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# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=5
DESCRIPTION="Assembler to combine Sanger, Roche 454 and Illumina Solexa reads"
HOMEPAGE="http://www.genome.umd.edu/masurca.html"
SRC_URI="ftp://ftp.genome.umd.edu/pub/MaSuRCA/MaSuRCA-"${PV}".tar.gz
ftp://ftp.genome.umd.edu/pub/MaSuRCA/MaSuRCA_QuickStartGuide.pdf"
LICENSE="BSD GPL-2 GPL-3"
SLOT="0"
KEYWORDS=""
IUSE=""
DEPEND="dev-lang/perl
app-arch/bzip2"
RDEPEND="${DEPEND}
>=sci-biology/quorum-0.2.1
>=sci-biology/jellyfish-1.1.11"
# the ebuild mimics "${S}"/install.sh
src_configure(){
cd jellyfish || die
econf
cd ../CA/kmer || die
econf
cd ../../SuperReads || die
econf
cd ../quorum || die
econf --enable-relative-paths --with-relative-jf-path
}
src_compile(){
cd jellyfish || die
default
cd ../CA/kmer || die
default
cd ../../CA/src || die
default
cd ../SuperReads || die
default
cd ../quorum || die
default
}
src_install(){
dobin masurca
dodoc sr_config_example.txt
}
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