| # Copyright 1999-2013 Gentoo Foundation |
| # Distributed under the terms of the GNU General Public License v2 |
| # $Id$ |
| |
| EAPI=4 |
| |
| inherit flag-o-matic toolchain-funcs |
| |
| MY_PV=${PV//./_} |
| |
| DESCRIPTION="SHort Read Mapping Package" |
| HOMEPAGE="http://compbio.cs.toronto.edu/shrimp/" |
| SRC_URI="http://compbio.cs.toronto.edu/shrimp/releases/SHRiMP_${MY_PV}.src.tar.gz" |
| |
| LICENSE="shrimp" |
| SLOT="0" |
| KEYWORDS="amd64 x86" |
| IUSE="custom-cflags" |
| |
| # file collision on /usr/bin/utils #453044 |
| DEPEND=" |
| !sci-biology/emboss |
| !sci-mathematics/cado-nfs" |
| RDEPEND="${DEPEND}" |
| |
| S=${WORKDIR}/SHRiMP_${MY_PV} |
| |
| pkg_setup() { |
| if [[ ${CC} == *gcc* ]] && ! tc-has-openmp; then |
| elog "Please set CC to an OPENMP capable compiler (e.g. gcc[openmp] or icc" |
| die "C compiler lacks OPENMP support" |
| fi |
| } |
| |
| src_prepare() { |
| sed -e '1 a #include <stdint.h>' -i common/dag_glue.cpp || die |
| # respect LDFLAGS wrt 331823 |
| sed -i -e "s/LDFLAGS/LIBS/" -e "s/\$(LD)/& \$(LDFLAGS)/" \ |
| -e 's/-static//' Makefile || die |
| } |
| |
| src_compile() { |
| append-flags -fopenmp |
| use custom-cflags || append-flags -O3 # per instructions in BUILDING |
| tc-export CXX |
| emake CXXFLAGS="${CXXFLAGS}" LDFLAGS="${LDFLAGS}" |
| } |
| |
| src_install() { |
| rm bin/README |
| dobin bin/* |
| insinto /usr/share/${PN} |
| doins -r utils |
| dodoc HISTORY README TODO SPLITTING_AND_MERGING |
| } |