76 lines
2.1 KiB
Bash
76 lines
2.1 KiB
Bash
# Copyright 1999-2017 Gentoo Foundation
|
|
# Distributed under the terms of the GNU General Public License v2
|
|
|
|
EAPI=5
|
|
|
|
inherit eutils flag-o-matic toolchain-funcs
|
|
|
|
MY_P=${PN}_${PV}
|
|
|
|
DESCRIPTION="A sequence assembler for very short reads"
|
|
HOMEPAGE="http://www.ebi.ac.uk/~zerbino/velvet/"
|
|
SRC_URI="http://www.ebi.ac.uk/~zerbino/velvet/${MY_P}.tgz"
|
|
|
|
LICENSE="GPL-2"
|
|
SLOT="0"
|
|
KEYWORDS="~amd64 ~x86"
|
|
IUSE="doc openmp"
|
|
|
|
RDEPEND=""
|
|
DEPEND="${RDEPEND}
|
|
doc? ( virtual/latex-base )"
|
|
|
|
S="${WORKDIR}"/${MY_P}
|
|
|
|
src_prepare() {
|
|
if ! use doc; then
|
|
sed -i -e '/default :/ s/doc//' "${S}"/Makefile || die
|
|
fi
|
|
elog "Upstream recommends using -O3 in CFLAGS"
|
|
echo
|
|
elog "To adjust the MAXKMERLENGTH, CATEGORIES, BIGASSEMBLY, LONGSEQUENCES parameters"
|
|
elog "as described in the PDF manual, please set the variables by prepending VELVET_ in"
|
|
elog "front of it. For example VELVET_MAXKMERLENGTH, VELVET_CATEGORIES, ..."
|
|
elog "Set them either in your environment or in /etc/portage/make.conf, then re-emerge"
|
|
elog "the package. For example:"
|
|
elog " VELVET_MAXKMERLENGTH=NN emerge [options] velvet"
|
|
|
|
if [[ $(tc-getCC) =~ gcc ]]; then
|
|
local eopenmp=-fopenmp
|
|
elif [[ $(tc-getCC) =~ icc ]]; then
|
|
local eopenmp=-openmp
|
|
else
|
|
elog "Cannot detect compiler type so not setting openmp support"
|
|
fi
|
|
append-flags -fPIC ${eopenmp}
|
|
append-ldflags ${eopenmp}
|
|
|
|
tc-export CC
|
|
|
|
MAKE_XOPTS=(
|
|
CC=$(tc-getCC)
|
|
CFLAGS="${CFLAGS}"
|
|
OPT="${CFLAGS}"
|
|
)
|
|
use openmp && MAKE_XOPTS+=( OPENMP=1 )
|
|
[[ ! -z "${VELVET_MAXKMERLENGTH}" ]] && MAKE_XOPTS+=( MAXKMERLENGTH=${VELVET_MAXKMERLENGTH} )
|
|
[[ ! -z "${VELVET_CATEGORIES}" ]] && MAKE_XOPTS+=( CATEGORIES=${VELVET_CATEGORIES} )
|
|
[[ ! -z "${VELVET_BIGASSEMBLY}" ]] && MAKE_XOPTS+=( BIGASSEMBLY=${VELVET_BIGASSEMBLY} )
|
|
[[ ! -z "${VELVET_LONGSEQUENCES}" ]] && MAKE_XOPTS+=( LONGSEQUENCES=${VELVET_LONGSEQUENCES} )
|
|
}
|
|
|
|
src_compile() {
|
|
emake "${MAKE_XOPTS[@]}" -j1
|
|
emake "${MAKE_XOPTS[@]}" -j1 color
|
|
}
|
|
|
|
src_test() {
|
|
emake "${MAKE_XOPTS[@]}" -j1 test
|
|
}
|
|
|
|
src_install() {
|
|
dobin velvet{g,h,g_de,h_de}
|
|
insinto /usr/share/${PN}
|
|
doins -r contrib
|
|
dodoc Manual.pdf CREDITS.txt ChangeLog
|
|
}
|