diff options
Diffstat (limited to 'sci-biology')
58 files changed, 316 insertions, 673 deletions
diff --git a/sci-biology/augustus/augustus-2.5.5.ebuild b/sci-biology/augustus/augustus-2.5.5.ebuild index 5bf36e85cb9b..ed345330c4a7 100644 --- a/sci-biology/augustus/augustus-2.5.5.ebuild +++ b/sci-biology/augustus/augustus-2.5.5.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2019 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=7 @@ -11,7 +11,7 @@ SRC_URI="http://augustus.gobics.de/binaries/${PN}.${PV}.tar.gz" LICENSE="Artistic" SLOT="0" -KEYWORDS="amd64 x86" +KEYWORDS="amd64 ~x86" IUSE="examples" S="${WORKDIR}/${PN}.${PV}" diff --git a/sci-biology/bcftools/Manifest b/sci-biology/bcftools/Manifest index 8d5aa1eec079..0f3c24a476a9 100644 --- a/sci-biology/bcftools/Manifest +++ b/sci-biology/bcftools/Manifest @@ -1,2 +1 @@ -DIST bcftools-1.16.tar.bz2 7325862 BLAKE2B 0e1240448d4efb352d3d0cd83decd286f7544fff3676f0a5cca51dec9c445c47c37ac24a3317aa7b41182c576e7e57dba460fc98aca069dc2f8fe0625c0b0f06 SHA512 998d5ac941f73798c35dd1db7ac7aba9067f275bd3055728aabfd8edd9f40484130df1fb57621d1a762a57b28ffcac358570915c341d420ae6f12bd17f7651a3 DIST bcftools-1.17.tar.bz2 7538043 BLAKE2B 82f65d53ebea0527ff000329f158ebdb1d603e04841a096cf8ca0434e7a5694ab43da7959ee10e9cb29328bf82301c03200e1203578a74e2e1118856b2641502 SHA512 39ae44a682e626a5261900e9412170a269e460b559d6607db697e6a12b1e512ffb3bdeb3486413e19b8adca26a8ccbb2bd4af24459decb74592c54473d2c6a68 diff --git a/sci-biology/bcftools/bcftools-1.16.ebuild b/sci-biology/bcftools/bcftools-1.16.ebuild deleted file mode 100644 index 6adee705bb46..000000000000 --- a/sci-biology/bcftools/bcftools-1.16.ebuild +++ /dev/null @@ -1,42 +0,0 @@ -# Copyright 1999-2023 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{9..11} ) - -inherit python-single-r1 - -DESCRIPTION="Utilities for variant calling and manipulating VCF and BCF files" -HOMEPAGE="http://www.htslib.org" -SRC_URI="https://github.com/samtools/${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-$(ver_cut 1-2)*:= - sys-libs/zlib - ${PYTHON_DEPS}" -DEPEND="${RDEPEND}" -BDEPEND="${PYTHON_DEPS}" - -src_prepare() { - default - - python_fix_shebang misc/{gff2gff,guess-ploidy,plot-roh}.py - - # remove bundled htslib - rm -r htslib-* || die -} - -src_configure() { - econf \ - --disable-bcftools-plugins \ - --disable-libgsl \ - --with-htslib=system -} diff --git a/sci-biology/bedtools/bedtools-2.30.0.ebuild b/sci-biology/bedtools/bedtools-2.30.0.ebuild index 5a8174fbdfe0..b86b87e72dc4 100644 --- a/sci-biology/bedtools/bedtools-2.30.0.ebuild +++ b/sci-biology/bedtools/bedtools-2.30.0.ebuild @@ -34,6 +34,7 @@ BDEPEND=" PATCHES=( "${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 336fb1afefa4..1a153471c26b 100644 --- a/sci-biology/biopandas/Manifest +++ b/sci-biology/biopandas/Manifest @@ -1,2 +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/bioperl-db/bioperl-db-1.6.9-r2.ebuild b/sci-biology/bioperl-db/bioperl-db-1.6.9-r2.ebuild index 6359865b90e0..435dc4a67173 100644 --- a/sci-biology/bioperl-db/bioperl-db-1.6.9-r2.ebuild +++ b/sci-biology/bioperl-db/bioperl-db-1.6.9-r2.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 @@ -15,7 +15,7 @@ DESCRIPTION="Perl tools for bioinformatics - Perl API that accesses the BioSQL s HOMEPAGE="http://www.bioperl.org/" SLOT="0" -KEYWORDS="amd64 x86" +KEYWORDS="amd64 ~x86" IUSE="test" RESTRICT="test" diff --git a/sci-biology/bioperl-network/bioperl-network-1.6.9-r1.ebuild b/sci-biology/bioperl-network/bioperl-network-1.6.9-r1.ebuild index 513429a9e292..fc51a12da036 100644 --- a/sci-biology/bioperl-network/bioperl-network-1.6.9-r1.ebuild +++ b/sci-biology/bioperl-network/bioperl-network-1.6.9-r1.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 @@ -14,7 +14,7 @@ DESCRIPTION="Perl tools for bioinformatics - Analysis of protein-protein interac HOMEPAGE="http://www.bioperl.org/" SLOT="0" -KEYWORDS="amd64 x86" +KEYWORDS="amd64 ~x86" RESTRICT="test" # bug 298326 RDEPEND=" diff --git a/sci-biology/bioperl-run/bioperl-run-1.6.9-r1.ebuild b/sci-biology/bioperl-run/bioperl-run-1.6.9-r1.ebuild index 2541aab82506..9c32c7eaa5f7 100644 --- a/sci-biology/bioperl-run/bioperl-run-1.6.9-r1.ebuild +++ b/sci-biology/bioperl-run/bioperl-run-1.6.9-r1.