4.0.0 org.broadinstitute.sting sting-root 3.2-SNAPSHOT public/sting-root sting-aggregator pom Sting Aggregator public ${project.basedir} StingText.properties false -build-timestamp "${maven.build.timestamp}" package generate-resources process-resources process-test-resources true ${sting.packagecommittests.skipped} ${sting.packagecommittests.skipped} ${sting.packagecommittests.skipped} true true true ${sting.serialcommittests.skipped} ${sting.serialcommittests.skipped} ${sting.serialcommittests.skipped} true true 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 system org.apache.maven.plugins maven-resources-plugin default-resources resources ${sting.process-resources.phase} default-testResources testResources ${sting.process-test-resources.phase} copy-resource-bundle-log4j copy-resources none ${project.reporting.outputDirectory}/apidocs ${sting.basedir}/sting-utils/src/main/config/org/broadinstitute/sting/utils/help org.apache.maven.plugins maven-javadoc-plugin extract-resource-bundle javadoc none ${resource.bundle.skip} org.broadinstitute.sting.utils.help.ResourceBundleExtractorDoclet ${project.build.outputDirectory} ${project.groupId} gatk-framework ${project.version} 2g false true -build-timestamp "${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 default-jar ${sting.jar.phase} test-jar test-jar ${sting.jar.phase} true org.apache.maven.plugins maven-shade-plugin sting-executable shade none true org.broadinstitute.sting:gsalib:tar.gz:* org.broadinstitute.sting:*: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 src/main/assembly/binary-dist.xml com.pyx4j maven-junction-plugin link-public-testdata link none ${basedir}/public/testdata ${sting.basedir}/public/gatk-framework/src/test/resources unlink-public-testdata unlink none ${basedir}/public/testdata ${sting.basedir}/public/gatk-framework/src/test/resources link-private-testdata link none ${basedir}/private/testdata ${sting.basedir}/private/gatk-private/src/test/resources unlink-private-testdata unlink none ${basedir}/private/testdata ${sting.basedir}/private/gatk-private/src/test/resources link-public-qscript link none ${basedir}/public/scala/qscript ${sting.basedir}/public/queue-framework/src/main/qscripts unlink-public-qscript unlink none ${basedir}/public/scala/qscript ${sting.basedir}/public/queue-framework/src/main/qscripts link-private-qscript link none ${basedir}/private/scala/qscript ${sting.basedir}/private/queue-private/src/main/qscripts unlink-private-qscript unlink none ${basedir}/private/scala/qscript ${sting.basedir}/private/queue-private/src/main/qscripts link-binary-jar link none ${sting.basedir}/target/${sting.binary-dist.name}.${project.packaging} ${project.build.directory}/${project.build.finalName}.${project.packaging} link-git-release link none ${project.build.directory}/${sting.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 ${sting.basedir}/public/package-tests/pom.xml true true ${sting.basedir}/${maven.repo.local} ${test} ${it.test} false false ${sting.packagetests.artifactId} ${project.build.testOutputDirectory} ${project.basedir} ${sting.queuetests.run} ${maven.surefire.debug} ${maven.failsafe.debug} package-unittests run test ${project.build.directory}/invoker-reports/unit/${test} ${sting.packageunittests.skipped} true ${sting.packageunittests.skipped} package-integrationtests integration-test verify verify ${project.build.directory}/invoker-reports/integration/${it.test} ${sting.packageintegrationtests.skipped} true ${sting.packageintegrationtests.skipped} package-queuetests integration-test verify verify ${project.build.directory}/invoker-reports/queuetest/${it.test} ${sting.packagequeuetests.skipped} true ${sting.packagequeuetests.skipped} package-largescaletests integration-test verify verify ${project.build.directory}/invoker-reports/largescale/${it.test} ${sting.packagelargescaletests.skipped} true ${sting.packagelargescaletests.skipped} package-knowledgebasetests integration-test verify verify ${project.build.directory}/invoker-reports/knowledgebase/${it.test} ${sting.packageknowledgebasetests.skipped} true ${sting.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.apache.maven.plugins maven-failsafe-plugin com.pyx4j maven-junction-plugin link-public-testdata process-test-resources unlink-public-testdata clean link-public-qscript process-test-resources unlink-public-qscript clean 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.sting.utils.help.GATKDoclet ${project.groupId} gatk-package ${project.version} false true private -build-timestamp "${maven.build.timestamp}" -absolute-version ${build.version} ${gatkdocs.include.hidden} -settings-dir ${sting.basedir}/settings/helpTemplates -destination-dir ${project.build.directory}/gatkdocs protected ${basedir}/protected/pom.xml protected private ${basedir}/private/pom.xml private com.pyx4j maven-junction-plugin link-private-testdata process-test-resources unlink-private-testdata clean link-private-qscript process-test-resources unlink-private-qscript clean packagetests-enabled sting.packagetests.enabled true true true none none none none