| # Copyright 1999-2013 Gentoo Foundation |
| # Distributed under the terms of the GNU General Public License v2 |
| # $Id$ |
| |
| 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 recommendes using -O3 in CFLAGS" |
| echo |
| elog "To adjust the MAXKMERLENGTH or CATEGORIES parameters as described in the manual," |
| elog "please set the variables VELVET_MAXKMERLENGTH or VELVET_CATEGORIES in your" |
| elog "environment or /etc/make.conf, then re-emerge the package. For example:" |
| elog " VELVET_MAXKMERLENGTH=NN emerge [options] velvet" |
| MAKEOPTS+=" -j1" |
| |
| 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}" |
| ) |
| if [[ ${VELVET_MAXKMERLENGTH} != "" ]]; then MAKE_XOPTS+=( MAXKMERLENGTH=${VELVET_MAXKMERLENGTH} ); fi |
| if [[ ${VELVET_CATEGORIES} != "" ]]; then MAKE_XOPTS+=( CATEGORIES=${VELVET_CATEGORIES} ); fi |
| } |
| |
| src_compile() { |
| emake "${MAKE_XOPTS[@]}" |
| emake "${MAKE_XOPTS[@]}" color |
| } |
| |
| src_test() { |
| emake "${MAKE_XOPTS[@]}" test |
| } |
| |
| src_install() { |
| dobin velvet{g,h,g_de,h_de} |
| insinto /usr/share/${PN} |
| doins -r contrib |
| dodoc Manual.pdf CREDITS.txt ChangeLog |
| } |
