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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 python-r1
PERL_EXPORT_PHASE_FUNCTIONS=no
inherit perl-module eutils toolchain-funcs
DESCRIPTION="Whole genome assembler, Hawkeye and AMOScmp to compare multiple assemblies"
HOMEPAGE="http://amos.sourceforge.net/"
SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz"
LICENSE="Artistic"
SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE="mpi qt4"
DEPEND="
mpi? ( virtual/mpi )
dev-libs/boost
qt4? ( dev-qt/qtcore:4[qt3support]
dev-qt/qt3support:4 )
sci-biology/blat
sci-biology/jellyfish"
RDEPEND="${DEPEND}
dev-lang/perl
dev-perl/DBI
dev-perl/Statistics-Descriptive
sci-biology/mummer"
MAKEOPTS+=" -j1"
src_prepare() {
epatch \
"${FILESDIR}"/${P}-gcc-4.7.patch \
"${FILESDIR}"/${P}-goBambus2.py-indent-and-cleanup.patch
# $ gap-links
# ERROR: Could not open file LIBGUESTFS_PATH=/usr/share/guestfs/appliance/
# $
}
# --with-jellyfish location of Jellyfish headers
src_install() {
default
python_replicate_script "${ED}"/usr/bin/goBambus2
# bambus needs TIGR::FASTAreader.pm and others
# configure --libdir sadly copies both *.a files and *.pm into /usr/lib64/AMOS/ and /usr/lib64/TIGR/, work around it
perl_set_version
insinto ${VENDOR_LIB}/AMOS
doins "${D}"/usr/lib64/AMOS/*.pm
insinto ${VENDOR_LIB}/TIGR
doins "${D}"/usr/lib64/TIGR/*.pm
# move also /usr/lib64/AMOS/AMOS.py to /usr/bin
mv "${D}"/usr/lib64/AMOS/*.py "${D}"/usr/bin || die
# zap the mis-placed files ('make install' is at fault)
rm -f "${D}"/usr/lib64/AMOS/*.pm
rm -rf "${D}"/usr/lib64/TIGR
echo AMOSCONF="${EPREFIX}"/etc/amos.acf > "${S}"/99amos || die
mkdir -p "${ED}"/etc || die
touch "${ED}"/etc/amos.acf || die
doenvd "${S}/99amos"
}
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