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# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/sci-biology/abyss/abyss-1.3.3.ebuild,v 1.5 2013/08/11 14:55:22 jlec Exp $
EAPI="4"
inherit autotools eutils toolchain-funcs
DESCRIPTION="Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler"
HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/abyss/"
SRC_URI="http://www.bcgsc.ca/downloads/abyss/${P}.tar.gz"
LICENSE="abyss"
SLOT="0"
IUSE="+mpi openmp"
KEYWORDS="~amd64 ~x86"
DEPEND="
dev-cpp/sparsehash
mpi? ( virtual/mpi )"
RDEPEND="${DEPEND}"
# todo: --enable-maxk=N configure option
# todo: fix automagic mpi toggling
src_prepare() {
tc-export AR
epatch \
"${FILESDIR}"/${P}-gcc-4.7.patch \
"${FILESDIR}"/${P}-ac_prog_ar.patch \
"${FILESDIR}"/${P}-samtoafg.patch
sed -i -e "s/-Werror//" configure.ac || die #365195
sed -i -e "/dist_pkgdoc_DATA/d" Makefile.am || die
eautoreconf
}
src_configure() {
econf \
--docdir="${EPREFIX}/usr/share/doc/${PF}" \
$(use_enable openmp)
}
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