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# Copyright 1999-2012 Gentoo Foundation
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# Distributed under the terms of the GNU General Public License v2
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# $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 $
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EAPI="2"
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inherit eutils multilib toolchain-funcs
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DESCRIPTION="A de novo whole-genome shotgun DNA sequence assembler, also known as the Celera Assembler and CABOG"
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HOMEPAGE="http://sourceforge.net/projects/wgs-assembler/"
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SRC_URI="mirror://sourceforge/${PN}/wgs-${PV}.tar.bz2"
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LICENSE="GPL-2"
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SLOT="0"
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IUSE=""
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KEYWORDS="~amd64 x86"
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DEPEND="x11-libs/libXt
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!x11-terms/terminator"
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RDEPEND="${DEPEND}
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app-shells/tcsh
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dev-perl/Log-Log4perl"
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S="${WORKDIR}/wgs-${PV}"
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src_configure() {
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sed -i -e "s/CC *= *gcc/CC = $(tc-getCC)/" \
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-e "s/CXX *= *g++/CXX = $(tc-getCXX)/" \
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"${S}"/src/c_make.as || die
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sed -i -e "s/CC *:=.*/CC := $(tc-getCC)/" \
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-e "s/CXX *:=.*/CXX := $(tc-getCXX)/" \
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"${S}"/kmer/configure.sh || die
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cd "${S}/kmer"
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./configure.sh || die
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}
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src_compile() {
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# not really an install target
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emake -C kmer -j1 install || die
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emake -C src -j1 SITE_NAME=LOCAL || die
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}
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src_install() {
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OSTYPE=$(uname)
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MACHTYPE=$(uname -m)
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MACHTYPE=${MACHTYPE/x86_64/amd64}
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MY_S="${OSTYPE}-${MACHTYPE}"
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sed -i 's|#!/usr/local/bin/|#!/usr/bin/env |' $(find $MY_S -type f) || die
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sed -i '/sub getBinDirectory ()/ a return "/usr/bin";' ${MY_S}/bin/runCA* || die
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sed -i '/sub getBinDirectoryShellCode ()/ a return "bin=/usr/bin\n";' ${MY_S}/bin/runCA* || die
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sed -i '1 a use lib "/usr/share/'${PN}'/lib";' $(find $MY_S -name '*.p*') || die
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dobin kmer/${MY_S}/bin/* || die
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insinto /usr/$(get_libdir)/${PN}
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doins kmer/${MY_S}/lib/* || die
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# Collisions
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# dolib.a kmer/${MY_S}/lib/* || die
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insinto /usr/include/${PN}
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doins kmer/${MY_S}/include/*
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insinto /usr/share/${PN}
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doins -r ${MY_S}/bin/spec
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insinto /usr/share/${PN}/lib
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doins -r ${MY_S}/bin/TIGR || die
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rm -rf ${MY_S}/bin/{TIGR,spec}
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dobin ${MY_S}/bin/* || die
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dolib.a ${MY_S}/lib/* || die
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dodoc README
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}
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