/biopandas/ +" +SRC_URI="https://github.com/BioPandas/biopandas/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" + +RDEPEND=" + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/pandas[${PYTHON_USEDEP}] +" + +distutils_enable_tests nose diff --git a/sci-biology/biopandas/metadata.xml b/sci-biology/biopandas/metadata.xml index 1b4a0fc84ad0..5133b4eff6ab 100644 --- a/sci-biology/biopandas/metadata.xml +++ b/sci-biology/biopandas/metadata.xml @@ -6,11 +6,11 @@ <name>Gentoo Biology Project</name> </maintainer> <upstream> - <remote-id type="pypi">BioPandas</remote-id> + <remote-id type="pypi">biopandas</remote-id> <maintainer status="unknown"> <email>mail@sebastianraschka.com</email> <name>Sebastian Raschka</name> </maintainer> - <remote-id type="github">rasbt/biopandas</remote-id> + <remote-id type="github">BioPandas/biopandas</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/biopython/Manifest b/sci-biology/biopython/Manifest index 014c48aa8401..0c16022dea2c 100644 --- a/sci-biology/biopython/Manifest +++ b/sci-biology/biopython/Manifest @@ -1 +1 @@ -DIST biopython-1.79.tar.gz 16738730 BLAKE2B 8c97fc23e458f7bc98b0ed0226bd6fb42f6c6f3ce03d562b13fac66c5061451595cd5bd01cad07bbe1fc6b20f4de21b0f03766b5a20e602545da888047a57185 SHA512 81e2718f4015bb038637b4d1181e6bea48018fec1e769c5f0ab75442a769336899191f1222e82e1b9569c1fac470500d7582420e5cbe9bce0056b41751adeaaa +DIST biopython-1.81.tar.gz 19324875 BLAKE2B be3a85f5b60638987d6186af498411b494f8d27389f24cd1b9e658bc6b1a29c799ec8b20a9ac0b955c6d4c239706f4dbb5b75f6d56908f63d731b1d56c9fd587 SHA512 1595fad6631bfb6cf4e1a92ed72e6093e2a0c24f3c0bd4182267ec9742fb03dff16099eedde139598aa6b5b8380bbac9e48246cb9ab8b44109333d60adfd00ed diff --git a/sci-biology/biopython/biopython-1.79.ebuild b/sci-biology/biopython/biopython-1.81.ebuild index c6a93b3af58d..8b90d610c6ae 100644 --- a/sci-biology/biopython/biopython-1.79.ebuild +++ b/sci-biology/biopython/biopython-1.81.ebuild @@ -3,13 +3,12 @@ EAPI=8 -PYTHON_COMPAT=( python3_{9..10} ) +PYTHON_COMPAT=( python3_{9..11} ) -inherit distutils-r1 optfeature +inherit distutils-r1 optfeature pypi DESCRIPTION="Python modules for computational molecular biology" HOMEPAGE="https://www.biopython.org/ https://pypi.org/project/biopython/" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" LICENSE="HPND" SLOT="0" diff --git a/sci-biology/bowtie/Manifest b/sci-biology/bowtie/Manifest index e62703395825..274e5e7b9fb6 100644 --- a/sci-biology/bowtie/Manifest +++ b/sci-biology/bowtie/Manifest @@ -1 +1,2 @@ DIST bowtie2-2.4.4-source.zip 10515984 BLAKE2B be4ceb9d3155d2a9a1f580e5032251b04b89ce0c8c9c89fc3551b34fe3bd71a683362488be7aad6daef24734c6f95c19223f20e67f198f745c4432381243039c SHA512 1b5dadd7e41b90bb9b05f50bfa171fe219cfd03aa8bb6f800de4baaffeb975eef6efc4fb8b49cb0d18833f74a1741cbe1556b87388f59188e04a55dcee6a02da +DIST bowtie2-2.5.1-source.zip 10528859 BLAKE2B 9dc22bfef4b3a1cfaa606cb235acd1d7688015678d82e8ca80d3d7cf269e1f45d6cb60bc29eb334fb6f0c25d5afd8202e83a83e53668c8965857b8885d2692c8 SHA512 31cc642e318ab50e7ef6035a9c2095024d46d92a317011ed0c3ac3ccb3d427a13bf724d0158d29a4f1e07115ddcb85229b95bcb2d4351164fcadd6568293565f diff --git