From 0dc9a5177e72dac73b0ce8e8de20925b5e6df227 Mon Sep 17 00:00:00 2001
From: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Wed, 10 Feb 2016 18:05:29 +0100
Subject: sci-biology/cg-cat: new package

Package-Manager: portage-2.2.26
---
 sci-biology/cg-cat/Manifest               |  1 +
 sci-biology/cg-cat/cg-cat-20150130.ebuild | 43 +++++++++++++++++++++++++++++++
 sci-biology/cg-cat/metadata.xml           | 12 +++++++++
 3 files changed, 56 insertions(+)
 create mode 100644 sci-biology/cg-cat/Manifest
 create mode 100644 sci-biology/cg-cat/cg-cat-20150130.ebuild
 create mode 100644 sci-biology/cg-cat/metadata.xml

diff --git a/sci-biology/cg-cat/Manifest b/sci-biology/cg-cat/Manifest
new file mode 100644
index 000000000..f1d64bb80
--- /dev/null
+++ b/sci-biology/cg-cat/Manifest
@@ -0,0 +1 @@
+DIST r2cat.tar.gz 409067 SHA256 d7db5b5a5c8475b5f7e8f49f474be01b7bc785b43a4ae68bd7de5672e7d491f3 SHA512 a837d216664fede82e147204e8f1ba07b2d5ad92ee3db6f3a1285ff4acc4fb5b70715ac272d727304901548d68cb4865c051ef24690226692c4c4d693c7988f1 WHIRLPOOL 34a103cce1556fa8fef9f1d087ea5dad307497c39f00f2e04474592faada8d515cc6022a4bcc2656e3997e4891692240cdde21711d091464cd3f88a739d4bb0a
diff --git a/sci-biology/cg-cat/cg-cat-20150130.ebuild b/sci-biology/cg-cat/cg-cat-20150130.ebuild
new file mode 100644
index 000000000..39444eccf
--- /dev/null
+++ b/sci-biology/cg-cat/cg-cat-20150130.ebuild
@@ -0,0 +1,43 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit java-pkg-2 java-ant-2
+
+DESCRIPTION="r2cat and treecat, scaffolding tools for ordering and orienting contigs"
+HOMEPAGE="http://bibiserv.techfak.uni-bielefeld.de/cgcat"
+SRC_URI="http://bibiserv.techfak.uni-bielefeld.de/applications/cgcat/resources/downloads/r2cat.tar.gz"
+# SRC_URI="http://bibiserv.techfak.uni-bielefeld.de/applications/cgcat/resources/downloads/r2cat.jar"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND=">=virtual/jre-1.6:*"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"/r2cat
+
+src_prepare(){
+	sed -e "s#/vol/bioapps#"${D}"/usr#" -e "s#/vol/bibidev/r2cat#"${D}"/usr#" -i Makefile
+}
+
+src_compile(){
+	emake
+}
+
+src_install(){
+	# emake install dies with:
+	# jarsigner -tsa https://timestamp.geotrust.com/tsa -keystore /homes/phuseman/.gnupg/jarsigner_keystore_cg-cat  cg-cat.jar cgcat
+	# Enter Passphrase for keystore: jarsigner: you must enter key password
+	# Makefile:44: recipe for target 'cg-cat.jar' failed
+	mkdir -p "${D}"/usr/share/r2cat
+	emake install_cebitec
+	emake install_bibiserv
+}
+
+# java -Xmx1024M -jar r2cat.jar
+# java -Xmx1024M -cp r2cat.jar de.bielefeld.uni.cebitec.treecat.Treecat -Xmx -d64
diff --git a/sci-biology/cg-cat/metadata.xml b/sci-biology/cg-cat/metadata.xml
new file mode 100644
index 000000000..1699e58b2
--- /dev/null
+++ b/sci-biology/cg-cat/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>
-- 
cgit v1.2.3-65-gdbad