| # Copyright 1999-2015 Gentoo Foundation |
| # Distributed under the terms of the GNU General Public License v2 |
| # $Id$ |
| |
| EAPI=5 |
| |
| PYTHON_COMPAT=( python2_7 ) |
| |
| inherit flag-o-matic python-single-r1 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 +cpu_flags_x86_sse2" |
| |
| REQUIRED_USE="${PYTHON_REQUIRED_USE}" |
| |
| # file collision on /usr/bin/utils #453044 |
| DEPEND="!sci-mathematics/cado-nfs" |
| RDEPEND="${DEPEND} |
| ${PYTHON_DEPS}" |
| |
| S=${WORKDIR}/SHRiMP_${MY_PV} |
| |
| pkg_pretend() { |
| use cpu_flags_x86_sse2 || die "This package needs sse2 support in your CPU" |
| } |
| |
| pkg_setup() { |
| if [[ ${CC} == *gcc* ]] && ! tc-has-openmp; then |
| elog "Please set CC to an OPENMP capable compiler (e.g. gcc[openmp] or icc" |
| die "C compiler lacks OPENMP support" |
| fi |
| python-single-r1_pkg_setup |
| } |
| |
| src_prepare() { |
| sed \ |
| -e '1 a #include <stdint.h>' \ |
| -i common/dag_glue.cpp || die |
| # respect LDFLAGS wrt 331823 |
| sed \ |
| -e "s/LDFLAGS/LIBS/" \ |
| -e "s/\$(LD)/& \$(LDFLAGS)/" \ |
| -e 's/-static//' \ |
| -i Makefile || die |
| |
| append-flags -fopenmp |
| if ! use custom-cflags; then |
| append-flags -O3 |
| replace-flags -O* -O3 |
| fi |
| tc-export CXX |
| |
| cd utils || die |
| sed -e '/^#!/d' -i *py || die |
| sed -e '1i#!/usr/bin/python' -i *py || die |
| } |
| |
| src_compile() { |
| emake CXXFLAGS="${CXXFLAGS}" LDFLAGS="${LDFLAGS}" |
| } |
| |
| src_install() { |
| local i |
| newdoc bin/README README.bin && rm bin/README |
| dobin bin/* utils/split-contigs utils/temp-sink |
| dodoc HISTORY README TODO SPLITTING_AND_MERGING SCORES_AND_PROBABILITES |
| |
| pushd utils > /dev/null |
| |
| python_doscript *py |
| |
| rm *.py *.o *.c split-contigs temp-sink || die |
| insinto /usr/share/${PN} |
| doins -r * |
| } |