sci-biology/shrimp: Vesion Bump

Package-Manager: portage-2.2.0_alpha141/cvs/Linux x86_64
Manifest-Sign-Key: 0x70EB7916

1 files changed, 64 insertions, 0 deletions

diff --git a/sci-biology/shrimp/shrimp-2.2.3.ebuild b/sci-biology/shrimp/shrimp-2.2.3.ebuild
new file mode 100644
index 000000000000..ce8cbe51b610
--- /dev/null
+++ b/sci-biology/shrimp/shrimp-2.2.3.ebuild
@@ -0,0 +1,64 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/shrimp/shrimp-2.2.3.ebuild,v 1.1 2012/10/18 18:17:38 jlec Exp $
+
+EAPI=4
+
+PYTHON_DEPEND=2
+
+inherit flag-o-matic python 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="as-is"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="custom-cflags"
+
+S=${WORKDIR}/SHRiMP_${MY_PV}
+
+pkg_setup() {
+	if [[ ${CC} == *gcc* ]] &&	! tc-has-openmp; then
+		elog "Please set CC to an OPENMP capable compiler (e.g. gcc[openmp] or icc"
+		die "C compiler lacks OPENMP support"
+	fi
+	python_set_active_version 2
+	python_pkg_setup
+}
+
+src_prepare() {
+	sed -e '1 a #include <stdint.h>' -i common/dag_glue.cpp || die
+	# respect LDFLAGS wrt 331823
+	sed -i -e "s/LDFLAGS/LIBS/" -e "s/\$(LD)/& \$(LDFLAGS)/" \
+		-e 's/-static//' Makefile || die
+	python_convert_shebangs -r -- 2 utils
+}
+
+src_compile() {
+	append-flags -fopenmp
+	if ! use custom-cflags; then
+		append-flags -O3
+		replace-flags -O2 -O3
+	fi
+	tc-export CXX
+	emake CXXFLAGS="${CXXFLAGS}" LDFLAGS="${LDFLAGS}"
+}
+
+src_install() {
+	local i
+	dobin bin/* utils/split-contigs utils/temp-sink
+	dodoc HISTORY README TODO SPLITTING_AND_MERGING SCORES_AND_PROBABILITES
+
+	pushd utils > /dev/null
+	for i in *py; do
+		newbin ${i} ${i%.py}
+	done
+
+	rm *.py *.o *.c split-contigs temp-sink || die
+	insinto /usr/share/${PN}
+	doins -r *
+}