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| author |   David Seifert <soap@gentoo.org> | 2018-10-28 21:24:40 +0100 |
|---|---|---|
| committer | David Seifert <soap@gentoo.org> | 2018-10-28 21:24:40 +0100 |
| commit | 59ee040ec29f25e981534026d9be99b4ca36b458 (patch) | |
| tree | 2c3eec35068ec00be3717441337d82b45ab86ef6 /sci-biology | |
| parent | sci-biology/samtools: Version bump to 1.9 (diff) | |
| download | gentoo-59ee040ec29f25e981534026d9be99b4ca36b458.tar.gz gentoo-59ee040ec29f25e981534026d9be99b4ca36b458.tar.bz2 gentoo-59ee040ec29f25e981534026d9be99b4ca36b458.zip | |
sci-biology/bcftools: Version bump to 1.9
Closes: https://bugs.gentoo.org/647714
Signed-off-by: David Seifert <soap@gentoo.org>
Package-Manager: Portage-2.3.50, Repoman-2.3.11
Diffstat (limited to 'sci-biology')
| -rw-r--r-- | sci-biology/bcftools/Manifest | 1 | ||||
| -rw-r--r-- | sci-biology/bcftools/bcftools-1.9.ebuild | 47 | ||||
| -rw-r--r-- | sci-biology/bcftools/files/bcftools-1.9-fix-shebangs.patch | 8 |
3 files changed, 56 insertions, 0 deletions
diff --git a/sci-biology/bcftools/Manifest b/sci-biology/bcftools/Manifest index 333bb377e499..eef8daed7a75 100644 --- a/sci-biology/bcftools/Manifest +++ b/sci-biology/bcftools/Manifest @@ -1 +1,2 @@ DIST bcftools-1.5.tar.bz2 2975685 BLAKE2B 937b7db770dcaddafbd00b67c3b88501a3190564b2ca629b83e52b48b414a604dd203cd067e357e2b7d02c700387576fca458d1cab2982dafa3b2c215b528722 SHA512 66b8bc61b9fbb381679a6781f77a18f66e8105567992da011413bc573d99b619558a1cf58e9e1373ae347a8b81638dd91977802a07a4578ddc9c61fb53403233 +DIST bcftools-1.9.tar.bz2 3134355 BLAKE2B dd551b509b1ee554f70be9da28a6eaf81dfcec43fc0d1aa972d64ef846f9db47f39177345e8c1ca754d11defb9c0823976ae94d6b3e7cd99313eed4f381182ed SHA512 fd662fb0d214eb75ac04fc4494e8dbaca84d10698ca14801427341def6a5df4af99e7bd4cd873da5422ae921deb49b940cedb926da356b1eabfac525a38f806c diff --git a/sci-biology/bcftools/bcftools-1.9.ebuild b/sci-biology/bcftools/bcftools-1.9.ebuild new file mode 100644 index 000000000000..53e47bc01a81 --- /dev/null +++ b/sci-biology/bcftools/bcftools-1.9.ebuild @@ -0,0 +1,47 @@ +# Copyright 1999-2018 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +PYTHON_COMPAT=( python2_7 ) + +inherit python-single-r1 + +DESCRIPTION="Utilities for variant calling and manipulating VCF and BCF files" +HOMEPAGE="http://www.htslib.org" +SRC_URI="https://github.com/samtools/${PN}/releases/download/${PV}/${P}.tar.bz2" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND=" + dev-lang/perl + =sci-libs/htslib-${PV}*:= + sys-libs/zlib:= + ${PYTHON_DEPS}" +DEPEND="${RDEPEND}" + +PATCHES=( + "${FILESDIR}"/${PN}-1.5-buildsystem.patch + "${FILESDIR}"/${PN}-1.9-fix-shebangs.patch +) + +src_prepare() { + default + + python_fix_shebang misc/{guess-ploidy,plot-roh}.py + + # remove bundled htslib + rm -r htslib-* || die +} + +src_configure() { + econf \ + --disable-bcftools-plugins \ + --disable-libgsl \ + --disable-configure-htslib \ + --with-htslib=system +} diff --git a/sci-biology/bcftools/files/bcftools-1.9-fix-shebangs.patch b/sci-biology/bcftools/files/bcftools-1.9-fix-shebangs.patch new file mode 100644 index 000000000000..76610187c493 --- /dev/null +++ b/sci-biology/bcftools/files/bcftools-1.9-fix-shebangs.patch @@ -0,0 +1,8 @@ +--- a/misc/vcfutils.pl ++++ b/misc/vcfutils.pl +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + # + # Copyright (C) 2010 Broad Institute. + # Copyright (C) 2011, 2014 Genome Research Ltd. |