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authorMartin Mokrejš <mmokrejs@fold.natur.cuni.cz>2017-05-16 01:27:17 +0200
committerMartin Mokrejš <mmokrejs@fold.natur.cuni.cz>2017-05-16 01:27:17 +0200
commitc1d81c6bb160f87609eb3005d0ac9457649aeda2 (patch)
tree74fca678c10ecc6f32c7bb4c62d3b3dae2d8f582
parentsci-biology/SOAPdenovo2: a bit cleanup of the build process (diff)
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sci-biology/MaSuRCA: version bump
The package is actually a bundle of many, including SOAPdenovo2 somewhat patched so that it compiles (unlike vanilla 2.04-r240). Package-Manager: Portage-2.3.5, Repoman-2.3.2
-rw-r--r--sci-biology/MaSuRCA/MaSuRCA-2.3.2b.ebuild57
-rw-r--r--sci-biology/MaSuRCA/MaSuRCA-3.2.2.ebuild34
-rw-r--r--sci-biology/MaSuRCA/Manifest2
3 files changed, 35 insertions, 58 deletions
diff --git a/sci-biology/MaSuRCA/MaSuRCA-2.3.2b.ebuild b/sci-biology/MaSuRCA/MaSuRCA-2.3.2b.ebuild
deleted file mode 100644
index 38a3d70..0000000
--- a/sci-biology/MaSuRCA/MaSuRCA-2.3.2b.ebuild
+++ /dev/null
@@ -1,57 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="Assembler to combine Sanger, Roche 454 and Illumina Solexa reads"
-HOMEPAGE="http://www.genome.umd.edu/masurca.html"
-SRC_URI="ftp://ftp.genome.umd.edu/pub/MaSuRCA/MaSuRCA-"${PV}".tar.gz
- ftp://ftp.genome.umd.edu/pub/MaSuRCA/MaSuRCA_QuickStartGuide.pdf"
-
-LICENSE="BSD GPL-2 GPL-3"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND="dev-lang/perl
- app-arch/bzip2"
-RDEPEND="${DEPEND}
- >=sci-biology/quorum-0.2.1
- >=sci-biology/jellyfish-1.1.11"
-
-# the ebuild mimics "${S}"/install.sh
-src_configure(){
- cd jellyfish || die
- econf
-
- cd ../CA/kmer || die
- econf
-
- cd ../../SuperReads || die
- econf
-
- cd ../quorum || die
- econf --enable-relative-paths --with-relative-jf-path
-}
-
-src_compile(){
- cd jellyfish || die
- default
-
- cd ../CA/kmer || die
- default
-
- cd ../../CA/src || die
- default
-
- cd ../SuperReads || die
- default
-
- cd ../quorum || die
- default
-}
-
-src_install(){
- dobin masurca
- dodoc sr_config_example.txt
-}
diff --git a/sci-biology/MaSuRCA/MaSuRCA-3.2.2.ebuild b/sci-biology/MaSuRCA/MaSuRCA-3.2.2.ebuild
new file mode 100644
index 0000000..d9e6677
--- /dev/null
+++ b/sci-biology/MaSuRCA/MaSuRCA-3.2.2.ebuild
@@ -0,0 +1,34 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+DESCRIPTION="de Bruijn and OLC assembler for Sanger, Roche 454, Illumina, Pacbio, Nanopore"
+HOMEPAGE="http://www.genome.umd.edu/masurca.html"
+SRC_URI="${P}.tar.gz
+ ftp://ftp.genome.umd.edu/pub/MaSuRCA/MaSuRCA_QuickStartGuide.pdf"
+
+LICENSE="BSD GPL-2 GPL-3"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND=">=dev-lang/perl-5.8
+ app-arch/bzip2"
+RDEPEND="${DEPEND}"
+
+RESTRICT="fetch"
+
+# the ebuild mimics "${S}"/install.sh
+src_configure(){
+ ./install.sh || die
+}
+
+src_compile(){
+ ./install.sh || die
+}
+
+src_install(){
+ dobin masurca
+ dodoc sr_config_example.txt
+}
diff --git a/sci-biology/MaSuRCA/Manifest b/sci-biology/MaSuRCA/Manifest
index 3366274..b18db4a 100644
--- a/sci-biology/MaSuRCA/Manifest
+++ b/sci-biology/MaSuRCA/Manifest
@@ -1,2 +1,2 @@
-DIST MaSuRCA-2.3.2b.tar.gz 7506105 SHA256 837cb144d3dba206a778e88a06f2af67f2cc9ca4f5e6e97dd48ad4ac783aec70 SHA512 042040899a8fafe99145390701f2ced0d100cebf4abad4d5d02ccfe3cfe4406e0a887740752ae81a75fc055629c1580c3f99dff007e4330190c732164cad0f35 WHIRLPOOL ef123be71b4deaaec961451fdc6250162d222345ba1307c59dc8f4ba6deddc52f25ee269b9d5b5ce44bab1f2332018c10da0cc9386e1a49718338c88516507b4
+DIST MaSuRCA-3.2.2.tar.gz 23269939 SHA256 b0535e9cca6fa3699290d5a31f3d30b6270ba3c75f8197d8bd142ba81eed5202 SHA512 274184de19e20e7e6eb31bdd62f69e02ea77657da1821207edb5c0f3a9c0d829426d14e4551d594411a17ca2ae8fdc81c3b2b19ae6c3978b641e60b8a80a2032 WHIRLPOOL 7e24c3150771083ed5cf9792c98db9db79d3b25178e693c5de93899f6bf028cc90b15027b6e68bbf36e4fff60010351db2cee6f60d5e5248b66eb308298021f8
DIST MaSuRCA_QuickStartGuide.pdf 152644 SHA256 3a1e9fa83608f6138355aa0e6c5b1db337e2fca67d0a7275c0b54e85780e421d SHA512 e911a7b092f68a1f60e45c996e25b53b65260fad9e465488d30a066b00db2cdef0e0bb422d9731d37cfa3958eac74943d54019ac9e538560b66da0a64d6ce800 WHIRLPOOL a7d1ef0798b0ee0810b0fe6ac6bda4e0b6f4655a7109d5dc5dfc797ed6669ad5353a2f3b988e9efe1dcde485dc69bdc2b1d3887ee2d026e99cf8a14fe4075a95