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# Copyright 1999-2013 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
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
}
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