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>[email protected]</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="github">broadgsa/gatk</remote-id> - </upstream> -</pkgmetadata>
