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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/wgs-assembler/wgs-assembler-7.0-r1.ebuild,v 1.3 2012/11/13 19:19:00 nativemad Exp $
EAPI=4
PYTHON_DEPEND=2
inherit eutils python toolchain-funcs
MY_PV="8.3rc1"
DESCRIPTION="De novo whole-genome shotgun DNA sequence assembler also known as Celera Assembler and CABOG"
HOMEPAGE="http://sourceforge.net/projects/wgs-assembler/"
#SRC_URI="mirror://sourceforge/${PN}/wgs-${PV}.tar.bz2"
SRC_URI="http://sourceforge.net/projects/wgs-assembler/files/wgs-assembler/wgs-8.3/wgs-8.3rc1.tar.bz2"
LICENSE="GPL-2"
SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE="static-libs"
DEPEND="
x11-libs/libXt
!x11-terms/terminator"
RDEPEND="${DEPEND}
app-shells/tcsh
dev-perl/Log-Log4perl"
S="${WORKDIR}/wgs-${MY_PV}"
pkg_setup() {
python_set_active_version 2
python_pkg_setup
}
src_prepare() {
# epatch \
# "${FILESDIR}"/${P}-build.patch
tc-export CC CXX
}
src_configure() {
cd "${S}/kmer"
./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
# avoid file collision
rm -f ${D}/usr/bin/jellyfish
}
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