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authorMartin Mokrejš <mmokrejs@fold.natur.cuni.cz>2017-05-15 16:17:46 +0200
committerMartin Mokrejš <mmokrejs@fold.natur.cuni.cz>2017-05-15 16:17:46 +0200
commit89745927430667600a2190593e887ccf4eac14e5 (patch)
tree8a9b744c0c74f0c046fb860e5de883d81a9b2976
parentdev-lang/yaggo: new package required by sci-biology/jellyfish-2.2.6 (diff)
downloadsci-89745927430667600a2190593e887ccf4eac14e5.zip
sci-89745927430667600a2190593e887ccf4eac14e5.tar.gz
sci-89745927430667600a2190593e887ccf4eac14e5.tar.bz2
sci-biology/jellyfish: version bump, add new CDEPEND on dev-lang/yaggo
Package-Manager: Portage-2.3.5, Repoman-2.3.2
-rw-r--r--sci-biology/jellyfish/Manifest2
-rw-r--r--sci-biology/jellyfish/jellyfish-2.2.6.ebuild (renamed from sci-biology/jellyfish/jellyfish-2.2.0.ebuild)18
2 files changed, 14 insertions, 6 deletions
diff --git a/sci-biology/jellyfish/Manifest b/sci-biology/jellyfish/Manifest
index 580d4f7..e66d33c 100644
--- a/sci-biology/jellyfish/Manifest
+++ b/sci-biology/jellyfish/Manifest
@@ -2,5 +2,5 @@ DIST JellyfishUserGuide.pdf 142367 SHA256 6f4365f1839b0370fff50fcd25ffcf2dad4192
DIST jellyfish-1.1.11.tar.gz 1067138 SHA256 496645d96b08ba35db1f856d857a159798c73cbc1eccb852ef1b253d1678c8e2 SHA512 aea7373e5ffb9deba7e164425bd7d4219d9be1e48ca666ff41e70bbc77026bc581273fb5a07c47894e2b31dd1339d4f1bc1a7b0501f10a482353ecde082eed1a WHIRLPOOL d2f31e39c1d4ce4fab78abd33c62c79bf950fdfab4f5283713e67deab8e1dabc3fd1c6cf09de964a6707793426abca24c05afe0dcf5365e04ae97dda15da2040
DIST jellyfish-2.1.3.tar.gz 955773 SHA256 00530abd01c1253646f29fa4554e96fd31148ed92402940e6f357bd5cab38e9b SHA512 2b6fea6c2686de7b568988543d5a9466676eb17252ecce3243b0dc7e3c833aed02ae6570749df58c2921289db0167b39848ccd80eb3cc568cdbaa0045114b702 WHIRLPOOL 4a1e6568932db0cc4773e89e4b8f049e96ed929723ffd518ce7e0ed12bd29041d0774fba1069251a336e448dd75703a350917ffc3db5a35f2cfac828572da566
DIST jellyfish-2.1.4.tar.gz 958038 SHA256 c4e692170d33efa9e6e4f0b134d8e257fb802832af17fdc53ac468bf8f0f29a5 SHA512 28bbaf6ed5c69caec24a09ceb2dfa99b160f3a9c2764d3f30ab205374a6f17dfc5c6d7405e75fd5161882350db160442a91568dd65ea9851e8cb74eb71f25742 WHIRLPOOL c588f4642ff0474e0565f63d2c17db03b90fa302dff9c678766e589142bc9f71a0b48e2088b24b2df15955cae85ab43aaa1ae79066113a144c8ee8bfa75594f3
-DIST jellyfish-2.2.0.tar.gz 1085913 SHA256 465b8169efae48bae301f1dc8031d1341dd3db624696e5ee973422f17fe3d0ad SHA512 42a91d45721dc6f1cd8eb79eacd01819a102129eb6be001abb7b12a9ba9921300b26864f285d95fac460577c56bf05578792e0a99541d8251cb88715883554a0 WHIRLPOOL 9279df2bc4081f2167f673340df062a4c1772b0cb723429f706f0534fed273c52c9129d44d6bd3e0c235dd91f6a1e82b577328a84b3d00698a6126116f48c4cd
+DIST jellyfish-2.2.6.tar.gz 660858 SHA256 800bc60aaec273dc04296ee7493e714457f2fe88551f76693e5d9f9a679dd35e SHA512 7d61d823feaaab05fbb43eaca22823a988bd05da318431e74092b42c7e33ce39f387ac15db30906341f084223b7c2726e199592555aea4b21a5b517e8d0c08f9 WHIRLPOOL a10bbafc2b6cf461a4d9256f03891080eef7353508ab0382d3ccab5823f327c89045b2c7393794fd7938c0eb0027304f5c2cc425ccdfca52c441a267d72eac72
DIST jellyfish-manual-1.1.pdf 241464 SHA256 60738f790ba50baeba04de60fdc3f620fe670d3067501d472c7b42a401600c88 SHA512 b697c51af5bd85b779fea4f03772ac8e21713f906773350931a7d67adecb4268b051e766173122ad2ba9d168235f534ff6eaa070496d6318cf8a76c8690ab61c WHIRLPOOL 01b0fff7373b40b125be3b5d44bc0af62704e84e449943235cc8b8331ff73c6d5d4be4e69040d8bc54ae1e12e377cbe4fd66108b7fcee8379d69568e8809bb5c
diff --git a/sci-biology/jellyfish/jellyfish-2.2.0.ebuild b/sci-biology/jellyfish/jellyfish-2.2.6.ebuild
index fd71046..99e258e 100644
--- a/sci-biology/jellyfish/jellyfish-2.2.0.ebuild
+++ b/sci-biology/jellyfish/jellyfish-2.2.6.ebuild
@@ -1,13 +1,13 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=6
-inherit eutils flag-o-matic
+inherit eutils flag-o-matic autotools
DESCRIPTION="k-mer counter within reads for assemblies"
HOMEPAGE="http://www.genome.umd.edu/jellyfish.html"
-SRC_URI="ftp://ftp.genome.umd.edu/pub/${PN}/${P}.tar.gz
+SRC_URI="https://github.com/gmarcais/Jellyfish/archive/v2.2.6.tar.gz -> ${P}.tar.gz
ftp://ftp.genome.umd.edu/pub/jellyfish/JellyfishUserGuide.pdf"
# older version is hidden in trinityrnaseq_r20140413p1/trinity-plugins/jellyfish-1.1.11
@@ -17,18 +17,26 @@ SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE="cpu_flags_x86_sse"
-DEPEND=""
+CDEPEND="dev-lang/yaggo"
DEPEND="${RDEPEND}
virtual/pkgconfig"
+S="${WORKDIR}/Jellyfish-${PV}"
+
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[@]}
- eapply_user
}
src_install(){