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| author |   David Seifert <soap@gentoo.org> | 2022-03-19 12:38:06 +0100 |
|---|---|---|
| committer | David Seifert <soap@gentoo.org> | 2022-03-19 12:38:06 +0100 |
| commit | 668ca73d47c048362cec2674c3bced215423a533 (patch) | |
| tree | be64ac091fafab1601ec5f508eb4aefd654f939f | |
| parent | sci-biology/bcftools: add 1.15 (diff) | |
| download | gentoo-668ca73d47c048362cec2674c3bced215423a533.tar.gz gentoo-668ca73d47c048362cec2674c3bced215423a533.tar.bz2 gentoo-668ca73d47c048362cec2674c3bced215423a533.zip | |
sci-biology/bedtools: drop 2.29.2
Signed-off-by: David Seifert <soap@gentoo.org>
| -rw-r--r-- | sci-biology/bedtools/Manifest | 1 | ||||
| -rw-r--r-- | sci-biology/bedtools/bedtools-2.29.2.ebuild | 50 | ||||
| -rw-r--r-- | sci-biology/bedtools/files/bedtools-2.29.2-samtools-1.10.patch | 13 |
3 files changed, 0 insertions, 64 deletions
diff --git a/sci-biology/bedtools/Manifest b/sci-biology/bedtools/Manifest index d2d1a7150f72..571c4c92d6b5 100644 --- a/sci-biology/bedtools/Manifest +++ b/sci-biology/bedtools/Manifest @@ -1,2 +1 @@ -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-2.29.2.ebuild b/sci-biology/bedtools/bedtools-2.29.2.ebuild deleted file mode 100644 index c90bc512fe34..000000000000 --- a/sci-biology/bedtools/bedtools-2.29.2.ebuild +++ /dev/null @@ -1,50 +0,0 @@ -# Copyright 1999-2020 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}"/${PN}-2.29.2-python.patch - "${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 -} diff --git a/sci-biology/bedtools/files/bedtools-2.29.2-samtools-1.10.patch b/sci-biology/bedtools/files/bedtools-2.29.2-samtools-1.10.patch deleted file mode 100644 index 7cc0e23de2d4..000000000000 --- a/sci-biology/bedtools/files/bedtools-2.29.2-samtools-1.10.patch +++ /dev/null @@ -1,13 +0,0 @@ ---- a/test/intersect/new_test-intersect.sh -+++ b/test/intersect/new_test-intersect.sh -@@ -975,8 +975,8 @@ - # Test intersect preserve the text header in bam - ############################################################ - echo -e " intersect.new.t78...\c" --echo -e "@HD VN:1.5 SO:coordinate" > exp --echo "@HD VN:1.5 SO:coordinate" | samtools view -b | $BT intersect -a /dev/stdin -b b.bed | samtools view -H >obs -+echo -e "@HD VN:1.5 SO:coordinate" > exp -+echo "@HD VN:1.5 SO:coordinate" | samtools view --no-PG -b | $BT intersect -a /dev/stdin -b b.bed | samtools view --no-PG -H >obs - check exp obs - rm exp obs - [[ $FAILURES -eq 0 ]] || exit 1; |