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# Copyright 1999-2013 Gentoo Foundation
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# Distributed under the terms of the GNU General Public License v2
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# $Header: /var/cvsroot/gentoo-x86/sci-biology/shrimp/shrimp-2.2.3.ebuild,v 1.2 2013/01/23 10:06:29 patrick Exp $
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EAPI=4
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PYTHON_DEPEND=2
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inherit flag-o-matic python toolchain-funcs
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MY_PV=${PV//./_}
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DESCRIPTION="SHort Read Mapping Package"
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HOMEPAGE="http://compbio.cs.toronto.edu/shrimp/"
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SRC_URI="http://compbio.cs.toronto.edu/shrimp/releases/SHRiMP_${MY_PV}.src.tar.gz"
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LICENSE="as-is"
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SLOT="0"
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KEYWORDS="~amd64 ~x86"
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IUSE="custom-cflags"
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# file collision on /usr/bin/utils #453044
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DEPEND="!sci-mathematics/cado-nfs"
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RDEPEND="${DEPEND}"
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S=${WORKDIR}/SHRiMP_${MY_PV}
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pkg_setup() {
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if [[ ${CC} == *gcc* ]] && ! tc-has-openmp; then
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elog "Please set CC to an OPENMP capable compiler (e.g. gcc[openmp] or icc"
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die "C compiler lacks OPENMP support"
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fi
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python_set_active_version 2
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python_pkg_setup
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}
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src_prepare() {
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sed -e '1 a #include <stdint.h>' -i common/dag_glue.cpp || die
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# respect LDFLAGS wrt 331823
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sed -i -e "s/LDFLAGS/LIBS/" -e "s/\$(LD)/& \$(LDFLAGS)/" \
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-e 's/-static//' Makefile || die
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python_convert_shebangs -r -- 2 utils
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}
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src_compile() {
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append-flags -fopenmp
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if ! use custom-cflags; then
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append-flags -O3
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replace-flags -O2 -O3
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fi
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tc-export CXX
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emake CXXFLAGS="${CXXFLAGS}" LDFLAGS="${LDFLAGS}"
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}
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src_install() {
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local i
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dobin bin/* utils/split-contigs utils/temp-sink
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dodoc HISTORY README TODO SPLITTING_AND_MERGING SCORES_AND_PROBABILITES
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pushd utils > /dev/null
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for i in *py; do
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newbin ${i} ${i%.py}
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done
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rm *.py *.o *.c split-contigs temp-sink || die
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insinto /usr/share/${PN}
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doins -r *
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}
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