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 @@ -14,7 +14,7 @@ DESCRIPTION="Perl wrapper modules for key bioinformatics applications" HOMEPAGE="http://www.bioperl.org/" SLOT="0" -KEYWORDS="amd64 x86" +KEYWORDS="amd64 ~x86" IUSE="minimal test" RESTRICT="test" diff --git a/sci-biology/bioperl/bioperl-1.6.9-r1.ebuild b/sci-biology/bioperl/bioperl-1.6.9-r1.ebuild index 2896271e137a..a692fe812401 100644 --- a/sci-biology/bioperl/bioperl-1.6.9-r1.ebuild +++ b/sci-biology/bioperl/bioperl-1.6.9-r1.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 @@ -15,7 +15,7 @@ DESCRIPTION="Perl tools for bioinformatics - Core modules" HOMEPAGE="http://www.bioperl.org/" SLOT="0" -KEYWORDS="amd64 x86" +KEYWORDS="amd64 ~x86" IUSE="minimal graphviz sqlite ${SUBPROJECTS}" REQUIRED_USE="minimal? ( !graphviz )" diff --git a/sci-biology/biopython/Manifest b/sci-biology/biopython/Manifest index c693a5a8a963..0c16022dea2c 100644 --- a/sci-biology/biopython/Manifest +++ b/sci-biology/biopython/Manifest @@ -1,2 +1 @@ -DIST biopython-1.79.tar.gz 16738730 BLAKE2B 8c97fc23e458f7bc98b0ed0226bd6fb42f6c6f3ce03d562b13fac66c5061451595cd5bd01cad07bbe1fc6b20f4de21b0f03766b5a20e602545da888047a57185 SHA512 81e2718f4015bb038637b4d1181e6bea48018fec1e769c5f0ab75442a769336899191f1222e82e1b9569c1fac470500d7582420e5cbe9bce0056b41751adeaaa DIST biopython-1.81.tar.gz 19324875 BLAKE2B be3a85f5b60638987d6186af498411b494f8d27389f24cd1b9e658bc6b1a29c799ec8b20a9ac0b955c6d4c239706f4dbb5b75f6d56908f63d731b1d56c9fd587 SHA512 1595fad6631bfb6cf4e1a92ed72e6093e2a0c24f3c0bd4182267ec9742fb03dff16099eedde139598aa6b5b8380bbac9e48246cb9ab8b44109333d60adfd00ed diff --git a/sci-biology/biopython/biopython-1.79.ebuild b/sci-biology/biopython/biopython-1.79.ebuild deleted file mode 100644 index c6a93b3af58d..000000000000 --- a/sci-biology/biopython/biopython-1.79.ebuild +++ /dev/null @@ -1,62 +0,0 @@ -# Copyright 1999-2023 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{9..10} ) - -inherit distutils-r1 optfeature - -DESCRIPTION="Python modules for computational molecular biology" -HOMEPAGE="https://www.biopython.org/ https://pypi.org/project/biopython/" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -LICENSE="HPND" -SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" - -RDEPEND=" - dev-python/matplotlib[${PYTHON_USEDEP}] - dev-python/networkx[${PYTHON_USEDEP}] - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/rdflib[${PYTHON_USEDEP}] - dev-python/pygraphviz[${PYTHON_USEDEP}] - >=dev-python/reportlab-3.5.13-r1[${PYTHON_USEDEP}] - dev-python/pydot[${PYTHON_USEDEP}]" -DEPEND="${RDEPEND}" -BDEPEND="sys-devel/flex" - -DOCS=( {CONTRIB,DEPRECATED,NEWS,README}.rst Doc/. ) - -python_test() { - distutils_install_for_testing - cp -r {Doc,Tests} "${TEST_DIR}"/lib/ || die - - # need to create symlinks for doctests - mkdir -p "${TEST_DIR}"/lib/Bio/Align || die - ln -r -s "${S}"/Bio/Align/substitution_matrices \ - "${TEST_DIR}"/lib/Bio/Align/substitution_matrices || die - - cd "${TEST_DIR}"/lib/Tests || die - rm test_BioSQL_{psycopg2.py,MySQLdb.py,mysql_connector.py} || die - "${EPYTHON}" run_tests.py --offline --verbose || die -} - -python_install_all() { - # remove files causing ecompressdir to fail - rm Doc/examples/ls_orchid.gbk.{gz,bz2} || die - - distutils-r1_python_install_all - - dodir /usr/share/${PN} - cp -r --preserve=mode Scripts Tests "${ED}"/usr/share/${PN} || die -} - -pkg_postinst() { - optfeature_header "For database support you need to install:" - optfeature "MySQL database support" dev-python/mysqlclient - optfeature "PostgreSQL database support" dev-python/psycopg:2 - - optfeature_header "Some applications need extra packages:" - optfeature "EMBOSS (The European Molecular Biology Open Software Suite)" sci-biology/emboss -} diff --git a/sci-biology/biopython/biopython-1.81.ebuild b/sci-biology/biopython/biopython-1.81-r1.ebuild index 8b90d610c6ae..115a4d3b1a4c 100644 --- a/sci-biology/biopython/biopython-1.81.ebuild +++ b/sci-biology/biopython/biopython-1.81-r1.ebuild @@ -4,6 +4,8 @@ EAPI=8 PYTHON_COMPAT=( python3_{9..11} ) +DISTUTILS_USE_PEP517="setuptools" +DISTUTILS_EXT=1 inherit distutils-r1 optfeature pypi @@ -27,17 +29,13 @@ BDEPEND="sys-devel/flex" DOCS=( {CONTRIB,DEPRECATED,NEWS,README}.rst Doc/. ) -python_test() { - distutils_install_for_testing - cp -r {Doc,Tests} "${TEST_DIR}"/lib/ || die - - # need to create symlinks for doctests - mkdir -p "${TEST_DIR}"/lib/Bio/Align || die - ln -r -s "${S}"/Bio/Align/substitution_matrices \ - "${TEST_DIR}"/lib/Bio/Align/substitution_matrices || die +PATCHES=( + "${FILESDIR}/${P}-reportlab4.patch" + "${FILESDIR}/${P}-python3.12.patch" +) - cd "${TEST_DIR}"/lib/Tests || die - rm test_BioSQL_{psycopg2.py,MySQLdb.py,mysql_connector.py} || die +python_test() { + cd Tests || die "${EPYTHON}" run_tests.py --offline --verbose || die } diff --git a/sci-biology/biopython/files/biopython-1.81-python3.12.patch b/sci-biology/biopython/files/biopython-1.81-python3.12.patch new file mode 100644 index 000000000000..8f903a4a39bd --- /dev/null +++ b/sci-biology/biopython/files/biopython-1.81-python3.12.patch @@ -0,0 +1,11 @@ +--- a/Tests/test_Entrez.orig.py 2023-02-13 04:07:42.000000000 +0100 ++++ b/Tests/test_Entrez.py 2023-06-30 14:42:58.177365639 +0200 +@@ -126,7 +126,7 @@ + :type params: dict + :param expected: Expected set of IDs, as colleciton of strings. + """ +- testcase.assertEquals(len(params["id"]), 1) ++ testcase.assertEqual(len(params["id"]), 1) + ids_str = params["id"][0] + # Compare up to ordering + testcase.assertCountEqual(ids_str.split(","), expected) diff --git a/sci-biology/biopython/files/biopython-1.81-reportlab4.patch b/sci-biology/biopython/files/biopython-1.81-reportlab4.patch new file mode 100644 index 000000000000..ef1994553614 --- /dev/null +++ b/sci-biology/biopython/files/biopython-1.81-reportlab4.patch @@ -0,0 +1,29 @@ +From 74fdf49ade95157c3c4b23a95831925be4899223 Mon Sep 17 00:00:00 2001 +From: Peter Cock <p.j.a.cock@googlemail.com> +Date: Mon, 5 Jun 2023 12:39:59 +0100 +Subject: [PATCH] Skip if ReportLab bitmap output module missing + +Would like to skip this earlier, but not so +easy in ReportLab v4 with a choice of backends +--- + Tests/test_GraphicsBitmaps.py | 5 ++++- + 1 file changed, 4 insertions(+), 1 deletion(-) + +diff --git a/Tests/test_GraphicsBitmaps.py b/Tests/test_GraphicsBitmaps.py +index 2ffdfb3dd71..76615a2fd1d 100644 +--- a/Tests/test_GraphicsBitmaps.py ++++ b/Tests/test_GraphicsBitmaps.py +@@ -111,9 +111,12 @@ def real_test(): + "Check the fonts needed by ReportLab if you want " + "bitmaps from Bio.Graphics\n" + str(err) + ) from None ++ elif str(err).startswith("cannot import desired renderPM backend rlPyCairo"): ++ raise MissingExternalDependencyError( ++ "Reportlab module rlPyCairo unavailable\n" + str(err) ++ ) from None + else: + raise +- + return True + + diff --git a/sci-biology/biosql/biosql-1.0.1-r2.ebuild b/sci-biology/biosql/biosql-1.0.1-r2.ebuild index fd42d5e58a9a..838f3b443ed8 100644 --- a/sci-biology/biosql/biosql-1.0.1-r2.ebuild +++ b/sci-biology/biosql/biosql-1.0.1-r2.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 @@ -9,7 +9,7 @@ SRC_URI="https://biosql.org/DIST/${P}.tar.bz2" LICENSE="LGPL-3" SLOT="0" -KEYWORDS="amd64 x86" +KEYWORDS="amd64 ~x86" IUSE="mysql postgres" # WARNING: bioperl-db is claimed to be incompatible with >=postgresql-8.3 (see INSTALL) diff --git a/sci-biology/clustal-omega/clustal-omega-1.2.4-r1.ebuild b/sci-biology/clustal-omega/clustal-omega-1.2.4-r1.ebuild index 2a4a2c108fed..4d5b2a779bf9 100644 --- a/sci-biology/clustal-omega/clustal-omega-1.2.4-r1.ebuild +++ b/sci-biology/clustal-omega/clustal-omega-1.2.4-r1.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 @@ -11,7 +11,7 @@ SRC_URI="http://www.clustal.org/omega/${P}.tar.gz" LICENSE="GPL-2" SLOT="0" -KEYWORDS="amd64 x86" +KEYWORDS="amd64 ~x86" DEPEND="dev-libs/argtable" RDEPEND="${DEPEND}" diff --git a/sci-biology/clustalw/clustalw-1.83-r4.ebuild b/sci-biology/clustalw/clustalw-1.83-r4.ebuild index 62c59747adf3..23c4ba9a3229 100644 --- a/sci-biology/clustalw/clustalw-1.83-r4.ebuild +++ b/sci-biology/clustalw/clustalw-1.83-r4.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 @@ -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}"/${PV}-as-needed.patch diff --git a/sci-biology/clustalw/clustalw-2.1-r2.ebuild b/sci-biology/clustalw/clustalw-2.1-r2.ebuild index 58a28e3ef7a5..16a957f6c636 100644 --- a/sci-biology/clustalw/clustalw-2.1-r2.ebuild +++ b/sci-biology/clustalw/clustalw-2.1-r2.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2022 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 @@ -9,7 +9,7 @@ SRC_URI="http://www.clustal.org/download/current/${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/clustalx/clustalx-2.1-r3.ebuild b/sci-biology/clustalx/clustalx-2.1-r3.ebuild index bd9b57aabe79..fa956bd186e8 100644 --- a/sci-biology/clustalx/clustalx-2.1-r3.ebuild +++ b/sci-biology/clustalx/clustalx-2.1-r3.