sci-biology/gatk: version bump to 3.8-1

Bump to the latest version before commandline syntax has been
changed (in gatk-4). The package builds at the cost of downloading
608.21 MiB during git tree download and 134MB when download maven
jar files into "${W}"/.m2 directory.

The ebuild works around permissions issue when mvn attempts to
access $HOME/.m2 which is outside sandbox.

The ebuild installs individual jar files and porobably using a
different target we could get out the GenomeAnalysisTK.jar
file as upstream actually releases as its binary.

Package-Manager: Portage-2.3.28, Repoman-2.3.9

4 files changed, 112 insertions, 48 deletions

diff --git a/sci-biology/gatk/Manifest b/sci-biology/gatk/Manifest
deleted file mode 100644
index 51545e7e5..000000000
--- a/sci-biology/gatk/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST gatk-3.6.tar.gz 7141883 SHA256 1690f8d0d29affc0c79b860c332e9409243d6dc919a8f65e338e5f941c70ecf8 SHA512 325b3ef4a2bd445475e20f32c1592e80e35b20d070ff8b4f731faa103220e55bd934ee18da8eae4482f67836b88e29c35265412dc104358bcd12e5e830a4b5c1 WHIRLPOOL acdec380dd51f07ea8666434db16d8c187d1b310bf268b3cb2ebaadb63055206693ceb3d53cd9ba4fcacbee37c8c825c30d6797f1ba9198e81092a11a9ac09a3
diff --git a/sci-biology/gatk/files/settings.xml b/sci-biology/gatk/files/settings.xml
new file mode 100644
index 000000000..9527ec0b7
--- /dev/null
+++ b/sci-biology/gatk/files/settings.xml
@@ -0,0 +1,9 @@
+<settings xmlns="http://maven.apache.org/SETTINGS/1.0.0"
+  xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+  xsi:schemaLocation="http://maven.apache.org/SETTINGS/1.0.0
+                      https://maven.apache.org/xsd/settings-1.0.0.xsd">
+  <localRepository>${user.home}/.m2/repository</localRepository>
+  <interactiveMode>false</interactiveMode>
+  <usePluginRegistry>false</usePluginRegistry>
+  <offline>true</offline>
+</settings>
diff --git a/sci-biology/gatk/gatk-3.6.ebuild b/sci-biology/gatk/gatk-3.6.ebuild
deleted file mode 100644
index bdbf14e9b..000000000
--- a/sci-biology/gatk/gatk-3.6.ebuild
+++ /dev/null
@@ -1,47 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-EANT_BUILD_TARGET="dist"
-EANT_NEEDS_TOOLS="true"
-JAVA_ANT_REWRITE_CLASSPATH="true"
-
-inherit java-pkg-2 java-ant-2 vcs-snapshot
-
-DESCRIPTION="The Genome Analysis Toolkit"
-HOMEPAGE="http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit"
-SRC_URI="https://github.com/broadgsa/gatk/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-IUSE=""
-KEYWORDS="~amd64"
-
-COMMON_DEPS=""
-DEPEND="
-	>=virtual/jdk-1.6
-	dev-java/maven-bin:*
-	dev-java/cofoja
-	${COMMON_DEPS}"
-RDEPEND="
-	>=virtual/jre-1.6
-	>=sci-biology/SnpEff-2.0.5
-	${COMMON_DEPS}"
-
-src_prepare() {
-	sh ant-bridge.sh || die # BUG: this download and compiles lot of stuff
-	java-pkg-2_src_prepare
-}
-
-src_install() {
-	mvn install -Dmaven.repo.local="${WORKDIR}"/.m2/repository || die
-	find public -name \*.jar | grep -v tests | grep -v cofoja | while read f; do \
-		java-pkg_dojar $f # FIXME: Java QA Notice: installing versioned jar 'gatk-tools-public-3.6.jar'
-	done
-}
-
-pkg_postinst(){
-	einfo "The ebuild also installs bundled SnpEff-2.0.5.jar file until the"
-	einfo "installation layout gets more testing"
-}
diff --git a/sci-biology/gatk/gatk-3.8.1.ebuild b/sci-biology/gatk/gatk-3.8.1.ebuild
new file mode 100644
index 000000000..b2610a770
--- /dev/null
+++ b/sci-biology/gatk/gatk-3.8.1.ebuild
@@ -0,0 +1,103 @@
+# Copyright 1999-2018 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=5
+
+inherit java-pkg-2 git-r3 # building from tar.gz snapshots is unsupported
+
+# fetch -3.8-1.tar.gz
+MY_PV=${PV/.1/-1}
+DESCRIPTION="The Genome Analysis Toolkit"
+HOMEPAGE="http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit"
+EGIT_REPO_URI="https://github.com/broadgsa/gatk.git"
+EGIT_COMMIT="41147a655594c2aae6e2cad8462bd1648570b32b"
