diff options
Diffstat (limited to 'sci-biology/bedtools')
| -rw-r--r-- | sci-biology/bedtools/Manifest | 3 | ||||
| -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, 66 deletions
diff --git a/sci-biology/bedtools/Manifest b/sci-biology/bedtools/Manifest index 31952fc3668b..c806da84e07a 100644 --- a/sci-biology/bedtools/Manifest +++ b/sci-biology/bedtools/Manifest @@ -1,8 +1,5 @@ AUX bedtools-2.29.2-buildsystem.patch 2002 BLAKE2B 7925c788858515ec4454ece3823680e99053790aeb30b2dcab06a52f6827c3cca85543c899fbabcc75ac5872cdfe632c9c5bf8b5dc24146c50a00dbd4ea56a1d SHA512 a76ec350aedfce4926f8fbaed742a992f81b2280727383f7aefd7f3629f7e04f300f9d3d9cce2a98c6fe2767cb6d2261074bd6242d6d5ae26a5095730c054a85 AUX bedtools-2.29.2-python.patch 1235 BLAKE2B 34381a33be915f983b2c93f04954486e7611f56b1bc3259887e5ac3aa54107e3392a784980779948136f97424485a31a53959f2f76b573cb44b7d83023c69005 SHA512 8c22230e3bc1eaeb7d85379eab402eb1e95443f88f60a9c04f628cd38a96b91d138149a1a46d941189a8cd6097e075a8bde8d4ad883757ec7b2c129268cdb37f -AUX bedtools-2.29.2-samtools-1.10.patch 659 BLAKE2B 5ec159e0a9bc9f4b5d661bcf93ba8a0cd08f62e8e6d3f92229b71d5dfb122d89eb6a68637e12394e6082cf9be99014787f9a780f7fb547ec61f5f8b8d405713d SHA512 0160c54ad3781e17df53b2525cbf0e6b5d1ebf5ce07257b16c35eed525623aa46b5ee32f158ab64b2e18a283eba0f8331a521ac8382cc31ca03cd88d1376c057 -DIST bedtools-2.29.2.tar.gz 20646485 BLAKE2B cdfff7a0f5300f31c2487e98bd28dc7e8b7f3575a098947c2c7b3a6e30272a80d35f07997d3a00bd42d91bf60899f32358b25b054b6f40b761cc66e2788508b3 SHA512 138ff029995e9889d2e43f884fa15bb5614d11cf75dfe18e2999aad0915e80f49444e67c9934c92ca8e28caad399394b493db8a1bee9f5304413a8c41c22c6d5 DIST bedtools-2.30.0.tar.gz 20648577 BLAKE2B 042bc31e846455cb1c20199f7a27a3850851f7c256a45b1e674c7aa48ecedc211b0fdfc5e25f915b588f21447e757ebff2bba16a65905bb10d3c88e4b17b1db1 SHA512 3993243cc3db12d194d6220aeae200e6af843d6d32d4e5a9a82d04c9d119f8ed47e618e87241edfa82cfac081bc9a40ada18f097d21b0cafc5f912ae012701c9 -EBUILD bedtools-2.29.2.ebuild 1232 BLAKE2B 77bf05d3c03b9f38a3ebd4ef4028666a2ae445aa9605f5d1d457bf7a26bdfc362fedfc5906994fddc24b29e18214484e3b464ce3d8644bc4ccb006dfb76051be SHA512 862ee4bbaee73a9274a8f9c9bbadedbd00f3d6d59380abcd48d35c9d922e7e2a849e4c8357f65657e55258afea611dbe34ed77735f1cb79fab5bada5cbfa79af EBUILD bedtools-2.30.0.ebuild 1184 BLAKE2B 128c85d2fae5a45068f3c6f0c64b93902dcfaf0eb1464fbc8546ac7b62827d62fbd01cab422e23153cc9e2975f3d43f628305a3986caf6df36923059f45d6a6c SHA512 77c36f5abcf230a4eff2f7215998ed8188d0e6dda8c1c1de94c16e6dd3b7b480bb6abed0d6bcf0baec2ebbb1d678c51a0c1b16aebc34785e49245e5d30b0626a MISC metadata.xml 407 BLAKE2B f3c2890ef1648dcfc7ae92c56fec8c111de2cb82ba4c8f7402756fa9db6f2ee43fa3ccb9a75db5d1e2ca7893ed3041efc22452814944e0e56f1a589353b47774 SHA512 925406053fd5c1aecb5ef26c522b3f410c6f9a639dc1ab7790a4124513c870af5b818adc53875c93ab19a36d444b8fb23c5ef10cc11ed50080785bbe60d1eb98 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; |