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# Copyright 1999-2013 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
EAPI=4
inherit eutils toolchain-funcs
DESCRIPTION="An ultrafast memory-efficient short read aligner"
HOMEPAGE="http://bowtie-bio.sourceforge.net/"
SRC_URI="mirror://sourceforge/bowtie-bio/${P}-src.zip"
LICENSE="Artistic"
SLOT="0"
IUSE=""
KEYWORDS="amd64 x86 ~x64-macos"
DEPEND="app-arch/unzip"
RDEPEND=""
# NB: Bundles code from Maq (http://maq.sf.net) and the SeqAn library (http://www.seqan.de)
# TODO: properly report system CFLAGS in -DCOMPILE_OPTIONS
src_prepare() {
epatch "${FILESDIR}"/${P}-gcc-47.patch
}
src_compile() {
unset CFLAGS
emake \
CC="$(tc-getCC)" \
CPP="$(tc-getCXX)" \
CXX="$(tc-getCXX)" \
EXTRA_FLAGS="${LDFLAGS}" \
RELEASE_FLAGS=""
}
src_install() {
dobin bowtie bowtie-*
exeinto /usr/share/${PN}/scripts
doexe scripts/*
newman MANUAL bowtie.1
dodoc AUTHORS NEWS TUTORIAL
}
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