commit: 668ca73d47c048362cec2674c3bced215423a533
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sat Mar 19 11:38:06 2022 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sat Mar 19 11:38:06 2022 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=668ca73d
sci-biology/bedtools: drop 2.29.2
Signed-off-by: David Seifert <soap <AT> gentoo.org>
sci-biology/bedtools/Manifest | 1 -
sci-biology/bedtools/bedtools-2.29.2.ebuild | 50 ----------------------
.../files/bedtools-2.29.2-samtools-1.10.patch | 13 ------
3 files changed, 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;