+# building outside of git is not possible,
+# see https://github.com/broadinstitute/picard/issues/605
+
+LICENSE="MIT"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64" # 608.21 MiB git download and 134MB "${W}"/.m2 download
+
+COMMON_DEPS=""
+DEPEND="
+	>=virtual/jdk-1.6
+	dev-java/maven-bin:* || ( dev-java/netbeans-java )
+	dev-java/cofoja
+	${COMMON_DEPS}"
+RDEPEND="
+	>=virtual/jre-1.6
+	>=sci-biology/SnpEff-2.0.5
+	${COMMON_DEPS}"
+
+#S="${WORKDIR}/${PN}-${MY_PV}"
+
+# https://maven.apache.org/settings.html
+# The two settings files are located at:
+#   The Maven installation directory: $M2_HOME/conf/settings.xml
+#   The user's home directory: ${user.home}/.m2/settings.xml
+#
+# localRepository: This value is the path of this build system's local repository. 
+#    The default value is ${user.home}/.m2/repository. This element is especially
+#    useful for a main build server allowing all logged-in users to build from a
+#    common local repository.
+# interactiveMode: true if Maven should attempt to interact with the user for input,
+#    false if not. Defaults to true.
+# usePluginRegistry: true if Maven should use the ${user.home}/.m2/plugin-registry.xml
+#    file to manage plugin versions, defaults to false. Note that for the current version
+#    of Maven 2.0, the plugin-registry.xml file should not be depended upon. Consider it
+#    dormant for now.
+# offline: true if this build system should operate in offline mode, defaults to false.
+#    This element is useful for build servers which cannot connect to a remote repository,
+#    either because of network setup or security reasons.
+
+src_prepare() {
+	mvn clean -Dmaven.repo.local="${WORKDIR}"/.m2/repository || die
+	sed -e 's#mvn_args="#mvn_args="-Dmaven.repo.local=${WORKDIR}/.m2/repository #' -i ant-bridge.sh || die
+	mkdir -p "${WORKDIR}"/.m2/repository || die
+	cp "${FILESDIR}"/settings.xml "${WORKDIR}"/.m2/repository/ || die
+	#export M2_HOME="${EPREFIX}"/usr/share/maven-bin-3.3
+	#export MAVEN_HOME="${EPREFIX}"/usr/share/maven-bin-3.3
+	export M2="${WORKDIR}"/.m2/repository # not recognized?
+	#export MAVEN_OPTS="-Xms256m -Xmx512m" # works but not needed actually
+	sh ant-bridge.sh || die # BUG: this downloads and compiles lot of stuff
+	java-pkg-2_src_prepare
+}
+
+src_install() {
+	mvn install -Dmaven.repo.local="${WORKDIR}"/.m2/repository || die
+	# Java QA Notice: installing versioned jar 'gatk-tools-public-3.8-1.jar'
+	# Java QA Notice: installing versioned jar 'gatk-queue-extensions-generator-3.8-1.jar'
+	# Java QA Notice: installing versioned jar 'gatk-engine-3.8-1.jar'
+	# Java QA Notice: installing versioned jar 'gatk-queue-extensions-public-3.8-1.jar'
+	# Java QA Notice: installing versioned jar 'gatk-utils-3.8-1.jar'
+	# Java QA Notice: installing versioned jar 'gatk-queue-3.8-1.jar'
+	find public -name \*.jar | grep -v tests | grep -v cofoja | while read f; do \
+		java-pkg_dojar $f
+	done
+}
+
+pkg_postinst(){
+	einfo "The ebuild also installs bundled SnpEff-2.0.5.jar file until the"
+	einfo "installation layout gets more testing"
+}
+
+# TODO: adjust the build system to output GenomeAnalysisTK.jar file like in an official
+#       binary release
+# # equery files gatk
+#   * Searching for gatk ...
+#   * Contents of sci-biology/gatk-3.8.1:
+#  /usr
+#  /usr/share
+#  /usr/share/gatk
+#  /usr/share/gatk/lib
+#  /usr/share/gatk/lib/external-example-1.0-SNAPSHOT.jar
+#  /usr/share/gatk/lib/gatk-engine-3.8-1.jar
+#  /usr/share/gatk/lib/gatk-queue-3.8-1.jar
+#  /usr/share/gatk/lib/gatk-queue-extensions-generator-3.8-1.jar
+#  /usr/share/gatk/lib/gatk-queue-extensions-public-3.8-1.jar
+#  /usr/share/gatk/lib/gatk-tools-public-3.8-1.jar
+#  /usr/share/gatk/lib/gatk-utils-3.8-1.jar
+#  /usr/share/gatk/lib/original-external-example-1.0-SNAPSHOT.jar
+#  /usr/share/gatk/lib/snpeff-2.0.5.jar
+#  /usr/share/gatk/package.env