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

[Martin Mokrejs]

commit:     a73a521f084a0e830acc97812812a694a7fe3e00
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat May  2 15:09:00 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat May  2 15:09:00 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=a73a521f

sci-biology/phusion: clarified missing LICENSE, have asked upstream for clarification

Package-Manager: portage-2.2.18

 sci-biology/phusion/ChangeLog           | 10 ++++++++
 sci-biology/phusion/metadata.xml        |  9 +++++++
 sci-biology/phusion/phusion-2.1c.ebuild | 42 +++++++++++++++++++++++++++++++++
 3 files changed, 61 insertions(+)

diff --git a/sci-biology/phusion/ChangeLog b/sci-biology/phusion/ChangeLog
new file mode 100644
index 0000000..b829645
--- /dev/null
+++ b/sci-biology/phusion/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/phusion
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*phusion-2.1c (02 May 2015)
+
+  02 May 2015; Martin Mokrejs <mmokrejs@×××××××××××××××.cz> +metadata.xml,
+  +phusion-2.1c.ebuild:
+  sci-biology/phusion: clarified missing LICENSE, have asked upstream for
+  clarification

diff --git a/sci-biology/phusion/metadata.xml b/sci-biology/phusion/metadata.xml
new file mode 100644
index 0000000..2bc8930
--- /dev/null
+++ b/sci-biology/phusion/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci-biology</herd>
+  <maintainer>
+    <email>mmokrejs@×××××××××××××××.cz</email>
+    <name>Martin Mokrejs</name>
+  </maintainer>
+</pkgmetadata>

diff --git a/sci-biology/phusion/phusion-2.1c.ebuild b/sci-biology/phusion/phusion-2.1c.ebuild
new file mode 100644
index 0000000..14fde04
--- /dev/null
+++ b/sci-biology/phusion/phusion-2.1c.ebuild
@@ -0,0 +1,42 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+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="ftp://ftp.sanger.ac.uk/pub/resources/software/phusion/phusion_pipeline_v2.1c.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"
+RDEPEND="${DEPEND}
+	sci-biology/phrap
+	dev-lang/perl"
+
+# contains bundled ssaha
+# file collision with sci-biology/shrimp on /usr/bin/fasta2fastq
+
+S="${WORKDIR}"/"phusion_pipeline_v2.1c"
+
+src_prepare(){
+	cp -pf /usr/bin/phrap src/phrap/phrap.manylong || die
+}
+
+src_compile(){
+	tcsh install.csh || csh install.csh || die
+}
+
+src_install(){
+	dobin bin/*
+	dodoc README.1st releaseNote_v2.1c doc/*
+}