a/sci-biology/bowtie/bowtie-2.5.1.ebuild b/sci-biology/bowtie/bowtie-2.5.1.ebuild new file mode 100644 index 000000000000..353362fd6026 --- /dev/null +++ b/sci-biology/bowtie/bowtie-2.5.1.ebuild @@ -0,0 +1,73 @@ +# Copyright 2021-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{9..11} ) + +inherit python-single-r1 toolchain-funcs + +DESCRIPTION="Popular short read aligner for Next-generation sequencing data" +HOMEPAGE="https://bowtie-bio.sourceforge.net/bowtie2/" +SRC_URI="mirror://sourceforge/project/${PN}-bio/bowtie2/${PV}/bowtie2-${PV}-source.zip" +S="${WORKDIR}/${PN}2-${PV}" + +LICENSE="GPL-3" +SLOT="2" +KEYWORDS="~amd64 ~x86" + +IUSE="test cpu_flags_x86_sse2 examples" +# Test script missing from tarball +# ./scripts/sim/run.sh: No such file or directory +RESTRICT="test" +REQUIRED_USE="cpu_flags_x86_sse2 ${PYTHON_REQUIRED_USE}" + +RDEPEND=" + ${PYTHON_DEPS} + dev-lang/perl + sys-libs/zlib +" +DEPEND="${RDEPEND}" +BDEPEND=" + app-arch/unzip + test? ( + dev-perl/App-cpanminus + dev-perl/B-COW + dev-perl/Clone + dev-perl/Config-General + dev-perl/File-Which + dev-perl/local-lib + dev-perl/Math-Random + dev-perl/Test-Deep + dev-perl/Text-Template + ) +" + +src_compile() { + emake \ + CXX="$(tc-getCXX)" \ + CXXFLAGS="" \ + CPPFLAGS="${CPPFLAGS}" \ + EXTRA_FLAGS="${LDFLAGS}" \ + RELEASE_FLAGS="${CXXFLAGS} -msse2" +} + +src_install() { + dobin bowtie2 bowtie2-* + + exeinto /usr/libexec/bowtie2 + doexe scripts/* + + HTML_DOCS=( doc/{manual.html,style.css} ) + einstalldocs + dodoc TUTORIAL + newman MANUAL bowtie2.1 + + python_fix_shebang "${ED}"/usr/bin/bowtie2-{build,inspect} + + if use examples; then + docinto examples + dodoc -r example/. + docompress -x /usr/share/doc/${PF}/examples + fi +} diff --git a/sci-biology/clustalw/clustalw-1.83-r4.ebuild b/sci-biology/clustalw/clustalw-1.83-r4.ebuild index 62c59747adf3..fe20213ae7b5 100644 --- a/sci-biology/clustalw/clustalw-1.83-r4.ebuild +++ b/sci-biology/clustalw/clustalw-1.83-r4.ebuild @@ -12,7 +12,7 @@ S="${WORKDIR}/${PN}${PV}" LICENSE="clustalw" SLOT="1" -KEYWORDS="amd64 ~ppc ppc64 sparc x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris" +KEYWORDS="amd64 ~ppc ppc64 sparc x86 ~amd64-linux ~x86-linux ~ppc-macos" PATCHES=( "${FILESDIR}"/${PV}-as-needed.patch diff --git a/sci-biology/clustalw/clustalw-2.1-r2.ebuild b/sci-biology/clustalw/clustalw-2.1-r2.ebuild index 58a28e3ef7a5..15c658788b5b 100644 --- a/sci-biology/clustalw/clustalw-2.1-r2.ebuild +++ b/sci-biology/clustalw/clustalw-2.1-r2.ebuild @@ -9,7 +9,7 @@ SRC_URI="http://www.clustal.org/download/current/${P}.tar.gz" LICENSE="GPL-3 LGPL-3" SLOT="2" -KEYWORDS="amd64 ~ppc ~ppc64 ~sparc x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris" +KEYWORDS="amd64 ~ppc ~ppc64 ~sparc x86 ~amd64-linux ~x86-linux ~ppc-macos" src_install() { default diff --git a/sci-biology/mrbayes/mrbayes-3.1.2-r2.ebuild b/sci-biology/mrbayes/mrbayes-3.1.2-r2.ebuild index 57c39ea21a94..1174d0de599e 100644 --- a/sci-biology/mrbayes/mrbayes-3.1.2-r2.ebuild +++ b/sci-biology/mrbayes/mrbayes-3.1.2-r2.ebuild @@ -11,7 +11,7 @@ SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz" LICENSE="GPL-2" SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos" IUSE="debug