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2020 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=7 @@ -13,7 +13,7 @@ SRC_URI=" LICENSE="GPL-3 LGPL-3" SLOT="0" -KEYWORDS="amd64 x86" +KEYWORDS="amd64 ~x86" IUSE="" DEPEND=" diff --git a/sci-biology/elph/elph-1.0.1-r2.ebuild b/sci-biology/elph/elph-1.0.1-r3.ebuild index 66309522b312..6cfc05845358 100644 --- a/sci-biology/elph/elph-1.0.1-r2.ebuild +++ b/sci-biology/elph/elph-1.0.1-r3.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 @@ -14,7 +14,10 @@ LICENSE="Artistic" SLOT="0" KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos" -PATCHES=( "${FILESDIR}"/${PN}-1.0.1-fix-build-system.patch ) +PATCHES=( + "${FILESDIR}"/${PN}-1.0.1-fix-build-system.patch + "${FILESDIR}"/${PN}-1.0.1-drop-register-keyword.patch +) src_configure() { tc-export CC CXX diff --git a/sci-biology/elph/files/elph-1.0.1-drop-register-keyword.patch b/sci-biology/elph/files/elph-1.0.1-drop-register-keyword.patch new file mode 100644 index 000000000000..c05a280d4679 --- /dev/null +++ b/sci-biology/elph/files/elph-1.0.1-drop-register-keyword.patch @@ -0,0 +1,102 @@ +Bug: https://bugs.gentoo.org/898116 + +--- a/GBase.cpp ++++ b/GBase.cpp +@@ -208,8 +208,8 @@ char* rstrstr(char* rstart, char *lend, char* substr) { /*like strstr, but star + + //hash function used for strings in GHash + int strhash(const char* str){ +- register int h=0; +- register int g; ++ int h=0; ++ int g; + while (*str) { + h=(h<<4)+*str++; + g=h&0xF0000000; +--- a/GString.cpp ++++ b/GString.cpp +@@ -364,8 +364,8 @@ GString& GString::appendfmt(const char *fmt,...) { + } + + GString& GString::trim(char c) { +- register int istart; +- register int iend; ++ int istart; ++ int iend; + for (istart=0; istart<length() && chars()[istart]==c;istart++); + if (istart==length()) { + make_unique(); //edit operation ahead +@@ -384,8 +384,8 @@ GString& GString::trim(char c) { + } + + GString& GString::trim(char* c) { +- register int istart; +- register int iend; ++ int istart; ++ int iend; + for (istart=0; istart<length() && strchr(c, chars()[istart])!=NULL ;istart++); + if (istart==length()) { + replace_data(0); //string was entirely trimmed +@@ -405,7 +405,7 @@ GString& GString::trim(char* c) { + GString& GString::trimR(char c) { + //only trim the right end + //register int istart; +- register int iend; ++ int iend; + for (iend=length()-1; iend>=0 && chars()[iend]==c;iend--); + if (iend==-1) { + replace_data(0); //string was entirely trimmed +@@ -423,7 +423,7 @@ GString& GString::trimR(char c) { + } + + GString& GString::trimR(char* c) { +- register int iend; ++ int iend; + for (iend=length()-1; iend>=0 && strchr(c,chars()[iend])!=NULL;iend--); + if (iend==-1) { + replace_data(0); //string was entirely trimmed +@@ -440,7 +440,7 @@ GString& GString::trimR(char* c) { + } + + GString& GString::trimL(char c) { +- register int istart; ++ int istart; + for (istart=0; istart<length() && chars()[istart]==c;istart++); + if (istart==length()) { + replace_data(0); //string was entirely trimmed +@@ -457,7 +457,7 @@ GString& GString::trimL(char c) { + } + + GString& GString::trimL(char* c) { +- register int istart; ++ int istart; + for (istart=0; istart<length() && strchr(c,chars()[istart])!=NULL;istart++); + if (istart==length()) { + replace_data(0); //string was entirely trimmed +@@ -598,7 +598,7 @@ bool GString::is_space() const { + if (my_data == &null_data) + return false; + +- for (register const char *p = chars(); *p; p++) ++ for (const char *p = chars(); *p; p++) + if (!isspace(*p)) + return false; + +@@ -889,7 +889,7 @@ GString& GString::append(const GString& s) { + + GString& GString::upper() { + make_unique(); //edit operation ahead +- for (register char *p = chrs(); *p; p++) ++ for (char *p = chrs(); *p; p++) + *p = (char) toupper(*p); + + return *this; +@@ -900,7 +900,7 @@ GString& GString::upper() { + GString& GString::lower() { + make_unique(); + +- for (register char *p = chrs(); *p; p++) ++ for (char *p = chrs(); *p; p++) + *p = (char) tolower(*p); + + return *this; diff --git a/sci-biology/eugene/eugene-4.1d-r1.ebuild b/sci-biology/eugene/eugene-4.1d-r1.ebuild index 40fb83ffc058..3800d7a2bdc3 100644 --- a/sci-biology/eugene/eugene-4.1d-r1.ebuild +++ b/sci-biology/eugene/eugene-4.1d-r1.