[gentoo-commits] proj/sci:master commit in: sci-biology/gatk/, sci-biology/gatk/files/

[Horea Christian]

commit:     09664039e99b1f7d3a0b36ee6f0ae3993be2904b
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Mon Sep 28 07:33:53 2020 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Mon Sep 28 07:33:53 2020 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=09664039

sci-biology/gatk: removed package with missing dep

Package-Manager: Portage-3.0.8, Repoman-3.0.1
Signed-off-by: Horea Christian <chr <AT> chymera.eu>

 sci-biology/gatk/files/settings.xml |   9 ----
 sci-biology/gatk/gatk-3.8.1.ebuild  | 102 ------------------------------------
 sci-biology/gatk/gatk-9999.ebuild   |  82 -----------------------------
 sci-biology/gatk/metadata.xml       |  11 ----
 4 files changed, 204 deletions(-)

diff --git a/sci-biology/gatk/files/settings.xml b/sci-biology/gatk/files/settings.xml
deleted file mode 100644
index 9527ec0b7..000000000
--- a/sci-biology/gatk/files/settings.xml
+++ /dev/null
@@ -1,9 +0,0 @@
-<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-3.8.1.ebuild b/sci-biology/gatk/gatk-3.8.1.ebuild
deleted file mode 100644
index 9ad24d86c..000000000
--- a/sci-biology/gatk/gatk-3.8.1.ebuild
+++ /dev/null
@@ -1,102 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# 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
-
-MY_PV=${PV/.1/-1} # convert 3.8.1 to 3.8-1
-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" # git tree for <=gatk-3
-# check out 3.8-1 branch but using a proper commit, not ${MY_PV}
-# https://github.com/broadinstitute/gatk/issues/4685#issuecomment-383188772
-EGIT_COMMIT="41147a655594c2aae6e2cad8462bd1648570b32b"
-# building outside of git is not possible,
-# see https://github.com/broadinstitute/picard/issues/605
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64" # 608.21 MiB git download and 134MB "${W}"/.m2 download
-
-DEPEND="
-	>=virtual/jdk-1.6
-	dev-java/maven-bin:* || ( dev-java/netbeans-java )
-	dev-java/cofoja
-	"
-RDEPEND="
-	>=virtual/jre-1.6
-	>=sci-biology/SnpEff-2.0.5
-	"
-
-#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

diff --git a/sci-biology/gatk/gatk-9999.ebuild b/sci-biology/gatk/gatk-9999.ebuild
deleted file mode 100644
index 70d42cb0a..000000000
--- a/sci-biology/gatk/gatk-9999.ebuild
+++ /dev/null
@@ -1,82 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 python3_{4,5,6} )
-
-inherit java-pkg-2 git-r3 # building from tar.gz snapshots is unsupported
-
-DESCRIPTION="The Genome Analysis Toolkit"
-HOMEPAGE="http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit"
-EGIT_REPO_URI="https://github.com/broadinstitute/gatk.git" # git tree for >=gatk-4
-EGIT_CLONE_TYPE="mirror"
-# building outside of git is not possible,
-# see https://github.com/broadinstitute/picard/issues/605
-#
-#
-# must run 'git clone https://github.com/broadinstitute/gatk.git gatk'
-# see https://github.com/broadinstitute/gatk/issues/4687
-
-LICENSE="BSD" # since gatk-4
-SLOT="0"
-
-# gatk-4 needs java-1.8
-DEPEND="
-	>=virtual/jdk-1.8
-	>=dev-vcs/git-2.5
-	>=dev-vcs/git-lfs-1.1.0
-	>=dev-java/maven-bin-3.1:* || ( dev-java/netbeans-java )
-	dev-java/cofoja
-	"
-RDEPEND="
-	>=virtual/jre-1.8
-	>=sci-biology/SnpEff-2.0.5
-	>=dev-lang/R-3.2.5
-	"
-
-#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() {
-	default
-}
-
-src_compile(){
-	# work around gradle writing $HOME/.gradle, requiring $HOME/.git and $HOME/.m2/
-	# https://github.com/samtools/htsjdk/issues/660#issuecomment-232155965
-	# make jure SDK-1.8 is available, JRE-1.8 is not enough
-	#
-	# https://github.com/broadinstitute/gatk#building
-	# gradlew tragets are bundle, localJar, sparkJar, ...
-	GRADLE_USER_HOME="${WORKDIR}" ./gradlew --stacktrace --debug bundle || 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
-	#
-	# install a bash-completion script gatk-completion.sh into proper place
-}

diff --git a/sci-biology/gatk/metadata.xml b/sci-biology/gatk/metadata.xml
deleted file mode 100644
index 5a54c7fec..000000000
--- a/sci-biology/gatk/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-biology@g.o</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="github">broadgsa/gatk</remote-id>
-	</upstream>
-</pkgmetadata>