1 files changed, 61 insertions, 0 deletions
diff --git a/sci-biology/picard/picard-2.17.11.ebuild b/sci-biology/picard/picard-2.17.11.ebuild
new file mode 100644
index 000000000..636bf879c
--- /dev/null
+++ b/sci-biology/picard/picard-2.17.11.ebuild
@@ -0,0 +1,61 @@
+# Copyright 1999-2018 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+#JAVA_PKG_IUSE="doc source"
+JAVA_PKG_IUSE=""
+
+inherit git-r3 java-pkg-2
+
+DESCRIPTION="Java-based command-line utilities that manipulate SAM/BAM/CRAM/VCF files"
+HOMEPAGE="http://picard.sourceforge.net
+	http://broadinstitute.github.io/picard"
+EGIT_REPO_URI="https://github.com/broadinstitute/picard.git"
+EGIT_BRANCH="${PV}"
+# building outside of git is not possible,
+# see https://github.com/broadinstitute/picard/issues/605
+#SRC_URI="https://github.com/broadinstitute/picard/archive/${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/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,htsjdk"
+
+src_prepare() {
+	default
+}
+
+src_compile(){
+	# work around gradle writing $HOME/.gradle, requiring $HOME/.git and $HOME/.m2/
+	# https://github.com/samtools/htsjdk/issues/660#issuecomment-232155965
+	# make jure SDK-1.8 is available, JRE-1.8 is not enough
+	GRADLE_USER_HOME="${WORKDIR}" ./gradlew --stacktrace --debug || die
+}
+
+src_install() {
+	cd build/libs || die
+	java-pkg_dojar "${PN}".jar
+	java-pkg_dojar "${PN}"-*-SNAPSHOT.jar
+
+	java-pkg_dolauncher ${PN} --main picard.cmdline.PicardCommandLine
+
+	#use source && java-pkg_dosrc "${S}"/src/java/*
+	#use doc && java-pkg_dojavadoc "${S}"/javadoc
+}