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| author |   David Seifert <soap@gentoo.org> | 2024-05-24 11:53:59 +0200 |
|---|---|---|
| committer | David Seifert <soap@gentoo.org> | 2024-05-24 11:53:59 +0200 |
| commit | baa67260b08ba489b0790e989e04dd1eb7f54c55 (patch) | |
| tree | 681c5ff8fa768bd5e21b1a4e3fc3275e9f537712 /sci-biology | |
| parent | net-vpn/i2p: restrict to >=virtual/jdk-11:* for #932030 (diff) | |
| download | gentoo-baa67260b08ba489b0790e989e04dd1eb7f54c55.tar.gz gentoo-baa67260b08ba489b0790e989e04dd1eb7f54c55.tar.bz2 gentoo-baa67260b08ba489b0790e989e04dd1eb7f54c55.zip | |
sci-biology/pysam: add 0.22.1
Signed-off-by: David Seifert <soap@gentoo.org>
Diffstat (limited to 'sci-biology')
| -rw-r--r-- | sci-biology/pysam/Manifest | 1 | ||||
| -rw-r--r-- | sci-biology/pysam/pysam-0.22.1.ebuild | 68 |
2 files changed, 69 insertions, 0 deletions
diff --git a/sci-biology/pysam/Manifest b/sci-biology/pysam/Manifest index 2bc79f89f441..fae7b9793388 100644 --- a/sci-biology/pysam/Manifest +++ b/sci-biology/pysam/Manifest @@ -1 +1,2 @@ DIST pysam-0.21.0.gh.tar.gz 3842829 BLAKE2B 83db290ec0bae71106276ed4f1721292c0d2fa55053c7451f0a8a79619b1c4d8444b99293ac5d8051bfb0b59e984e32a89798bab091e3a019b7c2a3fb7414d1c SHA512 b2ac986b6a352df1d2066a224d710648a88d8ad44273623a89ae0f4bb2645b00f0d0e1685c8ccedfd379259255957e653f3c3199621ac1d4c26098f538b6bfa7 +DIST pysam-0.22.1.gh.tar.gz 3885851 BLAKE2B 6f83c445c7e63e28823f443b0f106726303b0609f4040e9dca930c820d48c2adfe13d33ecffb514ce75c3b03968af050652689a0be39aaabca1af546e9188480 SHA512 fb8dc7c4a6ae908d8d409789f2706cce589d4b6a1057bcc4043f8a26a5b390f79d30d1a1cbe69cbf370caabf261ed8367685393240765080e94f1782ed7f0350 diff --git a/sci-biology/pysam/pysam-0.22.1.ebuild b/sci-biology/pysam/pysam-0.22.1.ebuild new file mode 100644 index 000000000000..9070476873e1 --- /dev/null +++ b/sci-biology/pysam/pysam-0.22.1.ebuild @@ -0,0 +1,68 @@ +# Copyright 1999-2024 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..12} ) + +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 -> ${P}.gh.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +RDEPEND="=sci-libs/htslib-1.20*:=" +DEPEND="${RDEPEND} + dev-python/setuptools[${PYTHON_USEDEP}]" +BDEPEND=" + dev-python/cython[${PYTHON_USEDEP}] + test? ( + =sci-biology/bcftools-1.20* + =sci-biology/samtools-1.20* + )" + +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' + + 'tests/AlignedSegment_test.py::TestBaseModifications' +) + +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 +} |