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3f9689daa1
Done via: ``` git grep -l 'virtual/zlib"' | xargs sed -i -e 's@virtual/zlib"@virtual/zlib:="@' ``` Signed-off-by: Michał Górny <mgorny@gentoo.org>
50 lines
1.2 KiB
Bash
50 lines
1.2 KiB
Bash
# Copyright 1999-2025 Gentoo Authors
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# Distributed under the terms of the GNU General Public License v2
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EAPI=8
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PYTHON_COMPAT=( python3_{11..13} )
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inherit python-any-r1 toolchain-funcs
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DESCRIPTION="Tools for manipulation and analysis of BED, GFF/GTF, VCF, SAM/BAM file formats"
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HOMEPAGE="https://bedtools.readthedocs.io/"
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SRC_URI="https://github.com/arq5x/${PN}2/releases/download/v${PV}/${P}.tar.gz"
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S="${WORKDIR}/${PN}2"
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LICENSE="GPL-2"
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SLOT="0"
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KEYWORDS="~amd64 ~x86"
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IUSE="test"
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RESTRICT="!test? ( test )"
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RDEPEND="
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app-arch/bzip2
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app-arch/xz-utils
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virtual/zlib:="
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DEPEND="${RDEPEND}"
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BDEPEND="
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${PYTHON_DEPS}
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test? ( >=sci-biology/samtools-1.10:0 )"
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# bedtools2 has a *terrible* build system and development practices.
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# Upstream has forked htslib 1.9 and extended it by adding clever callbacks
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# that make unbundling it nigh impossible. There are no signs of upstream porting
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# their fork to 1.10, which means we're stuck with the bundled version.
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PATCHES=(
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"${FILESDIR}"/${PN}-2.31.1-buildsystem.patch
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"${FILESDIR}"/${PN}-2.31.1-python.patch
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"${FILESDIR}"/${PN}-2.31.1-includes.patch
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)
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src_configure() {
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tc-export AR CC CXX RANLIB
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}
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src_install() {
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default
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insinto /usr/share/bedtools
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doins -r genomes
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}
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