mpi readline" DEPEND=" diff --git a/sci-biology/mrbayes/mrbayes-3.2.7.ebuild b/sci-biology/mrbayes/mrbayes-3.2.7.ebuild index ad87554eb31e..4fbad2f65473 100644 --- a/sci-biology/mrbayes/mrbayes-3.2.7.ebuild +++ b/sci-biology/mrbayes/mrbayes-3.2.7.ebuild @@ -9,7 +9,7 @@ SRC_URI="https://github.com/NBISweden/MrBayes/releases/download/v${PV}/${P}.tar. LICENSE="GPL-2" SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos" IUSE="debug mpi readline" # --with-readline was given, but MPI support requires readline to be disabled. REQUIRED_USE="mpi? ( !readline )" diff --git a/sci-biology/primer3/primer3-2.3.7-r1.ebuild b/sci-biology/primer3/primer3-2.3.7-r1.ebuild index b36e9291db94..3ce2c4fe5d39 100644 --- a/sci-biology/primer3/primer3-2.3.7-r1.ebuild +++ b/sci-biology/primer3/primer3-2.3.7-r1.ebuild @@ -11,7 +11,7 @@ SRC_URI="mirror://sourceforge/project/${PN}/${PN}/${PV}/${P}.tar.gz" LICENSE="GPL-2" SLOT="0" -KEYWORDS="~amd64 ~ppc ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris" +KEYWORDS="~amd64 ~ppc ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~ppc-macos" BDEPEND="dev-lang/perl" diff --git a/sci-biology/pysam/Manifest b/sci-biology/pysam/Manifest index f1a1fe7298b7..2bc79f89f441 100644 --- a/sci-biology/pysam/Manifest +++ b/sci-biology/pysam/Manifest @@ -1 +1 @@ -DIST pysam-0.19.1.gh.tar.gz 3649711 BLAKE2B dac3ab5a86ef95048e966fc007a0aa1c96ca8498f7c2672c2ed024f34b508bac42048e58b8ae0b538cea137a51e1874bb5c2c4976c7f3dc657a4c2cf5f9a27fb SHA512 719f3a15e7dd277a90cce7f938b674ff86ef6b8f2d3440c3a0bf2ea22c4fbc2b3c9e0cf297d958c99e09dcd6e9905f32e8c632158aa8d5af8210e79705e1c479 +DIST pysam-0.21.0.gh.tar.gz 3842829 BLAKE2B 83db290ec0bae71106276ed4f1721292c0d2fa55053c7451f0a8a79619b1c4d8444b99293ac5d8051bfb0b59e984e32a89798bab091e3a019b7c2a3fb7414d1c SHA512 b2ac986b6a352df1d2066a224d710648a88d8ad44273623a89ae0f4bb2645b00f0d0e1685c8ccedfd379259255957e653f3c3199621ac1d4c26098f538b6bfa7 diff --git a/sci-biology/pysam/files/pysam-0.21.0-cython-3.patch b/sci-biology/pysam/files/pysam-0.21.0-cython-3.patch new file mode 100644 index 000000000000..303a4fb0dcdc --- /dev/null +++ b/sci-biology/pysam/files/pysam-0.21.0-cython-3.patch @@ -0,0 +1,24 @@ +From 17bb13dcfdb56ac238458dcef23fe01893a892e9 Mon Sep 17 00:00:00 2001 +From: John Marshall <jmarshall@hey.com> +Date: Sat, 8 Apr 2023 11:00:46 +1200 +Subject: [PATCH] Remove incorrect type annotation + +The annotation already in pysam/libcbcf.pyi is correct. +Fixes #1179 as reopened on April 6th. +--- + pysam/libcbcf.pyx | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/pysam/libcbcf.pyx b/pysam/libcbcf.pyx +index 8c088af2..8ecfe5f3 100644 +--- a/pysam/libcbcf.pyx ++++ b/pysam/libcbcf.pyx +@@ -3479,7 +3479,7 @@ cdef class VariantRecordSample(object): + return bcf_format_get_alleles(self) + + @alleles.setter +- def alleles(self, value: tuple): ++ def alleles(self, value): + # Sets the genotype, supply a tuple of alleles to set. + # The supplied alleles need to be defined in the correspoding pysam.libcbcf.VariantRecord + # The genotype is reset when an empty tuple, None or (None,) is supplied diff --git