[gentoo-commits] proj/sci:master commit in: sci-biology/iCORN2/

[gentoo-commits] proj/sci:master commit in: sci-biology/iCORN2/

[Martin Mokrejs]

commit:     10ed6d59cf94bab5ba74ce81ef0f36cdbbbb562c
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Apr 10 18:03:55 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Apr 10 18:03:55 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=10ed6d59

sci-biology/iCORN2: new package with bundled gatk and picard jar files

Package-Manager: portage-2.2.28

 sci-biology/iCORN2/iCORN2-0.95.ebuild | 57 +++++++++++++++++++++++++++++++++++
 sci-biology/iCORN2/metadata.xml       | 12 ++++++++
 2 files changed, 69 insertions(+)

diff --git a/sci-biology/iCORN2/iCORN2-0.95.ebuild b/sci-biology/iCORN2/iCORN2-0.95.ebuild
new file mode 100644
index 0000000..61613a4
--- /dev/null
+++ b/sci-biology/iCORN2/iCORN2-0.95.ebuild
@@ -0,0 +1,57 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+DESCRIPTION="Iteratively map reads to a reference, fix mismatches and indels with GATK/picard"
+HOMEPAGE="http://icorn.sourceforge.net/
+		http://sourceforge.net/projects/icorn"
+SRC_URI="ftp://ftp.sanger.ac.uk/pub4/resources/software/pagit/ICORN2/icorn2.V${PV}.tgz
+	http://icorn.sourceforge.net/manual.html -> ${PN}_manual.html"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+DEPEND="
+	sci-biology/snpomatic
+	|| ( sci-biology/smalt sci-biology/smalt-bin )
+	sci-biology/samtools:=
+	sci-biology/gatk
+	sci-biology/picard"
+RDEPEND="${DEPEND}
+	dev-lang/perl
+	app-shells/tcsh"
+
+S="${WORKDIR}"/ICORN2
+
+src_unpack(){
+	default
+	# The bundled files GenomeAnalysisTK.jar from GATK
+	# contains bundled MarkDuplicates.jar from picard
+	# both .jar files were supposed to be in $ICORN2_HOME
+	rm -f *~ smalt || die
+}
+
+src_prepare(){
+	sed -e "s#java -jar \$ICORN2_HOME#java -jar /usr/share/${PN}/lib#" -i *.sh || die
+}
+
+# the tarball is a terrible mess
+src_install(){
+	dobin *.pl *.sh
+	insinto /usr/share/"${PN}"/lib
+	doins GenomeAnalysisTK.jar MarkDuplicates.jar
+	insinto /usr/share/"${PN}"/LSF
+	doins LSF/*
+	dodoc README.txt
+	newdoc "${DISTDIR}"/"${PN}"_manual.html manual.html
+}
+
+# http://icorn.sourceforge.net/documentation.html
+# Define the shell variable ICORN_HOME, PILEUP_HOME and SNPOMATIC_HOME
+pkg_postinst(){
+	einfo "Ideally install Artemis ACT viewer or gap4 from staden package"
+}

diff --git a/sci-biology/iCORN2/metadata.xml b/sci-biology/iCORN2/metadata.xml
new file mode 100644
index 0000000..f68a1b6
--- /dev/null
+++ b/sci-biology/iCORN2/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>