From 53b862b685eda906c6becbbc09b10521a0919e57 Mon Sep 17 00:00:00 2001
From: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Tue, 3 May 2016 21:01:51 +0200
Subject: sci-biology/conrad: new package, needs java spring

Package-Manager: portage-2.2.28
---
 sci-biology/conrad/Manifest        |  1 +
 sci-biology/conrad/conrad-1.ebuild | 51 ++++++++++++++++++++++++++++++++++++++
 sci-biology/conrad/metadata.xml    | 12 +++++++++
 3 files changed, 64 insertions(+)
 create mode 100644 sci-biology/conrad/Manifest
 create mode 100644 sci-biology/conrad/conrad-1.ebuild
 create mode 100644 sci-biology/conrad/metadata.xml

(limited to 'sci-biology')

diff --git a/sci-biology/conrad/Manifest b/sci-biology/conrad/Manifest
new file mode 100644
index 000000000..dbda934f8
--- /dev/null
+++ b/sci-biology/conrad/Manifest
@@ -0,0 +1 @@
+DIST conradSrcV1.zip 13315561 SHA256 fa978d5694d588f1047160f4cab2f8c8cdb613cda8c39a26f482e18e7e7dd742 SHA512 9a6cec2ecb601297e1055e2501c518156f6a4f8a3e30b77e8d2b83d347641f7f590595acdd3aa773296296b74826a3ad382bc538f90bcb439c5b135f83fb6b25 WHIRLPOOL 44712ed80c2e44628543373fe8791692ed8d8492983e3d9c1d70e59a77595a7b7cad2de93ec5a9163a621531739a4eeb9713e19be500d90c4dd631b5aa754461
diff --git a/sci-biology/conrad/conrad-1.ebuild b/sci-biology/conrad/conrad-1.ebuild
new file mode 100644
index 000000000..f9e19a18f
--- /dev/null
+++ b/sci-biology/conrad/conrad-1.ebuild
@@ -0,0 +1,51 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit java-pkg-2 java-ant-2
+
+DESCRIPTION="Gene predictor using ab initio and ad hoc evidence (RNA-Seq, BLAST) on gDNA"
+HOMEPAGE="http://www.broadinstitute.org/annotation/conrad
+	http://sourceforge.net/projects/conradcrf"
+SRC_URI="http://www.broadinstitute.org/annotation/conrad/conradSrcV1.zip"
+
+LICENSE="LGPL-2.1"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+RDEPEND="
+	>=virtual/jre-1.5:*
+	dev-java/commons-logging
+	>=dev-java/commons-lang-2.1:*
+	dev-java/colt
+	dev-java/dom4j
+	"
+	# spring # see bug #97004
+	# LBFGS
+DEPEND="${RDEPEND}
+	>=virtual/jdk-1.5:*
+	dev-java/ant-core
+	>=dev-java/jfreechart-1.0.3
+	>=dev-java/jcommon-1.0.6
+	>=dev-java/commons-math-1.1
+	"
+S="${WORKDIR}"
+
+src_prepare(){
+	sed -e s'#lib/conrad.jar#/usr/share/conrad/lib/conrad.jar#' -i bin/conrad.sh || die
+}
+
+src_compile(){
+	cd dev || die
+	ant compile || die
+}
+
+src_install() {
+	dobin bin/conrad.sh
+	java-pkg_dojar lib/conrad.jar
+	insinto /usr/share/conrad
+	dodoc -r docs models samples trainingFiles
+}
diff --git a/sci-biology/conrad/metadata.xml b/sci-biology/conrad/metadata.xml
new file mode 100644
index 000000000..f68a1b6fa
--- /dev/null
+++ b/sci-biology/conrad/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>
-- 
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