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

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 38a3d703e..000000000
--- 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 "${S}"/install.sh
-src_configure(){
-	cd jellyfish || die
-	econf
-
-	cd ../CA/kmer || die
-	econf
-
-	cd ../../SuperReads || die
-	econf
-
-	cd ../quorum || die
-	econf --enable-relative-paths --with-relative-jf-path
-}
-
-src_compile(){
-	cd jellyfish || die
-	default
-
-	cd ../CA/kmer || die
-	default
-
-	cd ../../CA/src || die
-	default
-
-	cd ../SuperReads || die
-	default
-
-	cd ../quorum || die
-	default
-}
-
-src_install(){
-	dobin masurca
-	dodoc sr_config_example.txt
-}
diff --git a/sci-biology/MaSuRCA/MaSuRCA-3.2.2.ebuild b/sci-biology/MaSuRCA/MaSuRCA-3.2.2.ebuild
new file mode 100644
index 000000000..d9e667792
--- /dev/null
+++ b/sci-biology/MaSuRCA/MaSuRCA-3.2.2.ebuild
@@ -0,0 +1,34 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+DESCRIPTION="de Bruijn and OLC assembler for Sanger, Roche 454, Illumina, Pacbio, Nanopore"
+HOMEPAGE="http://www.genome.umd.edu/masurca.html"
+SRC_URI="${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 3366274b4..b18db4ab7 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