a/sci-biology/pysam/pysam-0.19.1.ebuild b/sci-biology/pysam/pysam-0.21.0.ebuild index 1164fd6bc091..77292ed29613 100644 --- a/sci-biology/pysam/pysam-0.19.1.ebuild +++ b/sci-biology/pysam/pysam-0.21.0.ebuild @@ -17,20 +17,26 @@ LICENSE="MIT" SLOT="0" KEYWORDS="~amd64 ~x86" -RDEPEND="=sci-libs/htslib-1.15.1*:=" +RDEPEND="=sci-libs/htslib-1.17*:=" DEPEND="${RDEPEND} dev-python/cython[${PYTHON_USEDEP}] dev-python/setuptools[${PYTHON_USEDEP}]" BDEPEND=" test? ( - =sci-biology/bcftools-1.15.1* - =sci-biology/samtools-1.15.1* + =sci-biology/bcftools-1.17* + =sci-biology/samtools-1.17* )" distutils_enable_tests pytest DISTUTILS_IN_SOURCE_BUILD=1 +PATCHES=( + # backport + # https://github.com/pysam-developers/pysam/commit/17bb13dcfdb56ac238458dcef23fe01893a892e9 + "${FILESDIR}"/${P}-cython-3.patch +) + EPYTEST_DESELECT=( # only work with bundled htslib 'tests/tabix_test.py::TestRemoteFileHTTP' diff --git a/sci-biology/pysam/pysam-9999.ebuild b/sci-biology/pysam/pysam-9999.ebuild new file mode 100644 index 000000000000..a162ddf2158b --- /dev/null +++ b/sci-biology/pysam/pysam-9999.ebuild @@ -0,0 +1,72 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{9..11} ) + +inherit distutils-r1 + +if [[ ${PV} == *9999 ]]; then + inherit git-r3 + EGIT_REPO_URI="https://github.com/pysam-developers/pysam.git" +else + SRC_URI="https://github.com/pysam-developers/pysam/archive/v${PV}.tar.gz -> ${P}.gh.tar.gz" + KEYWORDS="~amd64 ~x86" +fi + +DESCRIPTION="Python interface for the SAM/BAM sequence alignment and mapping format" +HOMEPAGE=" + https://github.com/pysam-developers/pysam + https://pypi.org/project/pysam/" + +LICENSE="MIT" +SLOT="0" + +RDEPEND=">=sci-libs/htslib-1.17" +DEPEND="${RDEPEND} + dev-python/cython[${PYTHON_USEDEP}] + dev-python/setuptools[${PYTHON_USEDEP}]" +BDEPEND=" + test? ( + >=sci-biology/bcftools-1.17 + >=sci-biology/samtools-1.17 + )" + +distutils_enable_tests pytest + +DISTUTILS_IN_SOURCE_BUILD=1 + +EPYTEST_DESELECT=( + # only work with bundled htslib + 'tests/tabix_test.py::TestRemoteFileHTTP' + 'tests/tabix_test.py::TestRemoteFileHTTPWithHeader' +) + +python_prepare_all() { + # unbundle htslib + export HTSLIB_MODE="external" + export HTSLIB_INCLUDE_DIR="${ESYSROOT}"/usr/include + export HTSLIB_LIBRARY_DIR="${ESYSROOT}"/usr/$(get_libdir) + rm -r htslib || die + + # prevent setup.py from adding RPATHs (except $ORIGIN) + sed -e '/runtime_library_dirs=htslib_library_dirs/d' \ + -i setup.py || die + + if use test; then + einfo "Building test data" + emake -C tests/pysam_data + emake -C tests/cbcf_data + fi + + distutils-r1_python_prepare_all +} + +python_compile() { + # breaks with parallel build + # need to avoid dropping .so plugins into + # build-lib, which breaks tests + esetup.py build_ext --inplace -j1 + distutils-r1_python_compile -j1 +} diff --git a/sci-biology/rebase/rebase-1901-r2.ebuild b/sci-biology/rebase/rebase-1901-r2.ebuild index 1b4b75407947..a80aee6a3126 100644 --- a/sci-biology/rebase/rebase-1901-r2.ebuild +++ b/sci-biology/rebase/rebase-1901-r2.ebuild @@ -11,7 +11,7 @@ SRC_URI="https://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz" LICENSE="public-domain" SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris ~x86-solaris" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos" IUSE="emboss minimal" RESTRICT="binchecks strip" diff --git a/sci-biology/samtools/Manifest b/sci-biology/samtools/Manifest index 6836d74da51a..72408c9c9544 100644 --- a/sci-biology/samtools/Manifest +++ b/sci-biology/samtools/Manifest @@ -1,3 +1 @@ -DIST samtools-0.1.20.tar.gz 566387 BLAKE2B a62d74c408877754af50f5e5fea0e2289ec1e0c9f25013ed0d039bfe8ef61108600d917f8c9d356e98aca632795b4eb0f01ea1b54526a652577fb74a38a433c2 SHA512 15bd8cf401d14c1ab4faa591b6054f5ea9731c4e966f37f71d33d9081a270cfeb91e8a3d80c631e0725b49da81387f824c206e8c21553ad554d0cfc5c238a6e5 -DIST samtools-1.15.1.tar.bz2 7831692 BLAKE2B 0fe94ff05075b219c77d0da8500c64bdffd53927950b5a67f8708c5c326ebc90a40c193b3bcf0baf3d09baed6fa596d9d024cb529340c6887de88614c9ff4bd6 SHA512 54a8a394b6b5231bd942236ec353027caaf48b4552a00b35573a1e71d680320d8140a73409bb76066c82e86fe62cf74f2f8f2f1a1e4aec96e4e8b9aff0d44a46 -DIST samtools-1.16.1.tar.bz2 8217689 BLAKE2B 51ca62655d1f43dd0c6f9bd38b323b8a9d8f7486ce42496e21186da06ea881d94e096214720f3fb8d1dd12d7a23881bc3b25e27b1a845d56157ac7ffda7130c1 SHA512 f9d6b8652234c782a1b369f028073ad4a66c44e9620ae60f0ecb35e0874f04ca633713078b692fdc1a1cc4f884ebdbf3ecae6881f11fb3b4fd3d27c5b8da67ba +DIST samtools-1.17.tar.bz2 8605080 BLAKE2B 09cb0bff7bf7113a77f57fdb879765b28b65461a574e4a1ab20ae2327af46e5616e04f03eb68706d42ba0643e887d7921974a3d78c5f87d296a4c3b691215260 SHA512 107a6df858c6bd2556ba4e86cc1922c3184df095f347039fa94bfd24e5ee21e1a4a9fba5a7cce248a06ad47f99978d9aae570efee7e30e165f33ea848a2cd3c3 diff --git a/sci-biology/samtools/files/samtools-0.1.20-buildsystem.patch b/sci-biology/samtools/files/samtools-0.1.20-buildsystem.patch deleted file mode 100644 index eb9f6934a96f..000000000000 --- a/sci-biology/samtools/files/samtools-0.1.20-buildsystem.patch +++ /dev/null @@ -1,206 +0,0 @@ ---- samtools-0.1.20/bcftools/Makefile -+++ samtools-0.1.20/bcftools/Makefile -@@ -1,6 +1,6 @@ --CC= gcc --CFLAGS= -g -Wall -O2 #-m64 #-arch ppc --DFLAGS= -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -+CC?= gcc -+CFLAGS?= -g -Wall -O2 #-m64 #-arch ppc -+CPPFLAGS+= -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE - LOBJS= bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o - OMISC= .. - AOBJS= call1.o main.o $(OMISC)/kstring.o $(OMISC)/bgzf.o $(OMISC)/knetfile.o $(OMISC)/bedidx.o -@@ -11,14 +11,14 @@ - .SUFFIXES:.c .o - - .c.o: -- $(CC) -c $(CFLAGS) $(DFLAGS) -I.. $(INCLUDES) $< -o $@ -+ $(CC) -c $(CFLAGS) $(CPPFLAGS) -I.. $(INCLUDES) $< -o $@ - - all-recur lib-recur clean-recur cleanlocal-recur install-recur: - @target=`echo $@ | sed s/-recur//`; \ - wdir=`pwd`; \ - list='$(SUBDIRS)'; for subdir in $$list; do \ - cd $$subdir; \ -- $(MAKE) CC="$(CC)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \ -+ $(MAKE) CC="$(CC)" CPPFLAGS="$(CPPFLAGS)" CFLAGS="$(CFLAGS)" \ - INCLUDES="$(INCLUDES)" LIBPATH="$(LIBPATH)" $$target || exit 1; \ - cd $$wdir; \ - done; -@@ -31,7 +31,7 @@ - $(AR) -csru $@ $(LOBJS) - - bcftools:lib $(AOBJS) -- $(CC) $(CFLAGS) -o $@ $(AOBJS) -L. $(LIBPATH) -lbcf -lm -lz -lpthread -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(AOBJS) -L. $(LIBPATH) -lbcf -lm -lz -lpthread - - bcf.o:bcf.h - vcf.o:bcf.h ---- samtools-0.1.20/Makefile -+++ samtools-0.1.20/Makefile -@@ -4,10 +4,10 @@ - # make git-stamp - VERSION= - --CC= gcc --CFLAGS= -g -Wall $(VERSION) -O2 --#LDFLAGS= -Wl,-rpath,\$$ORIGIN/../lib --DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -+CC?