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# Copyright 1999-2018 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=5
PYTHON_COMPAT=( python2_7 )
inherit eutils python-single-r1 toolchain-funcs
MY_PV="${PV/_}" # convert from _rc2 to rc2
DESCRIPTION="De novo whole-genome shotgun DNA sequence OLC assembler"
HOMEPAGE="http://sourceforge.net/projects/wgs-assembler/"
SRC_URI="http://sourceforge.net/projects/${PN}/files/${PN}/wgs-8.3/wgs-${MY_PV}.tar.bz2"
LICENSE="GPL-2"
SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE="static-libs"
DEPEND="
x11-libs/libXt
!x11-terms/terminator"
RDEPEND="${DEPEND}
app-shells/tcsh
dev-perl/Log-Log4perl
sci-biology/jellyfish:2"
S="${WORKDIR}/wgs-${MY_PV}"
src_prepare() {
epatch "${FILESDIR}"/${P}-rename-jellyfish.patch
tc-export CC CXX
}
src_configure() {
cd "${S}/kmer" || die
./configure.sh || die
}
src_compile() {
# not really an install target
emake -C kmer -j1 install
emake -C src -j1 SITE_NAME=LOCAL
}
src_install() {
OSTYPE=$(uname)
MACHTYPE=$(uname -m)
MACHTYPE=${MACHTYPE/x86_64/amd64}
MY_S="${OSTYPE}-${MACHTYPE}"
sed -i 's|#!/usr/local/bin/|#!/usr/bin/env |' $(find $MY_S -type f) || die
sed -i '/sub getBinDirectory ()/ a return "/usr/bin";' ${MY_S}/bin/runCA* || die
sed -i '/sub getBinDirectoryShellCode ()/ a return "bin=/usr/bin\n";' ${MY_S}/bin/runCA* || die
sed -i '1 a use lib "/usr/share/'${PN}'/lib";' $(find $MY_S -name '*.p*') || die
dobin kmer/"${MY_S}"/bin/*
insinto /usr/$(get_libdir)/"${PN}"
use static-libs && doins kmer/"${MY_S}"/lib/*
insinto /usr/include/"${PN}"
doins kmer/"${MY_S}"/include/*
insinto /usr/share/${PN}/lib
doins -r "${MY_S}"/bin/TIGR
rm -rf "${MY_S}"/bin/TIGR || die
dobin "${MY_S}"/bin/*
use static-libs && dolib.a ${MY_S}/lib/*
dodoc README
# drop bundled jellyfish-2.0.0
rm "${ED}"/usr/bin/jellyfish || die
}
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