From d4725f7e03f4d243d29d408f4b9de39459e00d4c Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Sun, 19 Feb 2023 20:16:04 +0000 Subject: gentoo auto-resync : 19:02:2023 - 20:16:03 --- sci-biology/Manifest.gz | Bin 19497 -> 19495 bytes sci-biology/bcftools/Manifest | 2 - sci-biology/bcftools/bcftools-1.15.1.ebuild | 42 ----------------- sci-biology/pysam/Manifest | 4 +- sci-biology/pysam/pysam-0.19.1.ebuild | 66 -------------------------- sci-biology/pysam/pysam-0.20.0.ebuild | 69 ++++++++++++++++++++++++++++ sci-biology/samtools/Manifest | 2 - sci-biology/samtools/samtools-1.15.1.ebuild | 47 ------------------- 8 files changed, 71 insertions(+), 161 deletions(-) delete mode 100644 sci-biology/bcftools/bcftools-1.15.1.ebuild delete mode 100644 sci-biology/pysam/pysam-0.19.1.ebuild create mode 100644 sci-biology/pysam/pysam-0.20.0.ebuild delete mode 100644 sci-biology/samtools/samtools-1.15.1.ebuild (limited to 'sci-biology') diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz index 10d0948e70ea..58f4d20c7165 100644 Binary files a/sci-biology/Manifest.gz and b/sci-biology/Manifest.gz differ diff --git a/sci-biology/bcftools/Manifest b/sci-biology/bcftools/Manifest index 10584e16c542..f4aeb61e0c0a 100644 --- a/sci-biology/bcftools/Manifest +++ b/sci-biology/bcftools/Manifest @@ -1,5 +1,3 @@ -DIST bcftools-1.15.1.tar.bz2 6917252 BLAKE2B d2389df8d2a1bbc48fcaccad47d77ff99d700e82e04330189e7d93acdac97a13506c2b799fbba31bdc0988977c7df7c699e7b156f3530dd35e5f052c6f977731 SHA512 60fedacc41051675d372e68146ac8fa0dc019a7fb694fda487d89e62f34edaf5ac11cca38779e9bcfcf8b3148802fadabed12f7e46ad534ad5087b8d6383f97b DIST bcftools-1.16.tar.bz2 7325862 BLAKE2B 0e1240448d4efb352d3d0cd83decd286f7544fff3676f0a5cca51dec9c445c47c37ac24a3317aa7b41182c576e7e57dba460fc98aca069dc2f8fe0625c0b0f06 SHA512 998d5ac941f73798c35dd1db7ac7aba9067f275bd3055728aabfd8edd9f40484130df1fb57621d1a762a57b28ffcac358570915c341d420ae6f12bd17f7651a3 -EBUILD bcftools-1.15.1.ebuild 891 BLAKE2B f53122b55cb0ae73618c607332f51d1881e592b361bf325e762a4c1f6a19da1ba39df44068e87b410c67caa606ffa455dd678d7a7daaa0b266def26584785bc4 SHA512 065a1a9f36960e0c8f1600990bb4d6fd31305604c1cbf561110bc6943e810abf47632d147072cda42c09f3510a709455862212fd07d531e18c1109008370d5b4 EBUILD bcftools-1.16.ebuild 900 BLAKE2B 98f04325ca039867010c25c5ebff64725de637960c1980cce0faee7b8514d187ca3a309a3db79bb809ebcb9938869884c89b54f232fcf826aa34b38c5dde9c6e SHA512 82bb9a379019f0d9f9c601fad06d4041e5b890cb21618cc37f37f5f6ce0c3d5d9cd1d6223a19b8a53303e8ab3ce4046a21fbd3b7b18fd45243d57226d040ffc4 MISC metadata.xml 344 BLAKE2B 37f8e82e8a5a9ad572580a7e5ae6daa6911d672f17b8526f81b236cbc2e50a32c4cd2566aaed9f5feee016d7e2de7db2a40b60616e86c3e8cae307d60cebc70e SHA512 0160c9606089d610613d71dc0aa9c9c5e5266483fdc9c407b6e0ed911eac8f8b32ffaf5a49bbb427393c8240e9868df51f0fc68b2f45467f65d9b3d54b0ddde1 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/pysam/Manifest