= gcc -+CFLAGS?= -g -Wall $(VERSION) -O2 -+#LDFLAGS+= -Wl,-rpath,\$$ORIGIN/../lib -+CPPFLAGS+= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 - KNETFILE_O= knetfile.o - LOBJS= bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o \ - bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o \ -@@ -28,14 +28,14 @@ - .PHONY: all lib - - .c.o: -- $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@ -+ $(CC) -c $(CFLAGS) $(CPPFLAGS) $(INCLUDES) $< -o $@ - - all-recur lib-recur clean-recur cleanlocal-recur install-recur: - @target=`echo $@ | sed s/-recur//`; \ - wdir=`pwd`; \ - list='$(SUBDIRS)'; for subdir in $$list; do \ - cd $$subdir; \ -- $(MAKE) CC="$(CC)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \ -+ $(MAKE) CC="$(CC)" CPPFLAGS="$(CPPFLAGS)" CFLAGS="$(CFLAGS)" \ - INCLUDES="$(INCLUDES)" LIBPATH="$(LIBPATH)" $$target || exit 1; \ - cd $$wdir; \ - done; -@@ -48,22 +48,22 @@ - .PHONY:all lib clean cleanlocal - .PHONY:all-recur lib-recur clean-recur cleanlocal-recur install-recur - --lib:libbam.a -+lib:libbam-0.1-legacy.a - --libbam.a:$(LOBJS) -+libbam-0.1-legacy.a:$(LOBJS) - $(AR) -csru $@ $(LOBJS) - - samtools:lib-recur $(AOBJS) -- $(CC) $(CFLAGS) -o $@ $(AOBJS) $(LDFLAGS) libbam.a -Lbcftools -lbcf $(LIBPATH) $(LIBCURSES) -lm -lz -lpthread -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(AOBJS) -L. -lbam-0.1-legacy -Lbcftools -lbcf $(LIBPATH) $(LIBCURSES) -lm -lz -lpthread - - razip:razip.o razf.o $(KNETFILE_O) -- $(CC) $(CFLAGS) -o $@ $^ -lz -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $^ -lz - - bgzip:bgzip.o bgzf.o $(KNETFILE_O) -- $(CC) $(CFLAGS) -o $@ $^ -lz -lpthread -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $^ -lz -lpthread - - bgzf.o:bgzf.c bgzf.h -- $(CC) -c $(CFLAGS) $(DFLAGS) -DBGZF_CACHE $(INCLUDES) bgzf.c -o $@ -+ $(CC) -c $(CFLAGS) $(CPPFLAGS) -DBGZF_CACHE $(INCLUDES) bgzf.c -o $@ - - razip.o:razf.h - bam.o:bam.h razf.h bam_endian.h kstring.h sam_header.h -@@ -90,17 +90,17 @@ - faidx_main.o:faidx.h razf.h - - --libbam.1.dylib-local:$(LOBJS) -- libtool -dynamic $(LOBJS) -o libbam.1.dylib -lc -lz -+libbam-0.1-legacy.1.dylib-local:$(LOBJS) -+ libtool -dynamic $(LOBJS) -o libbam-0.1-legacy.1.dylib -lc -lz - --libbam.so.1-local:$(LOBJS) -- $(CC) -shared -Wl,-soname,libbam.so -o libbam.so.1 $(LOBJS) -lc -lz -+libbam-0.1-legacy.so.1-local:$(LOBJS) -+ $(CC) $(LDFLAGS) -shared -Wl,-soname,libbam-0.1-legacy.so -o libbam-0.1-legacy.so.1 $(LOBJS) -lc -lz -lm -lpthread - - dylib: - @$(MAKE) cleanlocal; \ - case `uname` in \ -- Linux) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" libbam.so.1-local;; \ -- Darwin) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" libbam.1.dylib-local;; \ -+ Linux) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" libbam-0.1-legacy.so.1-local;; \ -+ Darwin) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" libbam-0.1-legacy.1.dylib-local;; \ - *) echo 'Unknown OS';; \ - esac - ---- samtools-0.1.20/misc/Makefile -+++ samtools-0.1.20/misc/Makefile -@@ -1,8 +1,8 @@ --CC= gcc --CXX= g++ --CFLAGS= -g -Wall -O2 #-m64 #-arch ppc --CXXFLAGS= $(CFLAGS) --DFLAGS= -D_FILE_OFFSET_BITS=64 -+CC?