1 files changed, 51 insertions, 0 deletions
diff --git a/sci-biology/jellyfish/jellyfish-2.2.10.ebuild b/sci-biology/jellyfish/jellyfish-2.2.10.ebuild
new file mode 100644
index 000000000..692c9e9ee
--- /dev/null
+++ b/sci-biology/jellyfish/jellyfish-2.2.10.ebuild
@@ -0,0 +1,51 @@
+# Copyright 1999-2018 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit eutils flag-o-matic autotools
+
+DESCRIPTION="k-mer counter within reads for assemblies"
+HOMEPAGE="http://www.genome.umd.edu/jellyfish.html"
+SRC_URI="https://github.com/gmarcais/Jellyfish/releases/download/v${PV}/${P}.tar.gz"
+
+# older version is hidden in trinityrnaseq_r20140413p1/trinity-plugins/jellyfish-1.1.11
+
+LICENSE="GPL-3+ BSD"
+SLOT="2"
+KEYWORDS="~amd64 ~x86"
+IUSE="cpu_flags_x86_sse"
+
+RDEPEND=""
+DEPEND="${RDEPEND}
+	virtual/pkgconfig"
+
+src_prepare(){
+	eautoreconf
+	default
+}
+
+# TODO: enable compilation of Bindings to Ruby, Python and Perl
+# '--enable-ruby-binding', '--enable-python-binding' or '--enable-perl-binding',  '--enable-swig'
+src_configure(){
+	#  --with-sse              enable SSE
+	#  --with-half             enable half float (16 bits)
+	#  --with-int128           enable int128
+	local myconf
+	use cpu_flags_x86_sse && myconf+=( --with-sse )
+	econf econf ${myconf[@]}
+}
+
+src_install(){
+	default
+	mv "${ED}"/usr/bin/jellyfish "${ED}"/usr/bin/jellyfish2 || die
+	sed -e "s#jellyfish-${PV}#jellyfish#" -i "${ED}/usr/$(get_libdir)"/pkgconfig/jellyfish-2.0.pc || die
+	find "${ED}"/usr/include/"${P}"/"${PN}" -type f | while read f; do
+		sed -e "s#include <jellyfish/#include <jellyfish${SLOT}/#" -i $f || die
+	done
+	mkdir -p "${ED}/usr/include/${PN}${SLOT}" || die
+	mv "${ED}"/usr/include/"${P}"/"${PN}"/* "${ED}/usr/include/${PN}${SLOT}/" || die
+	rm -r "${ED}/usr/include/${P}" || die
+	mv "${ED}"/usr/share/man/man1/jellyfish.1 "${ED}"/usr/share/man/man1/jellyfish"${SLOT}".1 || die
+	dodoc doc/jellyfish.pdf
+}