sci-biology/jellyfish: install bundled PDF manual

And do not download an old version at all.

Package-Manager: Portage-2.3.31, Repoman-2.3.9

3 files changed, 54 insertions, 3 deletions

diff --git a/sci-biology/jellyfish/Manifest b/sci-biology/jellyfish/Manifest
index a6669d2ee..010ec694d 100644
--- a/sci-biology/jellyfish/Manifest
+++ b/sci-biology/jellyfish/Manifest
@@ -3,4 +3,5 @@ DIST jellyfish-1.1.11.tar.gz 1067138 BLAKE2B cda369674a939f0abda1c0ce12dbb170d67
 DIST jellyfish-2.1.3.tar.gz 955773 BLAKE2B f01891238aa819ddeb2ca3b45276f23fe209cb0015bc5874adbed6355bce44ab23c19020fd5a10779a93c29ca3d241e36fe72fb5b4ffee4a37b954980cb6b217 SHA512 2b6fea6c2686de7b568988543d5a9466676eb17252ecce3243b0dc7e3c833aed02ae6570749df58c2921289db0167b39848ccd80eb3cc568cdbaa0045114b702
 DIST jellyfish-2.1.4.tar.gz 958038 BLAKE2B 8cb3fa50858f8cc4fbb3e5e9c64f76e2d3ff4453767411a36fab1188673cbfd12f52270ee7f4269c606931f34e9805c878a05c6dcd3370b7b0de65f25ad7a1fb SHA512 28bbaf6ed5c69caec24a09ceb2dfa99b160f3a9c2764d3f30ab205374a6f17dfc5c6d7405e75fd5161882350db160442a91568dd65ea9851e8cb74eb71f25742
 DIST jellyfish-2.2.6.tar.gz 1082535 BLAKE2B 8ad044c470245132c843f93c639f9c0e502bcf41031a7a561b9c2bbfb46763d91651de5af51bf9d42bf560dbb7de9be5595aa00b9cf3a060db731a5087494780 SHA512 c3320facbbad1c6f2aede2edd7d2574bbff0e5a7f655d8b0224e511f07a319c4682adc1576a189367a546011c43d79f7b01474580dcc9c44f8e087397b475056
+DIST jellyfish-2.2.9.tar.gz 1146617 BLAKE2B 2c63ca99c86c6687f8300c746a248348dad2aaead01953fe6f4856e1e032a6985123b4a958bfc77af238280dc840bf35ce19852834cc620628e88a4ecc48356f SHA512 9da8259183d7b85940fdc3d8c6da8bcd11a8434dbd9b0d5344315b2803ef4e585eaa27fbcf38dcf699477c798e70b1e42fc4cf3226527c5e37eba65d80fd9623
 DIST jellyfish-manual-1.1.pdf 241464 BLAKE2B b33e6784674cb4a296b45c7799db9b1b9e0e01687093f236fe30fd34c56f71afd796b9f8fa30857918c9d49e767e527425fa0b09eb9195705ac85a6e314523eb SHA512 b697c51af5bd85b779fea4f03772ac8e21713f906773350931a7d67adecb4268b051e766173122ad2ba9d168235f534ff6eaa070496d6318cf8a76c8690ab61c
diff --git a/sci-biology/jellyfish/jellyfish-2.2.6-r1.ebuild b/sci-biology/jellyfish/jellyfish-2.2.6-r1.ebuild
index 54cc724eb..692c9e9ee 100644
--- a/sci-biology/jellyfish/jellyfish-2.2.6-r1.ebuild
+++ b/sci-biology/jellyfish/jellyfish-2.2.6-r1.ebuild
@@ -7,8 +7,7 @@ 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
-	ftp://ftp.genome.umd.edu/pub/jellyfish/JellyfishUserGuide.pdf"
+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
 
@@ -48,5 +47,5 @@ src_install(){
 	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"${SLOT}".1 || die
-	dodoc "${DISTDIR}"/JellyfishUserGuide.pdf
+	dodoc doc/jellyfish.pdf
 }
diff --git a/sci-biology/jellyfish/jellyfish-2.2.9.ebuild b/sci-biology/jellyfish/jellyfish-2.2.9.ebuild
new file mode 100644
index 000000000..692c9e9ee
--- /dev/null
+++ b/sci-biology/jellyfish/jellyfish-2.2.9.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
+}