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# Copyright 1999-2012 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/sci-biology/wgs-assembler/wgs-assembler-6.1.ebuild,v 1.4 2012/11/10 12:01:51 jlec Exp $
EAPI="2"
inherit eutils multilib toolchain-funcs
DESCRIPTION="A de novo whole-genome shotgun DNA sequence assembler, also known as the Celera Assembler and CABOG"
HOMEPAGE="http://sourceforge.net/projects/wgs-assembler/"
SRC_URI="mirror://sourceforge/${PN}/wgs-${PV}.tar.bz2"
LICENSE="GPL-2"
SLOT="0"
IUSE=""
KEYWORDS="~amd64 x86"
DEPEND="x11-libs/libXt
!x11-terms/terminator"
RDEPEND="${DEPEND}
app-shells/tcsh
dev-perl/Log-Log4perl"
S="${WORKDIR}/wgs-${PV}"
src_configure() {
sed -i -e "s/CC *= *gcc/CC = $(tc-getCC)/" \
-e "s/CXX *= *g++/CXX = $(tc-getCXX)/" \
"${S}"/src/c_make.as || die
sed -i -e "s/CC *:=.*/CC := $(tc-getCC)/" \
-e "s/CXX *:=.*/CXX := $(tc-getCXX)/" \
"${S}"/kmer/configure.sh || die
cd "${S}/kmer"
./configure.sh || die
}
src_compile() {
# not really an install target
emake -C kmer -j1 install || die
emake -C src -j1 SITE_NAME=LOCAL || die
}
src_install() {
OSTYPE=$(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/* || die
insinto /usr/$(get_libdir)/${PN}
doins kmer/${MY_S}/lib/* || die
# Collisions
# dolib.a kmer/${MY_S}/lib/* || die
insinto /usr/include/${PN}
doins kmer/${MY_S}/include/*
insinto /usr/share/${PN}
doins -r ${MY_S}/bin/spec
insinto /usr/share/${PN}/lib
doins -r ${MY_S}/bin/TIGR || die
rm -rf ${MY_S}/bin/{TIGR,spec}
dobin ${MY_S}/bin/* || die
dolib.a ${MY_S}/lib/* || die
dodoc README
}
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