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# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
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 *
}
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