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 @@ -11,7 +11,7 @@ SRC_URI="https://mulcyber.toulouse.inra.fr/frs/download.php/1359/${P}.tar.gz" LICENSE="Artistic" SLOT="0" -KEYWORDS="amd64 x86" +KEYWORDS="amd64 ~x86" RESTRICT="test" DEPEND=" diff --git a/sci-biology/express/Manifest b/sci-biology/express/Manifest deleted file mode 100644 index 9c2cc4ebf499..000000000000 --- a/sci-biology/express/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST express-1.5.1-src.tgz 931166 BLAKE2B 5eb185e4b001f26f0dd32885b256b9fa48c89f546d67d7f8472cade69dde25375a5fc8efed5f01b615d63b641b674f7034a13f9483eb7967a6fd784a55c8878e SHA512 59cf6511a879311247c65334285ea056d571d4fd950aa6243041fa10075ff0d1ddd2afbcfe12e5f7f3e7cdd22fe37fd7f6b43ed4a8eb28d7a33d72366dc549ee diff --git a/sci-biology/express/express-1.5.1.ebuild b/sci-biology/express/express-1.5.1.ebuild deleted file mode 100644 index 9511236b69f6..000000000000 --- a/sci-biology/express/express-1.5.1.ebuild +++ /dev/null @@ -1,38 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit cmake - -DESCRIPTION="Streaming RNA-Seq Analysis" -HOMEPAGE="https://pachterlab.github.io/eXpress/" -SRC_URI="https://pachterlab.github.io/eXpress/downloads/${P}/${P}-src.tgz" - -LICENSE="Artistic" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -DEPEND=" - dev-libs/boost:= - dev-libs/protobuf - dev-util/google-perftools - sci-biology/bamtools - sys-libs/zlib -" -RDEPEND="${DEPEND}" - -S="${WORKDIR}/${P}-src" - -PATCHES=( - "${FILESDIR}"/${P}-buildsystem.patch - "${FILESDIR}"/${P}-gcc6.patch -) - -src_configure() { - local mycmakeargs=( - -DBAMTOOLS_INCLUDE="${EPREFIX}/usr/include/bamtools" - ) - cmake_src_configure -} diff --git a/sci-biology/express/files/express-1.5.1-buildsystem.patch b/sci-biology/express/files/express-1.5.1-buildsystem.patch deleted file mode 100644 index fca5feadd111..000000000000 --- a/sci-biology/express/files/express-1.5.1-buildsystem.patch +++ /dev/null @@ -1,55 +0,0 @@ - CMakeLists.txt | 8 +++----- - src/CMakeLists.txt | 4 ++-- - 2 files changed, 5 insertions(+), 7 deletions(-) - -diff --git a/CMakeLists.txt b/CMakeLists.txt -index c768e28..65d5633 100644 ---- a/CMakeLists.txt -+++ b/CMakeLists.txt -@@ -6,14 +6,12 @@ set(${PROJECT_NAME}_VERSION_MAJOR 1) - set(${PROJECT_NAME}_VERSION_MINOR 5) - set(${PROJECT_NAME}_VERSION_PATCH 1) - --set(CMAKE_CXX_FLAGS "-Wall") -- - set(CMAKE_CXX_FLAGS_DEBUG "-g ${CMAKE_CXX_FLAGS}") - set(CMAKE_CXX_FLAGS_RHDEBINFO "-O3 -g ${CMAKE_CXX_FLAGS}") - set(CMAKE_CXX_FLAGS_MINSIZEREL "-Os ${CMAKE_CXX_FLAGS}") - - set(CMAKE_BUILD_TYPE Release) --set(Boost_USE_STATIC_LIBS ON) -+set(Boost_USE_STATIC_LIBS OFF) - - find_package(Boost 1.39 - COMPONENTS -@@ -33,10 +31,10 @@ endif(GPERFTOOLS_TCMALLOC_LIB) - - find_package(Protobuf) - if (PROTOBUF_FOUND) -- include_directories(${Boost_INCLUDE_DIRS} ${PROTOBUF_INCLUDE_DIR} "${CMAKE_CURRENT_SOURCE_DIR}/bamtools/include") -+ include_directories(${Boost_INCLUDE_DIRS} ${PROTOBUF_INCLUDE_DIR} ${BAMTOOLS_INCLUDE}) - set(PROTO_INT 1) - else (PROTOBUF_FOUND) -- include_directories(${Boost_INCLUDE_DIRS} "${CMAKE_CURRENT_SOURCE_DIR}/bamtools/include") -+ include_directories(${Boost_INCLUDE_DIRS} ${BAMTOOLS_INCLUDE}) - set(PROTO_INT 0) - endif(PROTOBUF_FOUND) - -diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt -index 1cc0c01..8929d1f 100644 ---- a/src/CMakeLists.txt -+++ b/src/CMakeLists.txt -@@ -16,11 +16,11 @@ endif (GPERFTOOLS_TCMALLOC) - if(WIN32) - set(LIBRARIES ${LIBRARIES} "${CMAKE_CURRENT_SOURCE_DIR}/../bamtools/lib/libbamtools.lib" "${CMAKE_CURRENT_SOURCE_DIR}/../win_build/zlibd.lib") - else(WIN32) -- set(LIBRARIES ${LIBRARIES} "${CMAKE_CURRENT_SOURCE_DIR}/../bamtools/lib/libbamtools.a" "pthread") -+ set(LIBRARIES ${LIBRARIES} "bamtools" "pthread") - endif(WIN32) - - if (PROTOBUF_FOUND) -- set(LIBRARIES ${LIBRARIES} "libprotobuf.a") -+ set(LIBRARIES ${LIBRARIES} "protobuf") - endif(PROTOBUF_FOUND) - - target_link_libraries(express ${LIBRARIES}) diff --git a/sci-biology/express/files/express-1.5.1-gcc6.patch b/sci-biology/express/files/express-1.5.1-gcc6.patch deleted file mode 100644 index 8a608b97b056..000000000000 --- a/sci-biology/express/files/express-1.5.1-gcc6.patch +++ /dev/null @@ -1,19 +0,0 @@ -Bug: https://bugs.gentoo.org/610692 - ---- a/src/targets.cpp -+++ b/src/targets.cpp -@@ -113,12 +113,12 @@ - - double ll = LOG_1; - double tot_mass = mass(with_pseudo); -- double tot_eff_len = cached_effective_length(lib.bias_table); -+ double tot_eff_len = cached_effective_length(static_cast<bool>(lib.bias_table)); - if (neighbors) { - foreach (const Target* neighbor, *neighbors) { - tot_mass = log_add(tot_mass, neighbor->mass(with_pseudo)); - tot_eff_len = log_add(tot_eff_len, -- neighbor->cached_effective_length(lib.bias_table)); -+ neighbor->cached_effective_length(static_cast<bool>(lib.bias_table))); - } - } - ll += tot_mass - tot_eff_len; diff --git a/sci-biology/express/metadata.xml b/sci-biology/express/metadata.xml deleted file mode 100644 index ccdff086e20b..000000000000 --- a/sci-biology/express/metadata.xml +++ /dev/null @@ -1,8 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-biology/finchtv/finchtv-1.3.1-r3.ebuild b/sci-biology/finchtv/finchtv-1.3.1-r3.ebuild index 60608c9aff2a..d3634ac607b1 100644 --- a/sci-biology/finchtv/finchtv-1.3.1-r3.ebuild +++ b/sci-biology/finchtv/finchtv-1.3.1-r3.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=7 @@ -14,7 +14,7 @@ SRC_URI="http://www.geospiza.com/finchtv/download/programs/linux/${MY_P}.tar.gz" LICENSE="finchtv" SLOT="0" -KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" +KEYWORDS="amd64 ~x86 ~amd64-linux ~x86-linux" S="${WORKDIR}/${MY_P}" diff --git a/sci-biology/glimmerhmm/glimmerhmm-3.0.1-r1.ebuild b/sci-biology/glimmerhmm/glimmerhmm-3.0.1-r1.ebuild index 5424e942a7f7..b6fc54eb65b1 100644 --- a/sci-biology/glimmerhmm/glimmerhmm-3.0.1-r1.ebuild +++ b/sci-biology/glimmerhmm/glimmerhmm-3.0.1-r1.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2019 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=7 @@ -13,7 +13,7 @@ SRC_URI="ftp://ftp.cbcb.umd.edu/pub/software/glimmerhmm/${MY_P}-${PV}.tar.gz" LICENSE="Artistic" SLOT="0" -KEYWORDS="amd64 x86" +KEYWORDS="amd64 ~x86" S="${WORKDIR}/${MY_P}" diff --git a/sci-biology/infernal/infernal-1.0.2-r1.ebuild b/sci-biology/infernal/infernal-1.0.2-r1.ebuild index 2e96418b6bb9..9aa5fd13f4db 100644 --- a/sci-biology/infernal/infernal-1.0.2-r1.ebuild +++ b/sci-biology/infernal/infernal-1.0.2-r1.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2020 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=7 @@ -11,7 +11,7 @@ SRC_URI="ftp://selab.janelia.org/pub/software/${PN}/${P}.tar.gz" LICENSE="GPL-3" SLOT="0" -KEYWORDS="amd64 x86" +KEYWORDS="amd64 ~x86" IUSE="mpi" RDEPEND="mpi? ( virtual/mpi )" diff --git a/sci-biology/mothur/mothur-1.27.0-r1.ebuild b/sci-biology/mothur/mothur-1.27.0-r1.ebuild index 12b628475aac..3f5603e9ecb5 100644 --- a/sci-biology/mothur/mothur-1.27.0-r1.ebuild +++ b/sci-biology/mothur/mothur-1.27.0-r1.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=7 @@ -12,7 +12,7 @@ S="${WORKDIR}/${PN^}.source" LICENSE="GPL-3" SLOT="0" -KEYWORDS="amd64 x86" +KEYWORDS="amd64 ~x86" IUSE="mpi +readline" RDEPEND=" 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/muscle/muscle-3.8.31.ebuild b/sci-biology/muscle/muscle-3.8.31.ebuild index 1638c655be32..e47f5f66cf46 100644 --- a/sci-biology/muscle/muscle-3.8.31.ebuild +++ b/sci-biology/muscle/muscle-3.8.31.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=7 @@ -13,7 +13,7 @@ SRC_URI="https://www.drive5.com/muscle/downloads${PV}/${MY_P}.tar.gz" LICENSE="public-domain" SLOT="0" -KEYWORDS="amd64 ~ppc x86" +KEYWORDS="amd64 ~ppc ~x86" RDEPEND="!sci-libs/libmuscle" diff --git a/sci-biology/pals/pals-1.0-r2.ebuild b/sci-biology/pals/pals-1.0-r2.ebuild index 4e367283bf01..94f972567ea7 100644 --- a/sci-biology/pals/pals-1.0-r2.ebuild +++ b/sci-biology/pals/pals-1.0-r2.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 @@ -12,7 +12,7 @@ S="${WORKDIR}" LICENSE="public-domain" SLOT="0" -KEYWORDS="amd64 x86" +KEYWORDS="amd64 ~x86" PATCHES=( "${FILESDIR}"/${PN}-1.0-fix-build-system.patch ) diff --git a/sci-biology/phyml/phyml-2.4.5-r4.ebuild b/sci-biology/phyml/phyml-2.4.5-r4.ebuild index d256370553ab..c0e9c38caf92 100644 --- a/sci-biology/phyml/phyml-2.4.5-r4.ebuild +++ b/sci-biology/phyml/phyml-2.4.5-r4.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2022 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 @@ -14,7 +14,7 @@ S="${WORKDIR}/${MY_P}" LICENSE="GPL-2" SLOT="0" -KEYWORDS="amd64 ~ppc x86" +KEYWORDS="amd64 ~ppc ~x86" PATCHES=( "${FILESDIR}"/${PN}-2.4.5-fix-build-system.patch ) diff --git a/sci-biology/piler/piler-1.0-r2.ebuild b/sci-biology/piler/piler-1.0-r2.ebuild index 845be78e1fe0..6f419d040b89 100644 --- a/sci-biology/piler/piler-1.0-r2.ebuild +++ b/sci-biology/piler/piler-1.0-r2.