4.0.0 org.broadinstitute.sting sting-aggregator 2.6-SNAPSHOT ../.. queue-framework jar Queue Framework ${project.basedir}/../.. ${project.build.directory}/generated-sources/gatk-extensions false queue-package ${project.groupId} gatk-framework ${project.version} org.scala-lang scala-compiler log4j log4j net.sf.jgrapht jgrapht org.apache.commons commons-email javax.mail mail ${project.groupId} gatk-queue-extgen ${project.version} runtime ${project.groupId} gatk-framework ${project.version} test-jar test org.testng testng test org.codehaus.mojo exec-maven-plugin generate-gatk-extensions exec generate-sources ${sting.generate-gatk-extensions.skipped} java -classpath org.broadinstitute.sting.queue.extensions.gatk.GATKExtensionsGenerator -l WARN -outDir ${gatk.extensions.sources} org.codehaus.mojo build-helper-maven-plugin add-gatk-extensions add-source generate-sources ${gatk.extensions.sources} org.apache.maven.plugins maven-assembly-plugin example-resources generate-resources org.scala-tools maven-scala-plugin com.pyx4j maven-junction-plugin link-public-qscript process-test-resources unlink-public-qscript clean org.apache.maven.plugins maven-resources-plugin copy-resource-bundle-log4j prepare-package org.apache.maven.plugins maven-javadoc-plugin extract-resource-bundle prepare-package org.apache.maven.plugins maven-jar-plugin test-jar org.apache.maven.plugins maven-invoker-plugin package-unittests package-integrationtests package-largescaletests package-pipelinetests protected ${basedir}/../../protected/gatk-protected/pom.xml ${project.groupId} gatk-protected ${project.version} true private ${basedir}/../../private/gatk-private/pom.xml ${project.groupId} gatk-private ${project.version} true 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