4.0.0 org.broadinstitute.sting sting-root 2.8-SNAPSHOT pom Sting Root 3.0.4 UTF-8 ${sourceEncoding} ${sourceEncoding} 1.7 1.7 yyyy/MM/dd HH:mm:ss ${project.basedir}/../.. true ${sting.committests.skipped} ${sting.committests.skipped} ${sting.committests.skipped} true false 4g -Xmx${test.maxmemory} org.scala-lang scala-compiler 2.10.2 org.scala-lang scala-library 2.10.2 com.google.code.cofoja cofoja 1.0-r139 net.sf sam 1.104.1628 net.sf picard 1.104.1628 edu.mit.broad picard-private-parts 2872 org.broad tribble 1.104.1628 org.broadinstitute variant 1.105.1642 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.apache.bcel bcel 5.2 org.reflections reflections 0.9.8 org.slf4j slf4j-log4j12 1.6.1 gov.nist 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 3.2.1 org.apache.commons commons-math 2.2 net.java.dev.jna jna 3.2.7 net.java.dev.jets3t jets3t 0.8.1 net.sf.gridscheduler drmaa 6.2u5p2 org.uncommons reportng 1.1.2 com.google.inject guice 3.0 org.apache.poi poi 3.8-beta3 org.apache.poi poi-ooxml 3.8-beta3 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 com.google.caliper caliper 0.5-rc1 test com.google.guava guava 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 org.apache.maven.plugins maven-jar-plugin 2.4 org.apache.maven.plugins maven-shade-plugin 2.1 org.apache.maven.plugins maven-assembly-plugin 2.4 org.apache.maven.plugins maven-surefire-plugin 2.16 true false false plain ${test.args} usedefaultlisteners false diff true ${sting.pipelinetests.run} ${java.io.tmpdir} default-test none unit-tests test ${sting.unittests.skipped} **/*UnitTest.class org.apache.maven.plugins maven-failsafe-plugin 2.16 true false false plain ${test.args} usedefaultlisteners false diff true ${sting.pipelinetests.run} ${java.io.tmpdir} integration-tests integration-test verify ${sting.integrationtests.skipped} **/*IntegrationTest.class pipeline-tests integration-test verify ${sting.pipelinetests.skipped} **/*PipelineTest.class large-scale-tests integration-test verify ${sting.largescaletests.skipped} **/*LargeScaleTest.class 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 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 ${git.version} git- com.google.code.sortpom maven-sortpom-plugin default sort verify true sting.public.repo.local Sting Public Local Repository file:${sting.basedir}/public/repo sting.private.repo.local Sting Private Local Repository file:${sting.basedir}/private/repo