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authorRobin H. Johnson <robbat2@gentoo.org>2015-08-08 13:49:04 -0700
committerRobin H. Johnson <robbat2@gentoo.org>2015-08-08 17:38:18 -0700
commit56bd759df1d0c750a065b8c845e93d5dfa6b549d (patch)
tree3f91093cdb475e565ae857f1c5a7fd339e2d781e /sci-biology/samtools/samtools-1.0-r1.ebuild
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proj/gentoo: Initial commit
This commit represents a new era for Gentoo: Storing the gentoo-x86 tree in Git, as converted from CVS. This commit is the start of the NEW history. Any historical data is intended to be grafted onto this point. Creation process: 1. Take final CVS checkout snapshot 2. Remove ALL ChangeLog* files 3. Transform all Manifests to thin 4. Remove empty Manifests 5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$ 5.1. Do not touch files with -kb/-ko keyword flags. Signed-off-by: Robin H. Johnson <robbat2@gentoo.org> X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed
Diffstat (limited to 'sci-biology/samtools/samtools-1.0-r1.ebuild')
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1 files changed, 73 insertions, 0 deletions
diff --git a/sci-biology/samtools/samtools-1.0-r1.ebuild b/sci-biology/samtools/samtools-1.0-r1.ebuild
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+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit eutils multilib python-r1 toolchain-funcs
+
+DESCRIPTION="Utilities for SAM (Sequence Alignment/Map), a format for large nucleotide sequence alignments"
+HOMEPAGE="http://www.htslib.org/"
+SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 x86 ~amd64-linux ~x86-linux ~x64-macos"
+IUSE="examples"
+
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+CDEPEND="
+ sys-libs/ncurses
+ sci-libs/htslib"
+
+RDEPEND="${CDEPEND}
+ dev-lang/lua
+ dev-lang/perl"
+DEPEND="${CDEPEND}
+ virtual/pkgconfig"
+
+src_prepare() {
+ find htslib-1.0 -delete || die
+
+ sed -i 's~/software/bin/python~/usr/bin/env python~' "${S}"/misc/varfilter.py || die
+
+ epatch "${FILESDIR}"/${P}-buildsystem.patch
+
+ tc-export CC AR
+
+ sed \
+ -e '/htslib.mk/d' \
+ -i Makefile || die
+
+}
+
+src_compile() {
+ local mymakeargs=(
+ LIBCURSES="$($(tc-getPKG_CONFIG) --libs ncurses)"
+ HTSDIR="${EPREFIX}/usr/include"
+ HTSLIB=$($(tc-getPKG_CONFIG) --libs htslib)
+ BAMLIB="libbam.so"
+ )
+ emake "${mymakeargs[@]}"
+}
+
+src_install() {
+ dobin samtools $(find misc -type f -executable)
+
+ python_replicate_script "${ED}"/usr/bin/varfilter.py
+ dolib.so libbam.so*
+
+ 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
+}