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# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=5
inherit toolchain-funcs
DESCRIPTION="STAR aligner: align RNA-seq reads to reference genome uncompressed suffix arrays"
HOMEPAGE="http://code.google.com/p/rna-star/"
SRC_URI="https://github.com/alexdobin/STAR/archive/STAR_"${PV}".tar.gz"
LICENSE="GPL-3"
SLOT="0"
KEYWORDS="~amd64"
IUSE=""
# sci-biology/htslib
DEPEND=""
RDEPEND="${DEPEND}"
S="${WORKDIR}"/STAR-STAR_"${PV}"
# contains bundled STAR-Fusion
src_prepare(){
sed -e "s/= gcc/= $(tc-getCC)/;s/-O2/${CFLAGS}/g" -i source/htslib/Makefile || die
sed -e "s/-O3/${CFLAGS}/g" -i source/Makefile || die
}
src_compile(){
cd source || die
emake STAR
}
src_install(){
dobin source/STAR
dodoc doc/STARmanual.pdf
}
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