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authorDavid Seifert <soap@gentoo.org>2018-10-28 21:24:40 +0100
committerDavid Seifert <soap@gentoo.org>2018-10-28 21:24:40 +0100
commit59ee040ec29f25e981534026d9be99b4ca36b458 (patch)
tree2c3eec35068ec00be3717441337d82b45ab86ef6 /sci-biology/bcftools
parentsci-biology/samtools: Version bump to 1.9 (diff)
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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/bcftools')
-rw-r--r--sci-biology/bcftools/Manifest1
-rw-r--r--sci-biology/bcftools/bcftools-1.9.ebuild47
-rw-r--r--sci-biology/bcftools/files/bcftools-1.9-fix-shebangs.patch8
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.