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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/amos/amos-3.1.0-r1.ebuild,v 1.1 2013/12/29 00:24:16 jlec Exp $
EAPI=5
PYTHON_COMPAT=( python2_7 )
inherit eutils python-r1
DESCRIPTION="A Modular, Open-Source whole genome assembler"
HOMEPAGE="http://amos.sourceforge.net/"
SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz"
LICENSE="Artistic"
SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE="qt4"
DEPEND="
dev-libs/boost
qt4? ( dev-qt/qtcore:4 )"
RDEPEND="${DEPEND}
dev-lang/perl
dev-perl/DBI
dev-perl/Statistics-Descriptive
sci-biology/blat
sci-biology/mummer"
MAKEOPTS+=" -j1"
src_prepare() {
epatch \
"${FILESDIR}"/${P}-gcc-4.7.patch \
"${FILESDIR}"/${P}-goBambus2.py-indent-and-cleanup.patch
}
# amos-3.1.0-r2/work/amos-3.1.0/src/Bambus/Untangler/DotLib.pm
# amos-3.1.0-r2/work/amos-3.1.0/src/Bambus/Untangler/AsmLib.pm
# amos-3.1.0-r2/work/amos-3.1.0/src/PerlModules/FASTAreader.pm
# amos-3.1.0-r2/work/amos-3.1.0/src/PerlModules/AmosFoundation.pm
# amos-3.1.0-r2/work/amos-3.1.0/src/PerlModules/Foundation.pm
# amos-3.1.0-r2/work/amos-3.1.0/src/PerlModules/AmosLib.pm
# amos-3.1.0-r2/work/amos-3.1.0/src/PerlModules/FASTArecord.pm
# amos-3.1.0-r2/work/amos-3.1.0/src/PerlModules/ParseFasta.pm
# amos-3.1.0-r2/work/amos-3.1.0/src/PerlModules/xfig.pm
# amos-3.1.0-r2/work/amos-3.1.0/src/PerlModules/FASTAwriter.pm
# amos-3.1.0-r2/work/amos-3.1.0/src/PerlModules/FASTAgrammar.pm
# amos-3.1.0-r2/work/amos-3.1.0/src/PerlModules/FASTAiterator.pm
# --with-jellyfish location of Jellyfish headers
src_install() {
default
python_replicate_script "${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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