b/sci-biology/pysam/Manifest index 02ce6871e04a..9bdae09a6265 100644 --- a/sci-biology/pysam/Manifest +++ b/sci-biology/pysam/Manifest @@ -1,3 +1,3 @@ -DIST pysam-0.19.1.gh.tar.gz 3649711 BLAKE2B dac3ab5a86ef95048e966fc007a0aa1c96ca8498f7c2672c2ed024f34b508bac42048e58b8ae0b538cea137a51e1874bb5c2c4976c7f3dc657a4c2cf5f9a27fb SHA512 719f3a15e7dd277a90cce7f938b674ff86ef6b8f2d3440c3a0bf2ea22c4fbc2b3c9e0cf297d958c99e09dcd6e9905f32e8c632158aa8d5af8210e79705e1c479 -EBUILD pysam-0.19.1.ebuild 1597 BLAKE2B 05400695c7825c0ffd97c774792476af0e91eed46673fdb52550d15b291f29e75227b3188f4db39298e676bfcf1fd8fe351fc7a3ca79ed4f7ba4cd53e78739b2 SHA512 28e4b669d32910e02eca460d62a0765219595b3c038d34a9faeeb3a45d6d91032a5e2fb6903067ab8e5aacf47b84a779c13938a030dd9017e2021784eaf0849d +DIST pysam-0.20.0.gh.tar.gz 3748498 BLAKE2B 1c1b99e5ec34641c196dd574e634cc87d49baa594243eca20ad1f99d2c01b8aadead70a729f389c93cf6f5e95f20d9c7e3d050a47821d1b0dcaaff39d88e6825 SHA512 3f8402057e1d5c807886d1d38180dbdbfa8557700fa97bd59cb42df4d7cc461dcbe54808a169ba5f9696651e801fd0431480cd033b601cd4e9c11bf8bbf14e49 +EBUILD pysam-0.20.0.ebuild 1767 BLAKE2B 45a292847762698e9629508f6b22624202509f946085995d8bd110fe4cd227e707546ecdae33b68036029b94bcf4824699a62031fd05144c6cfdd605b0c2e190 SHA512 3e54171befa77ac9d03114069064b5b166a4010c9fc8076540680660d8d90a7650264583d41bd6dce8d10e5c1a4723969cc2deb568d29283b91bf5b53351de35 MISC metadata.xml 442 BLAKE2B e3d339868a09d8930ff6d83f414f8166ed283a66d83d5b0fed0031024db151b17b1347f5e015f2b9c2152a041e2beb70696362be9b4e3fc225078bc5c520ad58 SHA512 4b1d08c5524e1bb04129e0d38f0584654b34979024afd2cf15bd482654ca8fac9c82e6db0661f7370f9fefa6949f1291ba3c18a9dca5d5041bd6f76554fa33c7 diff --git a/sci-biology/pysam/pysam-0.19.1.ebuild b/sci-biology/pysam/pysam-0.19.1.ebuild deleted file mode 100644 index 1164fd6bc091..000000000000 --- a/sci-biology/pysam/pysam-0.19.1.ebuild +++ /dev/null @@ -1,66 +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 distutils-r1 - -DESCRIPTION="Python interface for the SAM/BAM sequence alignment and mapping format" -HOMEPAGE=" - https://github.com/pysam-developers/pysam - https://pypi.org/project/pysam/" -SRC_URI="https://github.com/pysam-developers/pysam/archive/v${PV}.tar.gz -> ${P}.gh.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -RDEPEND="=sci-libs/htslib-1.15.1*:=" -DEPEND="${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* - )" - -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 $ORIGIN) - sed -e '/runtime_library_dirs=htslib_library_dirs/d' \ - -i setup.py || die - - if use test; then - einfo "Building test data" - emake -C tests/pysam_data - emake -C tests/cbcf_data - fi - - distutils-r1_python_prepare_all -} - -python_compile() { - # breaks with parallel build - # need to avoid dropping .so plugins into - # build-lib, which breaks tests - esetup.py build_ext --inplace -j1 - distutils-r1_python_compile -j1 -} diff --git a/sci-biology/pysam/pysam-0.20.0.ebuild