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

[Martin Mokrejs]

commit:     0a17f05714124c90b425b51925dea9557a003422
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Mar 23 17:05:44 2014 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Mar 23 17:05:44 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=0a17f057

sci-biology/fastqc: a skeleton for a new perl wrapper calling java libs, need help

Package-Manager: portage-2.2.7

---
 sci-biology/fastqc/ChangeLog            | 10 ++++++++++
 sci-biology/fastqc/fastqc-0.10.1.ebuild | 29 +++++++++++++++++++++++++++++
 sci-biology/fastqc/metadata.xml         |  9 +++++++++
 3 files changed, 48 insertions(+)

diff --git a/sci-biology/fastqc/ChangeLog b/sci-biology/fastqc/ChangeLog
new file mode 100644
index 0000000..69015c4
--- /dev/null
+++ b/sci-biology/fastqc/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/fastqc
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*fastqc-0.10.1 (23 Mar 2014)
+
+  23 Mar 2014; Martin Mokrejs <mmokrejs@×××××××××××××××.cz>
+  +fastqc-0.10.1.ebuild, +metadata.xml:
+  sci-biology/fastqc: a skeleton for a new perl wrapper calling java libs, need
+  help

diff --git a/sci-biology/fastqc/fastqc-0.10.1.ebuild b/sci-biology/fastqc/fastqc-0.10.1.ebuild
new file mode 100644
index 0000000..5274554
--- /dev/null
+++ b/sci-biology/fastqc/fastqc-0.10.1.ebuild
@@ -0,0 +1,29 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit java-pkg-2 eutils
+
+DESCRIPTION="Perl-based wrapper around java apps to quality control FASTA/FASTQ sequence files"
+HOMEPAGE="http://www.bioinformatics.babraham.ac.uk/projects/fastqc/"
+SRC_URI="http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v"${PV}"_source.zip"
+
+LICENSE="GPL-3+"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND="sci-biology/picard
+	>=virtual/jrei-1.6"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"/FastQC
+
+src_install(){
+	dobin fastqc
+	
+	# TODO: need to compile java in uk/ac/babraham/FastQC/
+	# and decide whether jbzip2-0.9.jar and sam-1.32.jar are standard java libs and from samtools or whetehr not
+}

diff --git a/sci-biology/fastqc/metadata.xml b/sci-biology/fastqc/metadata.xml
new file mode 100644
index 0000000..07b5255
--- /dev/null
+++ b/sci-biology/fastqc/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>