4.0.0 org.broadinstitute.gatk gatk-root 3.9-SNAPSHOT pom GATK Root 3.0.4 UTF-8 ${sourceEncoding} ${sourceEncoding} 1.8 1.8 yyyy/MM/dd HH:mm:ss ${project.basedir}/../.. true ${gatk.committests.skipped} ${gatk.committests.skipped} ${gatk.committests.skipped} true true false 1g 4g 4 50 10 -Xmx${test.maxmemory} -XX:+UseParallelOldGC -XX:ParallelGCThreads=${java.gc.threads} -XX:GCTimeLimit=${java.gc.timeLimit} -XX:GCHeapFreeLimit=${java.gc.heapFreeLimit} org.testng.reporters.FailedReporter,org.testng.reporters.JUnitXMLReporter,org.broadinstitute.gatk.utils.TestNGTestTransformer,org.broadinstitute.gatk.utils.GATKTextReporter,org.uncommons.reportng.HTMLReporter 2.10.1 2.10.2 org.scala-lang scala-compiler 2.10.2 org.scala-lang scala-library 2.10.2 com.google.code.cofoja cofoja 1.2-20140817 com.github.samtools htsjdk ${htsjdk.version} org.testng testng com.github.broadinstitute picard ${picard.version} com.intel.gkl gkl 0.5.9 log4j log4j 1.2.15 com.sun.jdmk jmxtools javax.jms jms com.sun.jmx jmxri javax.mail mail 1.4.4 colt colt 1.2.0 it.unimi.dsi fastutil 6.5.3 org.simpleframework simple-xml 2.0.4 org.reflections reflections 0.9.9-RC1 org.slf4j slf4j-api 1.6.1 org.slf4j slf4j-log4j12 1.7.5 gov.nist.math jama 1.0.2 net.sf.jgrapht jgrapht 0.8.3 org.freemarker freemarker 2.3.18 org.apache.commons commons-email 1.2 org.apache.commons commons-jexl 2.1.1 commons-lang commons-lang 2.5 commons-logging commons-logging 1.1.1 commons-io commons-io 2.1 commons-collections commons-collections 3.2.2 commons-httpclient commons-httpclient 3.1 org.apache.commons commons-math 2.2 org.apache.commons commons-math3 3.5 net.java.dev.jna jna 3.2.7 net.java.dev.jets3t jets3t 0.8.1 us.levk drmaa-gridengine 6.2u5 net.sf.snpeff snpeff 2.0.5 org.mongodb mongo-java-driver 2.7.3 com.google.code.gson gson 2.2.2 org.apache.httpcomponents httpclient 4.1.1 com.sun tools 1.4.2 system ${java.home}/../lib/tools.jar org.testng testng 6.8 test org.uncommons reportng 1.1.2 test org.testng testng com.google.inject guice 3.0 test com.google.caliper caliper 0.5-rc1 test com.google.guava guava org.testng testng test org.uncommons reportng test com.google.inject guice test org.codehaus.mojo exec-maven-plugin 1.2.1 com.lukegb.mojo gitdescribe-maven-plugin 2.0 org.codehaus.mojo build-helper-maven-plugin 1.8 org.apache.maven.plugins maven-clean-plugin 2.5 org.apache.maven.plugins maven-dependency-plugin 2.8 org.apache.maven.plugins maven-resources-plugin 2.6 org.apache.maven.plugins maven-javadoc-plugin 2.9.1 org.apache.maven.plugins maven-compiler-plugin 3.1 org.scala-tools maven-scala-plugin 2.15.2 -Xmx${scala.maxmemory} org.apache.maven.plugins maven-jar-plugin 2.4 org.apache.maven.plugins maven-shade-plugin 2.4.3 org.apache.maven.plugins maven-assembly-plugin 2.4 org.apache.maven.plugins maven-enforcer-plugin 1.3.1 org.apache.maven.plugins maven-surefire-plugin 2.16 true false false plain ${test.args} usedefaultlisteners false listener ${test.listeners} ${gatk.basedir} diff true ${gatk.queuetests.run} ${java.io.tmpdir} default-test none unit-tests test ${gatk.unittests.skipped} ${project.build.directory}/surefire-reports/unit/${test} **/*UnitTest.class unit org.apache.maven.plugins maven-failsafe-plugin 2.16 true false false plain ${test.args} usedefaultlisteners false listener ${test.listeners} ${gatk.basedir} diff true ${gatk.queuetests.run} ${java.io.tmpdir} integration-tests integration-test verify ${gatk.integrationtests.skipped} ${project.build.directory}/failsafe-reports/integration/${it.test} ${project.build.directory}/failsafe-reports/integration/failsafe-summary-${it.test}.xml **/*IntegrationTest.class integration queue-tests integration-test verify ${gatk.queuetests.skipped} ${project.build.directory}/failsafe-reports/queue/${it.test} ${project.build.directory}/failsafe-reports/queue/failsafe-summary-${it.test}.xml **/*QueueTest.class queue large-scale-tests integration-test verify ${gatk.largescaletests.skipped} ${project.build.directory}/failsafe-reports/largescale/${it.test} ${project.build.directory}/failsafe-reports/largescale/failsafe-summary-${it.test}.xml **/*LargeScaleTest.class largescale knowledge-base-tests integration-test verify ${gatk.knowledgebasetests.skipped} ${project.build.directory}/failsafe-reports/knowledgebasetests/${it.test} ${project.build.directory}/failsafe-reports/knowledgebasetests/failsafe-summary-${it.test}.xml **/*KnowledgeBaseTest.class knowledgebasetests com.google.code.sortpom maven-sortpom-plugin 2.2 false custom_1 \n ${sourceEncoding} true scope 4 false sort verify com.pyx4j maven-junction-plugin 1.0.3 org.apache.maven.plugins maven-invoker-plugin 1.8 org.apache.maven.plugins maven-install-plugin 2.5 org.apache.maven.plugins maven-site-plugin 3.3 com.lukegb.mojo gitdescribe-maven-plugin --long true git.version exported gitdescribe-initialize gitdescribe initialize gitdescribe-presite gitdescribe pre-site org.codehaus.mojo build-helper-maven-plugin fix-version-initialize regex-property initialize build.version ${git.version} git- fix-version-pre-site regex-property pre-site build.version ${git.version} git- com.google.code.sortpom maven-sortpom-plugin default sort verify org.apache.maven.plugins maven-install-plugin install-sysinternals-junction install-file initialize false ${gatk.basedir}/public/repo/sysinternals/junction/1.04/junction-1.04.exe ${gatk.basedir}/public/repo/sysinternals/junction/1.04/junction-1.04.pom exe true gatk.public.repo.local GATK Public Local Repository file:${gatk.basedir}/public/repo false true broad.artifactory.snapshots Broad Institute Artifactory SNAPSHOTs https://artifactory.broadinstitute.org/artifactory/libs-snapshot