diff options
Diffstat (limited to 'sci-biology/bedtools/bedtools-2.29.2.ebuild')
-rw-r--r-- | sci-biology/bedtools/bedtools-2.29.2.ebuild | 48 |
1 files changed, 48 insertions, 0 deletions
diff --git a/sci-biology/bedtools/bedtools-2.29.2.ebuild b/sci-biology/bedtools/bedtools-2.29.2.ebuild new file mode 100644 index 000000000000..de337827bf24 --- /dev/null +++ b/sci-biology/bedtools/bedtools-2.29.2.ebuild @@ -0,0 +1,48 @@ +# Copyright 1999-2020 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +PYTHON_COMPAT=( python3_{6..9} ) + +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}/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="test" +RESTRICT="!test? ( test )" + +RDEPEND=" + app-arch/bzip2 + app-arch/xz-utils + sys-libs/zlib" +DEPEND="${RDEPEND}" +BDEPEND="test? ( >=sci-biology/samtools-1.10:0 )" + +S="${WORKDIR}"/${PN}2 + +# 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}-2.29.2-buildsystem.patch + "${FILESDIR}"/${PN}-2.29.2-python.patch + "${FILESDIR}"/${PN}-2.29.2-samtools-1.10.patch +) + +src_configure() { + tc-export AR CC CXX RANLIB +} + +src_install() { + default + + insinto /usr/share/${PN} + doins -r genomes +} |