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# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
EAPI=5
AUTOTOOLS_AUTORECONF=true
inherit autotools-utils git-r3
DESCRIPTION="Genome assembly package live cvs sources"
HOMEPAGE="http://sourceforge.net/projects/amos"
SRC_URI=""
EGIT_REPO_URI="git://amos.git.sourceforge.net/gitroot/amos/amos"
LICENSE="Artistic"
SLOT="0"
KEYWORDS=""
IUSE="mpi qt4"
DEPEND="
mpi? ( virtual/mpi )
dev-libs/boost
qt4? ( dev-qt/qtcore:4 )
sci-biology/blat
sci-biology/jellyfish"
RDEPEND="${DEPEND}
dev-perl/DBI
dev-perl/Statistics-Descriptive
sci-biology/mummer"
# --with-jellyfish location of Jellyfish headers
src_install() {
default
python_replicate_script "${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
mkdir -p "${D}/usr/share/${PN}/perl/AMOS" || die
mv "${D}"/usr/lib64/AMOS/*.pm "${D}/usr/share/${PN}/perl/AMOS" || die
mkdir -p "${D}"/usr/share/"${PN}"/perl/TIGR || die
mv "${D}"/usr/lib64/TIGR/*.pm "${D}"/usr/share/"${PN}"/perl/TIGR || die
echo "PERL5LIB=/usr/share/${PN}/perl" > "${S}/99${PN}"
doenvd "${S}/99${PN}" || die
# move also /usr/lib64/AMOS/AMOS.py to /usr/bin
mv "${D}"/usr/lib64/AMOS/*.py "${D}"/usr/bin || die
}
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