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

[Martin Mokrejs]

commit:     6948e2872a1c6182e8e325edd5e48a21bd713443
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Apr 30 13:23:16 2017 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Apr 30 13:23:16 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=6948e287

sci-biology/samtools: version bump

Compiles fine against htslib-1.4 but because htslib-1.4 is not KEYWORDed
keeping samtools-1.4 masked as well.

Package-Manager: Portage-2.3.5, Repoman-2.3.2

 sci-biology/samtools/samtools-1.4.ebuild | 82 ++++++++++++++++++++++++++++++++
 1 file changed, 82 insertions(+)

diff --git a/sci-biology/samtools/samtools-1.4.ebuild b/sci-biology/samtools/samtools-1.4.ebuild
new file mode 100644
index 000000000..b0bd40b82
--- /dev/null
+++ b/sci-biology/samtools/samtools-1.4.ebuild
@@ -0,0 +1,82 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit eutils multilib python-r1 toolchain-funcs
+
+DESCRIPTION="Utilities for SAM (Sequence Alignment/Map) and BAM files"
+HOMEPAGE="http://www.htslib.org/"
+SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS=""
+# KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
+IUSE="examples"
+
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+CDEPEND="
+	sys-libs/ncurses:0=
+	>=sci-libs/htslib-${PV}"
+
+RDEPEND="${CDEPEND}
+	dev-lang/lua
+	dev-lang/perl"
+DEPEND="${CDEPEND}
+	virtual/pkgconfig"
+
+src_prepare() {
+	find htslib-* -delete || die
+
+	sed -i 's~/software/bin/python~/usr/bin/env python~' "${S}"/misc/varfilter.py || die
+
+	tc-export CC AR
+
+	sed \
+		-e '/htslib.mk/d' \
+		-i Makefile || die
+}
+
+src_compile() {
+	local mymakeargs=(
+		LIBCURSES="$($(tc-getPKG_CONFIG) --libs ncurses)"
+		HTSDIR="${EPREFIX}/usr/include"
+		HTSLIB=$($(tc-getPKG_CONFIG) --libs htslib)
+		BAMLIB="libbam.so"
+		CC=$(tc-getCC) CFLAGS="${CFLAGS}"
+		)
+	emake "${mymakeargs[@]}"
+}
+
+src_test() {
+	local mymakeargs=(
+		LIBCURSES="$($(tc-getPKG_CONFIG) --libs ncurses)"
+		HTSDIR="${EPREFIX}/usr/include"
+		HTSLIB=$($(tc-getPKG_CONFIG) --libs htslib)
+		BAMLIB="libbam.so"
+		)
+	LD_LIBRARY_PATH="${S}" emake "${mymakeargs[@]}" test
+}
+
+src_install() {
+	dobin samtools $(find misc -type f -executable)
+
+	python_replicate_script "${ED}"/usr/bin/varfilter.py
+	#dolib.so libbam.so*
+	dolib libbam.a
+
+	insinto /usr/include/bam
+	doins *.h
+
+	doman ${PN}.1
+	dodoc AUTHORS NEWS README
+
+	if use examples; then
+		insinto /usr/share/${PN}
+		doins -r examples
+	fi
+}