commit: 3f7de88151115f14fdb6036dcffa110a0104d55b Author: Wolfgang E. Sanyer <ezzieyguywuf <AT> gmail <DOT> com> AuthorDate: Tue Feb 23 16:49:45 2021 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> org> CommitDate: Tue Feb 23 16:49:45 2021 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=3f7de881
sci-biology/bedtools: bump to 2.30.0 * The samtools patch is no longer needed, as upstream has fixed this. Test suite passes without it now. Closes: https://github.com/gentoo/gentoo/pull/19616 Closes: https://bugs.gentoo.org/696188 Signed-off-by: Wolfgang E. Sanyer <ezzieyguywuf <AT> gmail.com> Signed-off-by: David Seifert <soap <AT> gentoo.org> sci-biology/bedtools/Manifest | 1 + sci-biology/bedtools/bedtools-2.30.0.ebuild | 49 +++++++++++++++++++++++++++++ 2 files changed, 50 insertions(+) diff --git a/sci-biology/bedtools/Manifest b/sci-biology/bedtools/Manifest index 5dc912159a4..d2d1a7150f7 100644 --- a/sci-biology/bedtools/Manifest +++ b/sci-biology/bedtools/Manifest @@ -1 +1,2 @@ DIST bedtools-2.29.2.tar.gz 20646485 BLAKE2B cdfff7a0f5300f31c2487e98bd28dc7e8b7f3575a098947c2c7b3a6e30272a80d35f07997d3a00bd42d91bf60899f32358b25b054b6f40b761cc66e2788508b3 SHA512 138ff029995e9889d2e43f884fa15bb5614d11cf75dfe18e2999aad0915e80f49444e67c9934c92ca8e28caad399394b493db8a1bee9f5304413a8c41c22c6d5 +DIST bedtools-2.30.0.tar.gz 20648577 BLAKE2B 042bc31e846455cb1c20199f7a27a3850851f7c256a45b1e674c7aa48ecedc211b0fdfc5e25f915b588f21447e757ebff2bba16a65905bb10d3c88e4b17b1db1 SHA512 3993243cc3db12d194d6220aeae200e6af843d6d32d4e5a9a82d04c9d119f8ed47e618e87241edfa82cfac081bc9a40ada18f097d21b0cafc5f912ae012701c9 diff --git a/sci-biology/bedtools/bedtools-2.30.0.ebuild b/sci-biology/bedtools/bedtools-2.30.0.ebuild new file mode 100644 index 00000000000..3647f43dabe --- /dev/null +++ b/sci-biology/bedtools/bedtools-2.30.0.ebuild @@ -0,0 +1,49 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +PYTHON_COMPAT=( python3_{7..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=" + ${PYTHON_DEPS} + test? ( >=sci-biology/samtools-1.10:0 )" + +S="${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}"/${PN}-2.29.2-python.patch +) + +src_configure() { + tc-export AR CC CXX RANLIB +} + +src_install() { + default + + insinto /usr/share/${PN} + doins -r genomes +}