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2022 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 @@ -12,7 +12,7 @@ S="${WORKDIR}" LICENSE="public-domain" SLOT="0" -KEYWORDS="amd64 x86" +KEYWORDS="amd64 ~x86" RDEPEND=" || ( diff --git a/sci-biology/pilercr/files/pilercr-1.0-drop-registers.patch b/sci-biology/pilercr/files/pilercr-1.0-drop-registers.patch new file mode 100644 index 000000000000..ab1535b4a767 --- /dev/null +++ b/sci-biology/pilercr/files/pilercr-1.0-drop-registers.patch @@ -0,0 +1,14 @@ +--- a/comp.cpp ++++ b/comp.cpp +@@ -28,7 +28,7 @@ void Complement(char *seq, int len) + /* Complement and reverse sequence */
+
+
+- { register unsigned char *s, *t;
++ { unsigned char *s, *t;
+ int c;
+
+
+old mode 100644 +new mode 100755 +Binary files a/pilercr and b/pilercr differ diff --git a/sci-biology/pilercr/pilercr-1.0-r2.ebuild b/sci-biology/pilercr/pilercr-1.0-r2.ebuild index 819fb3fbb03e..46c5dbc2b944 100644 --- a/sci-biology/pilercr/pilercr-1.0-r2.ebuild +++ b/sci-biology/pilercr/pilercr-1.0-r2.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 @@ -12,7 +12,7 @@ S="${WORKDIR}" LICENSE="public-domain" SLOT="0" -KEYWORDS="amd64 x86" +KEYWORDS="amd64 ~x86" PATCHES=( "${FILESDIR}"/${PN}-1.0-fix-build-system.patch diff --git a/sci-biology/pilercr/pilercr-1.0-r3.ebuild b/sci-biology/pilercr/pilercr-1.0-r3.ebuild new file mode 100644 index 000000000000..3d12c379b58c --- /dev/null +++ b/sci-biology/pilercr/pilercr-1.0-r3.ebuild @@ -0,0 +1,29 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit toolchain-funcs + +DESCRIPTION="Analysis of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs)" +HOMEPAGE="https://www.drive5.com/pilercr/" +SRC_URI="https://www.drive5.com/pilercr/pilercr1.06.tar.gz -> ${P}.tar.gz" +S="${WORKDIR}" + +LICENSE="public-domain" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +PATCHES=( + "${FILESDIR}"/${PN}-1.0-fix-build-system.patch + "${FILESDIR}"/${PN}-1.0-gcc43.patch + "${FILESDIR}"/${PN}-1.0-drop-registers.patch +) + +src_configure() { + tc-export CXX +} + +src_install() { + dobin pilercr +} 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/probcons/probcons-1.12-r1.ebuild b/sci-biology/probcons/probcons-1.12-r1.ebuild index 15960982abff..3f0f2670b7b0 100644 --- a/sci-biology/probcons/probcons-1.12-r1.ebuild +++ b/sci-biology/probcons/probcons-1.12-r1.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=7 @@ -14,7 +14,7 @@ S="${WORKDIR}/${PN}" LICENSE="public-domain" SLOT="0" -KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" +KEYWORDS="amd64 ~x86 ~amd64-linux ~x86-linux" # Gnuplot is explicitly runtime-only, it's run using system() RDEPEND=" diff --git a/sci-biology/pysam/Manifest b/sci-biology/pysam/Manifest index fc19ef776276..2bc79f89f441 100644 --- a/sci-biology/pysam/Manifest +++ b/sci-biology/pysam/Manifest @@ -1 +1 @@ -DIST pysam-0.20.0.gh.tar.gz 3748498 BLAKE2B 1c1b99e5ec34641c196dd574e634cc87d49baa594243eca20ad1f99d2c01b8aadead70a729f389c93cf6f5e95f20d9c7e3d050a47821d1b0dcaaff39d88e6825 SHA512 3f8402057e1d5c807886d1d38180dbdbfa8557700fa97bd59cb42df4d7cc461dcbe54808a169ba5f9696651e801fd0431480cd033b601cd4e9c11bf8bbf14e49 +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-0.20.0.ebuild b/sci-biology/pysam/pysam-0.21.0.ebuild index 6372f1602f70..77292ed29613 100644 --- a/sci-biology/pysam/pysam-0.20.0.ebuild +++ b/sci-biology/pysam/pysam-0.21.0.ebuild @@ -17,27 +17,30 @@ LICENSE="MIT" SLOT="0" KEYWORDS="~amd64 ~x86" -RDEPEND="=sci-libs/htslib-1.16*:=" +RDEPEND="=sci-libs/htslib-1.17*:=" DEPEND="${RDEPEND} dev-python/cython[${PYTHON_USEDEP}] dev-python/setuptools[${PYTHON_USEDEP}]" BDEPEND=" test? ( - =sci-biology/bcftools-1.16* - =sci-biology/samtools-1.16* + =sci-biology/bcftools-1.17* + =sci-biology/samtools-1.17* )" distutils_enable_tests pytest DISTUTILS_IN_SOURCE_BUILD=1 +PATCHES=( + # backport + # https://github.com/pysam-developers/pysam/commit/17bb13dcfdb56ac238458dcef23fe01893a892e9 + "${FILESDIR}"/${P}-cython-3.patch +) + EPYTEST_DESELECT=( # only work with bundled htslib 'tests/tabix_test.py::TestRemoteFileHTTP' 'tests/tabix_test.py::TestRemoteFileHTTPWithHeader' - # broken test - # https://github.com/pysam-developers/pysam/issues/1151#issuecomment-1365662253 - 'tests/AlignmentFilePileup_test.py::TestPileupObjects::testIteratorOutOfScope' ) python_prepare_all() { diff --git a/sci-biology/rebase/rebase-1901-r2.ebuild b/sci-biology/rebase/rebase-1901-r2.ebuild index 1b4b75407947..a80aee6a3126 100644 --- a/sci-biology/rebase/rebase-1901-r2.ebuild +++ b/sci-biology/rebase/rebase-1901-r2.ebuild @@ -11,7 +11,7 @@ SRC_URI="https://dev.gentoo.org/~jlec/distfiles/${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 d6c2ed1c0762..