[gentoo-commits] repo/gentoo:master commit in: sci-biology/bcftools/files/, sci-biology/bcftools/

[David Seifert]

commit:     59ee040ec29f25e981534026d9be99b4ca36b458
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sun Oct 28 20:24:40 2018 +0000
Commit:     David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sun Oct 28 20:24:40 2018 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=59ee040e

sci-biology/bcftools: Version bump to 1.9

Closes: https://bugs.gentoo.org/647714
Signed-off-by: David Seifert <soap <AT> gentoo.org>
Package-Manager: Portage-2.3.50, Repoman-2.3.11

 sci-biology/bcftools/Manifest                      |  1 +
 sci-biology/bcftools/bcftools-1.9.ebuild           | 47 ++++++++++++++++++++++
 .../bcftools/files/bcftools-1.9-fix-shebangs.patch |  8 ++++
 3 files changed, 56 insertions(+)

diff --git a/sci-biology/bcftools/Manifest b/sci-biology/bcftools/Manifest
index 333bb377e49..eef8daed7a7 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 00000000000..53e47bc01a8
--- /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 00000000000..76610187c49
--- /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.