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# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=6
inherit toolchain-funcs
DESCRIPTION="Popular short read aligner for Next-generation sequencing data"
HOMEPAGE="http://bowtie-bio.sourceforge.net/bowtie2/"
SRC_URI="mirror://sourceforge/project/${PN}-bio/${PN}2/${PV}/${PN}2-${PV}-source.zip"
LICENSE="GPL-3"
SLOT="2"
KEYWORDS="~amd64 ~x86"
IUSE="examples cpu_flags_x86_sse2 +tbb"
RDEPEND="dev-lang/perl
tbb? ( dev-cpp/tbb )"
DEPEND="${RDEPEND}
app-arch/unzip"
S="${WORKDIR}/${PN}2-${PV}"
DOCS=( AUTHORS NEWS TUTORIAL )
HTML_DOCS=( doc/{manual.html,style.css} )
PATCHES=( "${FILESDIR}/${PN}-2.2.9-fix-c++14.patch" )
pkg_pretend() {
if ! use cpu_flags_x86_sse2 ; then
eerror "This package requires a CPU supporting the SSE2 instruction set."
die "SSE2 support missing"
fi
}
src_compile() {
emake \
CC="$(tc-getCC)" \
CPP="$(tc-getCXX)" \
CXX="$(tc-getCXX)" \
CFLAGS="" \
CXXFLAGS="" \
EXTRA_FLAGS="${LDFLAGS}" \
RELEASE_FLAGS="${CXXFLAGS} -msse2" \
WITH_TBB="$(usex tbb 1 0)"
}
src_install() {
dobin ${PN}2 ${PN}2-*
exeinto /usr/libexec/${PN}2
doexe scripts/*
newman MANUAL ${PN}2.1
einstalldocs
if use examples; then
insinto /usr/share/${PN}2
doins -r example
fi
}
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