b/sci-biology/pysam/pysam-0.20.0.ebuild new file mode 100644 index 000000000000..6372f1602f70 --- /dev/null +++ b/sci-biology/pysam/pysam-0.20.0.ebuild @@ -0,0 +1,69 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{9..11} ) + +inherit distutils-r1 + +DESCRIPTION="Python interface for the SAM/BAM sequence alignment and mapping format" +HOMEPAGE=" + https://github.com/pysam-developers/pysam + https://pypi.org/project/pysam/" +SRC_URI="https://github.com/pysam-developers/pysam/archive/v${PV}.tar.gz -> ${P}.gh.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +RDEPEND="=sci-libs/htslib-1.16*:=" +DEPEND="${RDEPEND} + dev-python/cython[${PYTHON_USEDEP}] + dev-python/setuptools[${PYTHON_USEDEP}]" +BDEPEND=" + test? ( + =sci-biology/bcftools-1.16* + =sci-biology/samtools-1.16* + )" + +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' + # broken test + # https://github.com/pysam-developers/pysam/issues/1151#issuecomment-1365662253 + 'tests/AlignmentFilePileup_test.py::TestPileupObjects::testIteratorOutOfScope' +) + +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/samtools/Manifest b/sci-biology/samtools/Manifest index faa3a4d5981b..6bce14af3d22 100644 --- a/sci-biology/samtools/Manifest +++ b/sci-biology/samtools/Manifest @@ -1,8 +1,6 @@ AUX samtools-0.1.20-buildsystem.patch 6737 BLAKE2B 71445f57735903bccc2720a32f42b27093f670e383d2d194b5692b1ba536e3df44204711cf4574b3933e5ce00605b661b1a36d79ca7f193ce36816271a3f8214 SHA512 ecb05971fbea4570ec161a165cb581b38ed727bb7e5b769862984bf035414cd564ab809882dc3272f8b192feeb86e29247d7327afa73ff668b01c03c58bb177d 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 EBUILD samtools-0.1.20-r4.ebuild 2049 BLAKE2B d377712eaca931258b37645e6a6b3cc379fdb550ef83a0c272a3eb564d7753185fea53416973e4fdf2c25b79475a81ae72b646ce22c570c934e4eabce8a9ded6 SHA512 c0d387f715ebf1f746ea4e4a7eab85a86ef0bff646c9a69639b17ef02e93c39982941d7eb811a6d67b0e635c9c4e05924d2b89a6809c3bd0592db91894dab4aa -EBUILD samtools-1.15.1.ebuild 917 BLAKE2B ce0e56d9fd4d45f32d53e014648ea154b55363f9b48f1293f1687c2f2c668d7f498bb346bc291bf30c0be23499326cc38eb93065114c932269808825ece939e6 SHA512 dee59486e4942a45450b41aa1df296264dcc6396463a8e2e3ce93f4d7fb14acae252d4798492a19912999ca621c2188ef25ee6063fee7c9bc673ba57169a99c6 EBUILD samtools-1.16.1.ebuild 926 BLAKE2B 7856fb586ff9b879e353784635eb27d190da7d1dc41a42f103cb1116ebde092b94e086779883bc916d5223632d217ea3f3d5468278d174122845a48be6df2d3d SHA512 b6711d8b955e466cdd79a2a4a92fa9f7f98aaa302901c97f1bab439f7cc407ff65726957627a8182068a7eb5f5556e680b52d9f2514f461e4e2f33ac3dc4dfa3 MISC metadata.xml 409 BLAKE2B c94eab9ebda4844beb471694106e353ccbbaca53e69de680301c6cfab3f3b6224ec94fcd631c9de2811d309463e5ee6decf2e443bfc68921f3362c6a312cd3af SHA512 fb2d3686e1ee70e4e80266a26603b3e52b680b1537a4569493a3a0511b93e2acdb2be3136df7ae54905a9f86fb7e53fa054607262751ebd8f54903f1905dad24 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 -} -- cgit v1.2.3