[gentoo-commits] proj/sci:master commit in: sci-biology/phusion2/

["Martin Mokrejs" <mmokrejs@fold.natur.cuni.cz>]

commit:     fdbb0df35cd149e408bb18fdcfa8debc839c6026
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Feb 16 18:00:57 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Feb 16 18:00:57 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=fdbb0df3

sci-biology/phusion2: renamed a package; version bump; note that upstream sourceforge site contains additional components of the bundle

Package-Manager: portage-2.2.26

 sci-biology/phusion2/metadata.xml        | 12 ++++++++++
 sci-biology/phusion2/phusion2-3.0.ebuild | 40 ++++++++++++++++++++++++++++++++
 2 files changed, 52 insertions(+)

diff --git a/sci-biology/phusion2/metadata.xml b/sci-biology/phusion2/metadata.xml
new file mode 100644
index 0000000..1699e58
--- /dev/null
+++ b/sci-biology/phusion2/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="person">
+    <email>mmokrejs@fold.natur.cuni.cz</email>
+    <name>Martin Mokrejs</name>
+  </maintainer>
+<maintainer type="project">
+    <email>sci-biology@gentoo.org</email>
+    <name>Gentoo Biology Project</name>
+  </maintainer>
+</pkgmetadata>

diff --git a/sci-biology/phusion2/phusion2-3.0.ebuild b/sci-biology/phusion2/phusion2-3.0.ebuild
new file mode 100644
index 0000000..5f2d7ca
--- /dev/null
+++ b/sci-biology/phusion2/phusion2-3.0.ebuild
@@ -0,0 +1,40 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit eutils
+
+DESCRIPTION="Whole genome shotgun assembler using phrap (for Sanger-based reads)"
+HOMEPAGE="http://www.sanger.ac.uk/resources/software/phusion/"
+SRC_URI="http://downloads.sourceforge.net/project/${PN}/${P}.tar.gz"
+
+LICENSE="all-rights-reserved" # temporarily placed value
+# from http://genome.cshlp.org/content/13/1/81.full
+# Availability
+# Phusion is undergoing a rewrite of the code to make this a portable package. It will be made available free of charge to academic sites, but requires licensing for commercial use. For more information please contact the authors.
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND="app-shells/tcsh
+	sys-cluster/openmpi"
+RDEPEND="${DEPEND}
+	sci-biology/phrap
+	dev-lang/perl"
+
+# contains bundled ssaha
+# file collision with sci-biology/shrimp on /usr/bin/fasta2fastq
+
+S="${WORKDIR}"
+
+src_prepare(){
+	rm -f phusion2 *.o
+	sed -e 's/^CFLAGS =/# CFLAGS =/' -i Makefile || die
+}
+
+src_install(){
+	dobin ctgreads.pl phusion2
+	dodoc how_to_make_mates
+}