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# Copyright 1999-2014 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
EAPI=5
inherit eutils toolchain-funcs
DESCRIPTION="An ultrafast memory-efficient short read aligner"
HOMEPAGE="http://bowtie-bio.sourceforge.net/"
SRC_URI="mirror://sourceforge/project/${PN}-bio/${PN}2/${PV}/${PN}2-${PV}-source.zip"
LICENSE="GPL-3"
SLOT="2"
IUSE="examples"
KEYWORDS="~amd64 ~x86"
RDEPEND="dev-lang/perl"
DEPEND="${RDEPEND}
app-arch/unzip"
S="${WORKDIR}/${PN}2-${PV}"
pkg_pretend() {
grep "sse2" /proc/cpuinfo > /dev/null
if [[ $? -ne 0 ]] ; then
ewarn "Your processor does not support sse2. Bowtie will probably not work on this machine."
fi
}
src_prepare() {
epatch "${FILESDIR}/${P}-buildsystem.patch"
}
src_compile() {
emake \
CC="$(tc-getCC)" \
CPP="$(tc-getCXX)" \
EXTRA_FLAGS="${LDFLAGS}" \
RELEASE_FLAGS="${CXXFLAGS} -msse2"
}
src_install() {
dobin ${PN}2 ${PN}2-*
exeinto /usr/share/${PN}2/scripts
doexe scripts/*
newman MANUAL ${PN}2.1
dodoc AUTHORS NEWS TUTORIAL
dohtml doc/manual.html doc/style.css
if use examples; then
insinto /usr/share/${PN}2
doins -r example
fi
}
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