= gcc -+CXX?= g++ -+CFLAGS?= -g -Wall -O2 #-m64 #-arch ppc -+CXXFLAGS?= $(CFLAGS) -+CPPFLAGS+= -D_FILE_OFFSET_BITS=64 - OBJS= - PROG= md5sum-lite md5fa maq2sam-short maq2sam-long ace2sam wgsim bamcheck - INCLUDES= -I.. -@@ -11,7 +11,7 @@ - .SUFFIXES:.c .o - - .c.o: -- $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@ -+ $(CC) -c $(CFLAGS) $(CPPFLAGS) $(INCLUDES) $< -o $@ - - all:$(PROG) - -@@ -20,7 +20,7 @@ - wdir=`pwd`; \ - list='$(SUBDIRS)'; for subdir in $$list; do \ - cd $$subdir; \ -- $(MAKE) CC="$(CC)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \ -+ $(MAKE) CC="$(CC)" CPPFLAGS="$(CPPFLAGS)" CFLAGS="$(CFLAGS)" \ - INCLUDES="$(INCLUDES)" $$target || exit 1; \ - cd $$wdir; \ - done; -@@ -28,31 +28,31 @@ - lib: - - bamcheck:bamcheck.o -- $(CC) $(CFLAGS) -o $@ bamcheck.o -L.. -lm -lbam -lpthread -lz -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ bamcheck.o -L.. -lm -lbam-0.1-legacy -lpthread -lz - - bamcheck.o:bamcheck.c ../faidx.h ../khash.h ../sam.h ../razf.h - $(CC) $(CFLAGS) -c -I.. -o $@ bamcheck.c - - ace2sam:ace2sam.o -- $(CC) $(CFLAGS) -o $@ ace2sam.o -lz -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ ace2sam.o -lz - - wgsim:wgsim.o -- $(CC) $(CFLAGS) -o $@ wgsim.o -lm -lz -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ wgsim.o -lm -lz - - md5fa:md5.o md5fa.o md5.h ../kseq.h -- $(CC) $(CFLAGS) -o $@ md5.o md5fa.o -lz -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ md5.o md5fa.o -lz - - md5sum-lite:md5sum-lite.o -- $(CC) $(CFLAGS) -o $@ md5sum-lite.o -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ md5sum-lite.o - - md5sum-lite.o:md5.c md5.h - $(CC) -c $(CFLAGS) -DMD5SUM_MAIN -o $@ md5.c - - maq2sam-short:maq2sam.c -- $(CC) $(CFLAGS) -o $@ maq2sam.c -lz -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ maq2sam.c -lz - - maq2sam-long:maq2sam.c -- $(CC) $(CFLAGS) -DMAQ_LONGREADS -o $@ maq2sam.c -lz -+ $(CC) $(CFLAGS) -DMAQ_LONGREADS $(LDFLAGS) -o $@ maq2sam.c -lz - - md5fa.o:md5.h md5fa.c - $(CC) $(CFLAGS) -c -I.. -o $@ md5fa.c ---- samtools-0.1.20/misc/varfilter.py -+++ samtools-0.1.20/misc/varfilter.py -@@ -1,4 +1,4 @@ --#!/software/bin/python -+#!/usr/bin/env python - - # Author: lh3, converted to python and modified to add -C option by Aylwyn Scally - # diff --git a/sci-biology/samtools/samtools-0.1.20-r4.ebuild b/sci-biology/samtools/samtools-0.1.20-r4.ebuild deleted file mode 100644 index f4b779aa838b..000000000000 --- a/sci-biology/samtools/samtools-0.1.20-r4.ebuild +++ /dev/null @@ -1,73 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit multilib toolchain-funcs - -DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment