[gentoo-commits] proj/sci:master commit in: sci-biology/bcftools/

[Martin Mokrejs]

commit:     7d318bbea490d8786ab6336b355529b08df8ee38
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Jul 20 20:14:43 2017 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Jul 28 20:05:19 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=7d318bbe

sci-biology/bcftools: version bump

This should be kept unmasked as it uses bundled static lib of htslib-1.5
so practically avoid dependency on sci-libs/htslib-1.5.

Package-Manager: Portage-2.3.6, Repoman-2.3.2

 sci-biology/bcftools/bcftools-1.5.ebuild | 29 +++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)

diff --git a/sci-biology/bcftools/bcftools-1.5.ebuild b/sci-biology/bcftools/bcftools-1.5.ebuild
new file mode 100644
index 000000000..b194609b6
--- /dev/null
+++ b/sci-biology/bcftools/bcftools-1.5.ebuild
@@ -0,0 +1,29 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=5
+
+inherit toolchain-funcs
+
+DESCRIPTION="Utilities for variant calling and manipulating VCF and BCF files"
+HOMEPAGE="http://www.htslib.org"
+SRC_URI="https://github.com/samtools/bcftools/releases/download/"${PV}"/"${P}".tar.bz2"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+# compiles bundled sci-libs/htslib-"${PV}" as a static library and links it into binaries
+DEPEND="dev-lang/perl"
+RDEPEND="${DEPEND}"
+
+src_prepare(){
+	sed -e "s@gcc@$(tc-getCC)@" \
+		-e 's#prefix      = /usr/local#prefix      = "${EPREFIX}"/usr#' \
+		-e "s@CFLAGS   = -g -Wall -Wc++-compat -O2@#CFLAGS   = ${CFLAGS}@" -i Makefile || die
+
+	sed -e "s@gcc@$(tc-getCC)@" \
+		-e 's#prefix      = /usr/local#prefix      = "${EPREFIX}"/usr#' \
+		-e "s@CFLAGS   = -g -Wall -O2@#CFLAGS   = ${CFLAGS}@" -i htslib-*/Makefile || die
+}