1 files changed, 59 insertions, 0 deletions
diff --git a/sci-biology/picard/picard-2.8.1.ebuild b/sci-biology/picard/picard-2.8.1.ebuild
new file mode 100644
index 000000000..4d09e8d48
--- /dev/null
+++ b/sci-biology/picard/picard-2.8.1.ebuild
@@ -0,0 +1,59 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI="6"
+
+JAVA_PKG_IUSE="doc source"
+
+inherit java-pkg-2 java-ant-2
+
+DESCRIPTION="Java-based command-line utilities that manipulate SAM/BAM/CRAM/VCF files"
+HOMEPAGE="http://picard.sourceforge.net
+	http://broadinstitute.github.io/picard"
+SRC_URI="https://github.com/broadinstitute/picard/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+IUSE=""
+KEYWORDS=""
+
+CDEPEND="dev-java/snappy:1.1
+	dev-java/cofoja:0
+	dev-java/commons-jexl:2
+	dev-java/ant-core:0
+	dev-java/htsjdk:0"
+
+DEPEND=">=virtual/jdk-1.8
+	${CDEPEND}"
+
+RDEPEND=">=virtual/jre-1.8
+	${CDEPEND}"
+
+EANT_BUILD_TARGET="all"
+EANT_NEEDS_TOOLS="true"
+JAVA_ANT_REWRITE_CLASSPATH="true"
+EANT_GENTOO_CLASSPATH="snappy-1.1,cofoja,commons-jexl-2,ant-core,htsjdk"
+
+java_prepare() {
+	default
+	rm -r src/java/picard/util/TestNGUtil.java src/tests/java/* || die
+	epatch "${FILESDIR}"/${PV}-build.xml.patch
+}
+
+src_compile(){
+	# work around gradle writing $HOME/.gradle and requiring $HOME/.git
+	# https://github.com/samtools/htsjdk/issues/660#issuecomment-232155965
+	GRADLE_USER_HOME="${WORKDIR}" ./gradlew build || die
+}
+
+#src_install() {
+#	cd dist || die
+#	java-pkg_dojar ${PN}.jar
+#	java-pkg_dojar ${PN}-lib.jar
+#	
+#	java-pkg_dolauncher ${PN} --main picard.cmdline.PicardCommandLine
+#	
+#	use source && java-pkg_dosrc "${S}"/src/java/*
+#	use doc && java-pkg_dojavadoc "${S}"/javadoc
+#}