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-1.16.1.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/${PF}/examples -} - -pkg_postinst() { - elog "This version of samtools should *not* be your first choice for working" - elog "with NGS data. It is installed solely for programs requiring it." - elog "It is recommended that you use >=sci-biology/samtools-1.10." -} diff --git a/sci-biology/samtools/samtools-1.16.1.ebuild b/sci-biology/samtools/samtools-1.16.1.ebuild deleted file mode 100644 index 8047657df992..000000000000 --- a/sci-biology/samtools/samtools-1.16.1.ebuild +++ /dev/null @@ -1,47 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -inherit toolchain-funcs - -DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment formats" -HOMEPAGE="http://www.htslib.org/" -SRC_URI="https://github.com/samtools/${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-$(ver_cut 1-2)*:= - sys-libs/ncurses:=[unicode(+)] - sys-libs/zlib" -DEPEND="${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/sibsim4/sibsim4-0.20.ebuild b/sci-biology/sibsim4/sibsim4-0.20.ebuild index 679cb462e045..c90c13dce7ec 100644 --- a/sci-biology/sibsim4/sibsim4-0.20.ebuild +++ b/sci-biology/sibsim4/sibsim4-0.20.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=7 @@ -12,7 +12,7 @@ S="${WORKDIR}/SIBsim4-${PV}" LICENSE="GPL-2" SLOT="0" -KEYWORDS="amd64 x86" +KEYWORDS="amd64 ~x86" PATCHES=( "${FILESDIR}"/${P}-makefile.patch ) diff --git a/sci-biology/stride/stride-20011129-r1.ebuild b/sci-biology/stride/stride-20011129-r1.ebuild index 9638fd559b55..13bfc8e29073 100644 --- a/sci-biology/stride/stride-20011129-r1.ebuild +++ b/sci-biology/stride/stride-20011129-r1.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=7 @@ -13,7 +13,7 @@ SRC_URI=" LICENSE="STRIDE" SLOT="0" -KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux" +KEYWORDS="amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" RESTRICT="mirror bindist" S="${WORKDIR}" diff --git a/sci-biology/tree-puzzle/tree-puzzle-5.2.ebuild b/sci-biology/tree-puzzle/tree-puzzle-5.2.ebuild index b5e8e3931220..61e95bb658d5 100644 --- a/sci-biology/tree-puzzle/tree-puzzle-5.2.ebuild +++ b/sci-biology/tree-puzzle/tree-puzzle-5.2.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2022 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 @@ -11,7 +11,7 @@ SRC_URI="http://www.tree-puzzle.de/${P}.tar.gz" LICENSE="GPL-2" SLOT="0" -KEYWORDS="~amd64 ~ppc x86 ~amd64-linux ~x86-linux ~ppc-macos" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos" IUSE="mpi" RESTRICT="test" diff --git a/sci-biology/treeviewx/treeviewx-0.5.1-r3.ebuild b/sci-biology/treeviewx/treeviewx-0.5.1-r3.ebuild index 359aa98a784f..ada60056715e 100644 --- a/sci-biology/treeviewx/treeviewx-0.5.1-r3.ebuild +++ b/sci-biology/treeviewx/treeviewx-0.5.1-r3.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=7 @@ -13,7 +13,7 @@ S="${WORKDIR}/tv-${PV}" LICENSE="GPL-2" SLOT="0" -KEYWORDS="amd64 x86" +KEYWORDS="amd64 ~x86" RDEPEND="x11-libs/wxGTK:${WX_GTK_VER}[X]" DEPEND="${RDEPEND}" diff --git a/sci-biology/trf/trf-4.04-r2.ebuild b/sci-biology/trf/trf-4.04-r2.ebuild index 16cbb1c3cab9..79558a9d9f11 100644 --- a/sci-biology/trf/trf-4.04-r2.ebuild +++ b/sci-biology/trf/trf-4.04-r2.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 @@ -12,7 +12,7 @@ S="${WORKDIR}" LICENSE="trf" # http://tandem.bu.edu/trf/trf.license.html SLOT="0" -KEYWORDS="amd64 x86" +KEYWORDS="amd64 ~x86" RESTRICT="mirror bindist" QA_PREBUILT="opt/trf/.*" diff --git a/sci-biology/uchime/uchime-4.2.40-r1.ebuild b/sci-biology/uchime/uchime-4.2.40-r1.ebuild index fe35819b5eed..9742ee2575fc 100644 --- a/sci-biology/uchime/uchime-4.2.40-r1.ebuild +++ b/sci-biology/uchime/uchime-4.2.40-r1.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2022 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 @@ -14,6 +14,6 @@ S="${WORKDIR}/${MY_P}" LICENSE="public-domain" SLOT="0" -KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" +KEYWORDS="amd64 ~x86 ~amd64-linux ~x86-linux" PATCHES=( "${FILESDIR}"/CMakeLists.patch ) |