dev-java/htsjdk: added 2.1.0 version needed=bundled so far in cramtools-3.0

Package-Manager: portage-2.2.28

2 files changed, 49 insertions, 0 deletions

diff --git a/dev-java/htsjdk/Manifest b/dev-java/htsjdk/Manifest
index ef1ea94b4..e2608ae99 100644
--- a/dev-java/htsjdk/Manifest
+++ b/dev-java/htsjdk/Manifest
@@ -1,2 +1,3 @@
+DIST htsjdk-2.1.0.tar.gz 11134251 SHA256 e0b52c63c6472601c9e071b39e6545dd1d075a013b102b6606a31b7b23bdda65 SHA512 a13446fed6e0b8833012e26827d1ecdccbdb1e894f1a6c6b2d41359fb948834ac1cab364a1f5e7e51180b19979a27b34c3f51f326b30fd47c5c4fb71663fa0b9 WHIRLPOOL 15e0342183739096b5a0d1ad167c6b8318bd126c4eed6867d748736fda0bbfa885b06198a51a952e0a4579d547f8b7480aabbef8e31653a3e3f09056bad4c42c
 DIST htsjdk-2.2.2.tar.gz 11459641 SHA256 5ef1b1e6b1fcdb7f13952b61de3b2af581ba800e4f6ea37762fbbd6d4e3f6904 SHA512 69c4f6be9be16669fbbbcac2e668b564c09793763908b1c4703b760ea46fdbcf747d233f87c48888de3810379b02f2e0d8ebef4d1bf48215128e02cb4053bd10 WHIRLPOOL 023f922b8a9f04c5c995bd862576b8eb19fc97357843e1709ce2b54d9b51dd666b9e7a93e5e934dfef228840d78ea09e9dd68294f8f07d29ef9937b023ed8f73
 DIST htsjdk-2.5.1.tar.gz 9121664 SHA256 78ab25ba4c540805261faf6c7f2ae57755c26f654b93da6d41dc6ff21d59dc00 SHA512 6bc67deb28556664a018dd72a89f7c84f534262dc7f18072d4e1f4bdfc51298d8aeb7086a9d2764d92c44c69844577a9b9a005b00e13fc35f2bd240bde7a347f WHIRLPOOL e5da7f92e4be3271aa1387faaf6966b212a1fbe82d8dc3cea3115f75df9c8188323bb9402b8d34e58191e13b01411d6e529a78687d1f4b963cd239f4512ec88e
diff --git a/dev-java/htsjdk/htsjdk-2.1.0.ebuild b/dev-java/htsjdk/htsjdk-2.1.0.ebuild
new file mode 100644
index 000000000..ca2cdd9cf
--- /dev/null
+++ b/dev-java/htsjdk/htsjdk-2.1.0.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
+}