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

[Martin Mokrejs]

commit:     0097320955e9522a3b7b082a9ec3aa803dae2a0e
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Mar 23 22:36:38 2014 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Mar 23 22:36:38 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=00973209

sci-biology/inGAP-bin: new package; needs java team help

Package-Manager: portage-2.2.7

---
 sci-biology/inGAP-bin/ChangeLog              |  9 +++++++
 sci-biology/inGAP-bin/inGAP-bin-3.0.1.ebuild | 39 ++++++++++++++++++++++++++++
 sci-biology/inGAP-bin/metadata.xml           |  9 +++++++
 3 files changed, 57 insertions(+)

diff --git a/sci-biology/inGAP-bin/ChangeLog b/sci-biology/inGAP-bin/ChangeLog
new file mode 100644
index 0000000..c573f62
--- /dev/null
+++ b/sci-biology/inGAP-bin/ChangeLog
@@ -0,0 +1,9 @@
+# ChangeLog for sci-biology/inGAP-bin
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*inGAP-bin-3.0.1 (23 Mar 2014)
+
+  23 Mar 2014; Martin Mokrejs <mmokrejs@×××××××××××××××.cz>
+  +inGAP-bin-3.0.1.ebuild, +metadata.xml:
+  sci-biology/inGAP-bin: new package; needs java team help

diff --git a/sci-biology/inGAP-bin/inGAP-bin-3.0.1.ebuild b/sci-biology/inGAP-bin/inGAP-bin-3.0.1.ebuild
new file mode 100644
index 0000000..0c7903c
--- /dev/null
+++ b/sci-biology/inGAP-bin/inGAP-bin-3.0.1.ebuild
@@ -0,0 +1,39 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=3
+
+MY_PV="3_0_1"
+S="${WORKDIR}"/inGAP_"${MY_PV}"
+
+DESCRIPTION="Detect SNPs and indels from Next-gen sequences using a Bayesian algorithm"
+HOMEPAGE="http://sites.google.com/site/nextgengenomics/ingap
+	http://sourceforge.net/projects/ingap/"
+SRC_URI="http://sourceforge.net/projects/ingap/files/ingap/v"${PV}"/inGAP_"${MY_PV}".tgz"
+
+LICENSE="LGPL-3"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}
+	dev-java/jfreechart
+	dev-java/swing-layout
+	dev-java/jcommon
+	dev-java/itext
+	dev-java/bytecode
+	dev-java/biojava
+	dev-java/absolutelayout" # gnujaxp ?
+
+src_install(){
+	dobin inGAP.jar || die
+	# dobin external/bin/{primer3_core, run_cpp, trf}
+	mv manual.pdf inGAP_Manual.pdf || die
+	dodoc inGAP_Manual.pdf || die
+	insinto /usr/share/inGAP
+	doins doc/manual.htm
+	insinto /usr/share/inGAP/manual_files
+	doins doc/manual_files/*.png
+}

diff --git a/sci-biology/inGAP-bin/metadata.xml b/sci-biology/inGAP-bin/metadata.xml
new file mode 100644
index 0000000..2bc8930
--- /dev/null
+++ b/sci-biology/inGAP-bin/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>