74 lines
1.6 KiB
Bash
74 lines
1.6 KiB
Bash
# 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
|
|
}
|