[gentoo-commits] proj/sci:jlec/scilab commit in: sci-biology/rtg-tools/

[Justin Lecher]

commit:     cb2c0165a5a3e091ffbbd123a4ab0334a75eed24
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Jan 26 11:05:09 2018 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Jan 26 11:05:09 2018 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=cb2c0165

sci-biology/rtg-tools: package skeleton

Will need to ask upstream to provide common 'compile', 'install'
and 'all' targets into
https://github.com/RealTimeGenomics/rtg-tools/blob/master/build.xml

Any volunteers to unbundle the bundled stuff? At least it is not
gradle but good old ant. ;)

Package-Manager: Portage-2.3.20, Repoman-2.3.6

 sci-biology/rtg-tools/metadata.xml          | 12 ++++++++
 sci-biology/rtg-tools/rtg-tools-9999.ebuild | 44 +++++++++++++++++++++++++++++
 2 files changed, 56 insertions(+)

diff --git a/sci-biology/rtg-tools/metadata.xml b/sci-biology/rtg-tools/metadata.xml
new file mode 100644
index 000000000..138cb7705
--- /dev/null
+++ b/sci-biology/rtg-tools/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@×××××××××××××××.cz</email>
+		<name>Martin Mokrejs</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci-biology@g.o</email>
+		<name>Gentoo Biology Project</name>
+	</maintainer>
+</pkgmetadata>

diff --git a/sci-biology/rtg-tools/rtg-tools-9999.ebuild b/sci-biology/rtg-tools/rtg-tools-9999.ebuild
new file mode 100644
index 000000000..30843a98e
--- /dev/null
+++ b/sci-biology/rtg-tools/rtg-tools-9999.ebuild
@@ -0,0 +1,44 @@
+# Copyright 1999-2018 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit java-pkg-2 java-ant-2 eutils git-r3
+
+DESCRIPTION="Manipulate and analyze SAM/BAM/VCF files"
+HOMEPAGE="https://github.com/RealTimeGenomics/rtg-tools"
+EGIT_REPO_URI="https://github.com/RealTimeGenomics/rtg-tools.git"
+
+LICENSE="BSD-2"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND="
+		>=virtual/jdk-1.8:*
+		dev-java/ant-core
+		dev-java/jython"
+RDEPEND="${DEPEND}
+		>=virtual/jre-1.8:*"
+
+src_compile(){
+	ant runalltests || die
+}
+
+# "${S}"/lib/sam-2.9.1.jar
+# "${S}"/lib/findbugs-annotations.jar
+# "${S}"/lib/findbugs-jsr305.jar
+# "${S}"/lib/velocity-tools-generic.jar
+# "${S}"/lib/RPlot.jar
+# "${S}"/lib/commons-collections-3.2.1.jar
+# "${S}"/lib/velocity-1.7.jar
+# "${S}"/lib/commons-compress-1.4.1.jar
+# "${S}"/lib/commons-lang-2.4.jar
+# "${S}"/lib/jumble-annotations.jar
+# "${S}"/lib/sam-2.9.1-src.jar
+# "${S}"/lib/gzipfix.jar
+# "${S}"/buildLib/ant-contrib-1.0b3.jar
+# "${S}"/buildLib/handlechecker.jar
+# "${S}"/testLib/hamcrest-core-1.3.jar
+# "${S}"/testLib/junit.jar
+# "${S}"/testLib/spelling.jar