[gentoo-commits] proj/sci:master commit in: dev-java/htsjdk/

[Martin Mokrejs]

commit:     9ce6536356df2dffa9672161ae47b8de609c7682
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Jul 12 16:28:58 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Jul 12 16:28:58 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=9ce65363

dev-java/htsjdk: re-added back 2.2.2 version due to picard-2

Package-Manager: portage-2.2.28

 dev-java/htsjdk/htsjdk-2.2.2.ebuild | 48 +++++++++++++++++++++++++++++++++++++
 1 file changed, 48 insertions(+)

diff --git a/dev-java/htsjdk/htsjdk-2.2.2.ebuild b/dev-java/htsjdk/htsjdk-2.2.2.ebuild
new file mode 100644
index 0000000..ca2cdd9
--- /dev/null
+++ b/dev-java/htsjdk/htsjdk-2.2.2.ebuild
@@ -0,0 +1,48 @@
+# Copyright 1999-2016 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 API for high-throughput sequencing data (HTS) formats."
+HOMEPAGE="https://samtools.github.io/htsjdk/"
+SRC_URI="https://github.com/samtools/htsjdk/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64 ~x86"
+
+CDEPEND="dev-java/commons-jexl:2
+	dev-java/commons-compress:0
+	dev-java/commons-logging: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="commons-jexl-2,commons-compress,commons-logging"
+
+java_prepare() {
+	default
+	rm -v lib/{commons-compress,commons-jexl,commons-logging}*.jar || die
+}
+
+src_install() {
+	cd dist || die
+
+	for i in *.jar; do
+		java-pkg_newjar $i ${i/-[0-9]*.jar/.jar}
+	done
+
+	use source && java-pkg_dosrc "${S}"/src/java/*
+	use doc && java-pkg_dojavadoc "${S}"/javadoc
+}