dev-java/htsjdk: add a live ebuild, add a note

Not sure if current build system still creates $HOME/.git but from
reading github Issues it seem it is still needed: users are even asked
to run 'git clone' to work around the issue when gradle fails to do that.

Package-Manager: Portage-2.3.3, Repoman-2.3.1

2 files changed, 55 insertions, 2 deletions

diff --git a/dev-java/htsjdk/htsjdk-2.5.1.ebuild b/dev-java/htsjdk/htsjdk-2.5.1.ebuild
index 0f1e162dd..6ba163f80 100644
--- a/dev-java/htsjdk/htsjdk-2.5.1.ebuild
+++ b/dev-java/htsjdk/htsjdk-2.5.1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
@@ -36,7 +36,7 @@ java_prepare(){
 }
 
 src_compile(){
-	# work around gradle writing $HOME/.gradle
+	# work around gradle writing $HOME/.gradle and $HOME/.git
 	# https://github.com/samtools/htsjdk/issues/660#issuecomment-232155965
 	GRADLE_USER_HOME="${WORKDIR}" ./gradlew build || die
 }
diff --git a/dev-java/htsjdk/htsjdk-9999.ebuild b/dev-java/htsjdk/htsjdk-9999.ebuild
new file mode 100644
index 000000000..e9576743a
--- /dev/null
+++ b/dev-java/htsjdk/htsjdk-9999.ebuild
@@ -0,0 +1,53 @@
+# 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 git-r3 java-pkg-2 java-ant-2
+
+DESCRIPTION="Java API for high-throughput sequencing data (HTS) formats."
+HOMEPAGE="https://samtools.github.io/htsjdk/"
+EGIT_REPO_URI="https://github.com/samtools/htsjdk.git"
+
+LICENSE="MIT"
+SLOT="0"
+IUSE=""
+KEYWORDS="" # SANDBOX VIOLATION
+
+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
+}
+
+src_compile(){
+	# work around gradle writing $HOME/.gradle and $HOME/.git
+	# https://github.com/samtools/htsjdk/issues/660#issuecomment-232155965
+	GRADLE_USER_HOME="${WORKDIR}" ./gradlew || die
+}
+
+src_install() {
+	cd build/libs || die
+
+	#for i in *-SNAPSHOT.jar; do
+	#	java-pkg_newjar $i ${i/-[0-9]*.jar/.jar}
+	#done
+	java-pkg_newjar "${S}"/build/libs/*-SNAPSHOT.jar htsjdk.jar
+	use source && java-pkg_dosrc "${S}"/build/libs/*-sources.jar
+	use doc && java-pkg_dojavadoc "${S}"/build/libs/*-javadoc.jar
+}