sci-biology/picard: version bump (not working yet)

Bug: https://github.com/broadinstitute/picard/issues/605
Bug: https://bugs.gentoo.org/653012
Package-Manager: Portage-2.3.27, Repoman-2.3.9

3 files changed, 63 insertions, 61 deletions

diff --git a/sci-biology/picard/Manifest b/sci-biology/picard/Manifest
index 83c9ee5b6..2f14e87a2 100644
--- a/sci-biology/picard/Manifest
+++ b/sci-biology/picard/Manifest
@@ -1,3 +1,2 @@
-DIST picard-1.141.tar.gz 5692255 SHA256 128e761b4dbedda9a89cceb4d1648be213ec823ff105a35db9c9526955a42320 SHA512 5fed8ff0076ec5f096a5138b95ae07805f8f4d68db33b65f2e21325f49493c50f235519768823c2db981b2e543fbf05f55be7939d75cbd5d257ac84e633b9bf4 WHIRLPOOL 5716cc51da6e94b338aceb5a3d01da5ae048f011e3d3eee72a96144d4b6f80dddf898ea902fae08b127f93c771f521437bd299bdeaf005af6f24c76f9844b63d
-DIST picard-2.10.2.tar.gz 35031761 SHA256 bb452782dd5ce5c988c70b41308a06d23293dcfe7468398adf00d2722fe31a6b SHA512 eb3dc4f0bd951faf06d955d62bded8890ab2cc165b97c4232300dd0b49e852a2e636657022850147fe0b728d4b4d0c616c7c7a9ddf2ba716c385f680b5ae6836 WHIRLPOOL c04523b30a0e7da74e318c223bb2fa1d165222889612229353a0a8d99f1d17162a5e4df19379612e1afd75abaceb51d5579008035ab3d8857f1816d80e57e1ef
-DIST picard-2.2.2.tar.gz 6565857 SHA256 1d858fde23aa9938a87cd96e6c2fbbfcdea669c9f30d524c107af26bce3798de SHA512 4ee97443397b45236a2481fa64c80edbd7761d6562cc134d65f1d95fa101ccc82402bbf21ed6b186e15324f2c189737790066e18cd0143bb50768c20ee4b156b WHIRLPOOL 69df60c171a5e531b78ad670b260d717a749012d05028e1afba2484eb3a84a71e61ade13c7298b0e9bc6ff526367ca886d9440b996882d3f19455f8f46e3bd4f
+DIST picard-1.141.tar.gz 5692255 BLAKE2B 26bb6edd32b75895a52c549e61e5873b6b5d1127fa1458e671b24a2b792c86bb3db5f9f8b8f24f9419a4ce1680f6bbad98da8dc7da4bf9b14178e901a28d803e SHA512 5fed8ff0076ec5f096a5138b95ae07805f8f4d68db33b65f2e21325f49493c50f235519768823c2db981b2e543fbf05f55be7939d75cbd5d257ac84e633b9bf4
+DIST picard-2.2.2.tar.gz 6565857 BLAKE2B e18bd45c9422b97e129418804bb063806614a707dbb9bafd42ae77a0899328cbade45a3b9d8a91f6a07e3508b6b8b3e4b964ee0c9b838a0d6d9cd5eef04d83f6 SHA512 4ee97443397b45236a2481fa64c80edbd7761d6562cc134d65f1d95fa101ccc82402bbf21ed6b186e15324f2c189737790066e18cd0143bb50768c20ee4b156b
diff --git a/sci-biology/picard/picard-2.10.2.ebuild b/sci-biology/picard/picard-2.10.2.ebuild
deleted file mode 100644
index bddadedbb..000000000
--- a/sci-biology/picard/picard-2.10.2.ebuild
+++ /dev/null
@@ -1,58 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-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 --stacktrace --debug || 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 "${S}"/javadoc
-#}
diff --git a/sci-biology/picard/picard-2.17.11.ebuild b/sci-biology/picard/picard-2.17.11.ebuild
new file mode 100644
index 000000000..636bf879c
--- /dev/null
+++ b/sci-biology/picard/picard-2.17.11.ebuild
@@ -0,0 +1,61 @@
+# Copyright 1999-2018 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+#JAVA_PKG_IUSE="doc source"
+JAVA_PKG_IUSE=""
+
+inherit git-r3 java-pkg-2
+
+DESCRIPTION="Java-based command-line utilities that manipulate SAM/BAM/CRAM/VCF files"
+HOMEPAGE="http://picard.sourceforge.net
+	http://broadinstitute.github.io/picard"
+EGIT_REPO_URI="https://github.com/broadinstitute/picard.git"
+EGIT_BRANCH="${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
+}