formats" -HOMEPAGE="http://samtools.sourceforge.net/" -SRC_URI="https://github.com/samtools/samtools/archive/${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="MIT" -SLOT="0.1-legacy" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos" - -RDEPEND=" - sys-libs/ncurses:0= - dev-lang/perl" -DEPEND="${RDEPEND}" -BDEPEND="virtual/pkgconfig" - -PATCHES=( "${FILESDIR}"/${P}-buildsystem.patch ) - -src_prepare() { - default - tc-export CC AR -} - -src_compile() { - local _ncurses="$($(tc-getPKG_CONFIG) --libs ncurses)" - emake dylib LIBCURSES="${_ncurses}" - emake LIBCURSES="${_ncurses}" -} - -src_install() { - # install executables and hide them away from sight - dobin samtools bcftools/{bcftools,vcfutils.pl} misc/{*.py,*.pl,wgsim,ace2sam} \ - misc/{md5sum-lite,maq2sam-short,bamcheck,maq2sam-long,md5fa,plot-bamcheck} - mv "${ED}"/usr/{bin,${PN}-${SLOT}} || die - mkdir "${ED}"/usr/bin || die - mv "${ED}"/usr/{${PN}-${SLOT},bin/} || die - - # remove py2 script, has been removed upstream anyways - # https://github.com/samtools/samtools/issues/1125 - rm "${ED}"/usr/bin/${PN}-${SLOT}/varfilter.py || die - - # fix perl shebangs - pushd "${ED}"/usr/bin/${PN}-${SLOT} >/dev/null || die - local i - for i in plot-bamcheck *.pl; do - sed -e '1s:.*:#!/usr/bin/env perl:' -i "${i}" || die - done - popd >/dev/null || die - - dolib.so libbam-${SLOT}$(get_libname 1) - dosym libbam-${SLOT}$(get_libname 1) /usr/$(get_libdir)/libbam-${SLOT}$(get_libname) - - insinto /usr/include/bam-${SLOT} - doins *.h - - mv ${PN}{,-${SLOT}}.1 || die - doman ${PN}-${SLOT}.1 - einstalldocs - - dodoc -r examples - docompress -x /usr/share/doc/${PF}/examples -} - -pkg_postinst() { - elog "This version of samtools should *not* be your first choice for working" - elog "with NGS data. It is installed solely for programs requiring it." - elog "It is recommended that you use >=sci-biology/samtools-1.10." -} diff --git a/sci-biology/samtools/samtools-1.15.1.ebuild b/sci-biology/samtools/samtools-1.15.1.ebuild deleted file mode 100644 index 21d2b8a5077d..000000000000 --- a/sci-biology/samtools/samtools-1.15.1.ebuild +++ /dev/null @@ -1,47 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -inherit toolchain-funcs - -DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment formats" -HOMEPAGE="http://www.htslib.org/" -SRC_URI="https://github.com/samtools/${PN}/releases/download/${PV}/${P}.tar.bz2" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos" - -RDEPEND=" - dev-lang/perl - =sci-libs/htslib-${PV}*:= - sys-libs/ncurses:=[unicode(+)] - sys-libs/zlib" -DEPEND="${RDEPEND}" -BDEPEND="virtual/pkgconfig" - -src_prepare() { - default - - # remove bundled htslib - rm -r htslib-* || die -} - -src_configure() { - econf \ - --with-ncurses \ - --with-htslib=system \ - CURSES_LIB="$($(tc-getPKG_CONFIG) --libs ncursesw || die)" -} - -src_compile() { - emake AR="$(tc-getAR)" -} - -src_install() { - default - - dodoc -r examples - docompress -x /usr/share/doc/${PF}/examples -} diff --git a/sci-biology/samtools/samtools-1.16.1.ebuild b/sci-biology/samtools/samtools-1.17.ebuild index 8047657df992..e105621c7865 100644 --- a/sci-biology/samtools/samtools-1.16.1.ebuild +++ b/sci-biology/samtools/samtools-1.17.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2022 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 |