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author | V3n3RiX <venerix@koprulu.sector> | 2024-04-25 23:59:45 +0100 |
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committer | V3n3RiX <venerix@koprulu.sector> | 2024-04-25 23:59:45 +0100 |
commit | 6243676c91946098c06d42bc87b5eb99aac40bf0 (patch) | |
tree | e6de308ba22148b4898b67b049c7f017ece8fea2 /sci-biology/bedtools/bedtools-2.31.1.ebuild | |
parent | b987a550f067c3da93b0664cf1fdc8a624c0aa38 (diff) |
gentoo auto-resync : 25:04:2024 - 23:59:45
Diffstat (limited to 'sci-biology/bedtools/bedtools-2.31.1.ebuild')
-rw-r--r-- | sci-biology/bedtools/bedtools-2.31.1.ebuild | 49 |
1 files changed, 49 insertions, 0 deletions
diff --git a/sci-biology/bedtools/bedtools-2.31.1.ebuild b/sci-biology/bedtools/bedtools-2.31.1.ebuild new file mode 100644 index 000000000000..57ee6c3fde3f --- /dev/null +++ b/sci-biology/bedtools/bedtools-2.31.1.ebuild @@ -0,0 +1,49 @@ +# Copyright 1999-2024 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..12} ) + +inherit python-any-r1 toolchain-funcs + +DESCRIPTION="Tools for manipulation and analysis of BED, GFF/GTF, VCF, SAM/BAM file formats" +HOMEPAGE="https://bedtools.readthedocs.io/" +SRC_URI="https://github.com/arq5x/${PN}2/releases/download/v${PV}/${P}.tar.gz" +S="${WORKDIR}/${PN}2" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="test" +RESTRICT="!test? ( test )" + +RDEPEND=" + app-arch/bzip2 + app-arch/xz-utils + sys-libs/zlib" +DEPEND="${RDEPEND}" +BDEPEND=" + ${PYTHON_DEPS} + test? ( >=sci-biology/samtools-1.10:0 )" + +# bedtools2 has a *terrible* build system and development practices. +# Upstream has forked htslib 1.9 and extended it by adding clever callbacks +# that make unbundling it nigh impossible. There are no signs of upstream porting +# their fork to 1.10, which means we're stuck with the bundled version. +PATCHES=( + "${FILESDIR}"/${PN}-2.31.1-buildsystem.patch + "${FILESDIR}"/${PN}-2.31.1-python.patch + "${FILESDIR}"/${PN}-2.31.1-includes.patch +) + +src_configure() { + tc-export AR CC CXX RANLIB +} + +src_install() { + default + + insinto /usr/share/bedtools + doins -r genomes +} |