4.0.0 org.broadinstitute.gatk gatk-root 3.7-SNAPSHOT public/gatk-root gatk-aggregator pom GATK Aggregator public ${project.basedir} GATKText.properties false -build-timestamp "${maven.build.timestamp}" html ${gatk.basedir}/public/src/main/scripts/shell ${gatk.basedir}/public/src/main/assembly package prepare-package package generate-resources process-resources process-test-resources true ${gatk.packagecommittests.skipped} ${gatk.packagecommittests.skipped} ${gatk.packagecommittests.skipped} true true true ${gatk.serialcommittests.skipped} ${gatk.serialcommittests.skipped} ${gatk.serialcommittests.skipped} true true ${gatk.basedir}/target/executable ${gatk.basedir}/target/package ${gatk.basedir}/target com.sun tools org.apache.maven.plugins maven-clean-plugin gatkdocs ${basedir} javadoc.sh options packages ${basedir} dependency-reduced-pom.xml org.apache.maven.plugins maven-dependency-plugin unpack-direct-dependencies unpack-dependencies none true ${project.build.outputDirectory} jar runtime ${resource.bundle.path} executable-jar-lib copy-dependencies none ${gatk.executable.directory}/lib runtime false org.apache.maven.plugins maven-resources-plugin default-resources resources ${gatk.process-resources.phase} default-testResources testResources ${gatk.process-test-resources.phase} org.apache.maven.plugins maven-javadoc-plugin extract-resource-bundle javadoc none ${resource.bundle.skip} org.broadinstitute.gatk.utils.help.ResourceBundleExtractorDoclet ${project.build.outputDirectory} ${project.groupId} ${project.artifactId} ${project.version} 2g false true -build-timestamp "${maven.build.timestamp}" -absolute-version ${build.version} -out "${project.build.outputDirectory}/${resource.bundle.path}" org.apache.maven.plugins maven-compiler-plugin none com.google.java.contract.core.apt.AnnotationProcessor default-compile none default-testCompile none compile-package-info compile compile -Xpkginfo:always **/package-info.java compile-java compile compile **/package-info.java testCompile-java testCompile test-compile org.scala-tools maven-scala-plugin compile testCompile org.apache.maven.plugins maven-jar-plugin executable-jar jar none ${project.build.outputDirectory}/ignored_by_executable_jar ${gatk.executable.directory} ${gatk.binary-dist.name} ${app.main.class} true lib/ default-jar ${gatk.jar.phase} unshaded-default-jar jar none test-jar test-jar ${gatk.jar.phase} true org.apache.maven.plugins maven-shade-plugin package-jar shade none true false org.broadinstitute.gatk:gsalib:tar.gz:* org.broadinstitute.gatk:*:tar.bz2:example-resources *:* META-INF/services/javax.annotation.processing.Processor ${app.main.class} ${resource.bundle.path} org.apache.maven.plugins maven-assembly-plugin example-resources single none src/main/assembly/example-resources.xml binary-dist single none ${gatk.assembly.directory}/binary-dist.xml com.pyx4j maven-junction-plugin link-extensions-sources link none ${project.build.directory}/generated-sources/gatk-queue-extensions-public-src-main-scala ${gatk.basedir}/public/gatk-queue-extensions-public/src/main/scala link-executable-jar link none ${gatk.shortcut.directory}/${gatk.binary-dist.name}.${project.packaging} ${gatk.executable.directory}/${gatk.binary-dist.name}.${project.packaging} link-package-jar link none ${gatk.package.directory}/${gatk.binary-dist.name}.${project.packaging} ${project.build.directory}/${project.build.finalName}.${project.packaging} ${gatk.shortcut.directory}/${gatk.binary-dist.name}.${project.packaging} ${project.build.directory}/${project.build.finalName}.${project.packaging} link-git-release link none ${project.build.directory}/${gatk.binary-dist.name}-${build.version}.tar.bz2 ${project.build.directory}/${project.build.finalName}-binary-dist.tar.bz2 org.apache.maven.plugins maven-invoker-plugin true false ${gatk.basedir}/public/package-tests/pom.xml true true ${gatk.basedir}/${maven.repo.local} ${test} ${it.test} false false ${gatk.packagetests.artifactId} ${project.build.testOutputDirectory} ${project.basedir} ${gatk.queuetests.run} ${maven.surefire.debug} ${maven.failsafe.debug} package-unittests run test ${project.build.directory}/invoker-reports/unit/${test} ${gatk.packageunittests.skipped} true ${gatk.packageunittests.skipped} package-integrationtests integration-test verify verify ${project.build.directory}/invoker-reports/integration/${it.test} ${gatk.packageintegrationtests.skipped} true ${gatk.packageintegrationtests.skipped} package-queuetests integration-test verify verify ${project.build.directory}/invoker-reports/queuetest/${it.test} ${gatk.packagequeuetests.skipped} true ${gatk.packagequeuetests.skipped} package-largescaletests integration-test verify verify ${project.build.directory}/invoker-reports/largescale/${it.test} ${gatk.packagelargescaletests.skipped} true ${gatk.packagelargescaletests.skipped} package-knowledgebasetests integration-test verify verify ${project.build.directory}/invoker-reports/knowledgebase/${it.test} ${gatk.packageknowledgebasetests.skipped} true ${gatk.packageknowledgebasetests.skipped} org.apache.maven.plugins maven-install-plugin 2.5 install-package install-file none true ${project.groupId} ${project.artifactId} ${project.version} ${project.packaging} ${project.build.directory}/${project.build.finalName}.${project.packaging} org.codehaus.mojo exec-maven-plugin check-utils-engine-tools exec process-sources false ${gatk.shell.directory}/check_utils_engine_tools.sh delete-mavens-links exec process-test-resources false ${gatk.shell.directory}/delete_maven_links.sh org.apache.maven.plugins maven-failsafe-plugin org.apache.maven.plugins maven-clean-plugin com.google.code.sortpom maven-sortpom-plugin package-tests sort verify false public/package-tests/pom.xml org.apache.maven.plugins maven-javadoc-plugin 2.9.1 generate-gatk-docs aggregate false org.broadinstitute.gatk.tools.walkers.help.WalkerDoclet ${project.groupId} gatk-package-distribution ${project.version} false true private -build-timestamp "${maven.build.timestamp}" -absolute-version ${build.version} ${gatkdocs.include.hidden} -settings-dir ${gatk.basedir}/settings/helpTemplates -destination-dir ${project.build.directory}/gatkdocs -output-file-extension ${gatkdocs.extension} protected ${basedir}/protected/pom.xml protected private ${basedir}/private/pom.xml private fast disable.shadepackage none none packagetests-enabled gatk.packagetests.enabled true true true none none none none none none