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# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=6
inherit flag-o-matic toolchain-funcs
DESCRIPTION="Popular short read aligner for Next-generation sequencing data"
HOMEPAGE="http://bowtie-bio.sourceforge.net/"
SRC_URI="mirror://sourceforge/bowtie-bio/${P}-src.zip"
LICENSE="Artistic"
SLOT="1"
KEYWORDS="~amd64 ~x86 ~x64-macos"
IUSE="examples +tbb"
RDEPEND="tbb? ( dev-cpp/tbb )"
DEPEND="${RDEPEND}
sci-biology/seqan:1.4
app-arch/unzip"
DOCS=( AUTHORS NEWS TUTORIAL doc/README )
HTML_DOCS=( doc/{manual.html,style.css} )
PATCHES=(
"${FILESDIR}/${P}-_ContextLss-1.1-1.4.patch"
"${FILESDIR}/${P}-fix-setBegin-call.patch"
"${FILESDIR}/${P}-seqan-popcount.patch"
"${FILESDIR}/${P}-seqan-rename-ChunkPool.patch"
"${FILESDIR}/${P}-seqan-rename-fill-to-resize.patch"
"${FILESDIR}/${P}-spelling.patch"
"${FILESDIR}/${P}-tbb-tinythread-missing.patch"
"${FILESDIR}/${P}-unbundle-seqan.patch"
)
src_prepare() {
default
# remove bundled libraries, use system seqan 1.4
rm -rf SeqAn-1.1/ third_party/ || die
# innocuous non-security flags, prevent log pollution
append-cxxflags \
-Wno-unused-local-typedefs \
-Wno-unused-but-set-variable \
-Wno-unused-variable
}
src_compile() {
emake \
CC="$(tc-getCC)" \
CPP="$(tc-getCXX)" \
CFLAGS="" \
CXXFLAGS="" \
EXTRA_FLAGS="${LDFLAGS}" \
RELEASE_FLAGS="${CXXFLAGS}" \
WITH_TBB="$(usex tbb 1 0)"
}
src_install() {
dobin ${PN} ${PN}-*
exeinto /usr/libexec/${PN}
doexe scripts/*
newman MANUAL ${PN}.1
einstalldocs
if use examples; then
insinto /usr/share/${PN}
doins -r genomes indexes
fi
}
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