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<?xml version="1.0" encoding="UTF-8"?>
<project xmlns= "http://maven.apache.org/POM/4.0.0" xmlns:xsi= "http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation= "http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd" >
<modelVersion > 4.0.0</modelVersion>
<!--
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This pom is parent for all gatk poms
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See also:
http://maven.apache.org/pom.html#Inheritance_v
http://maven.apache.org/guides/introduction/introduction-to-the-pom.html#Project_Inheritance_vs_Project_Aggregation
http://stackoverflow.com/questions/1992213/maven-parent-pom-vs-modules-pom
-->
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<groupId > org.broadinstitute.gatk</groupId>
<artifactId > gatk-root</artifactId>
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<version > 3.8-SNAPSHOT</version>
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<packaging > pom</packaging>
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<name > GATK Root</name>
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<prerequisites >
<maven > 3.0.4</maven>
</prerequisites>
<properties >
<sourceEncoding > UTF-8</sourceEncoding>
<project.build.sourceEncoding > ${sourceEncoding}</project.build.sourceEncoding>
<project.reporting.outputEncoding > ${sourceEncoding}</project.reporting.outputEncoding>
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<maven.compiler.source > 1.8</maven.compiler.source>
<maven.compiler.target > 1.8</maven.compiler.target>
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<maven.build.timestamp.format > yyyy/MM/dd HH:mm:ss</maven.build.timestamp.format>
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<gatk.basedir > ${project.basedir}/../..</gatk.basedir>
<gatk.committests.skipped > true</gatk.committests.skipped>
<gatk.unittests.skipped > ${gatk.committests.skipped}</gatk.unittests.skipped>
<gatk.integrationtests.skipped > ${gatk.committests.skipped}</gatk.integrationtests.skipped>
<gatk.queuetests.skipped > ${gatk.committests.skipped}</gatk.queuetests.skipped>
<gatk.largescaletests.skipped > true</gatk.largescaletests.skipped>
<gatk.knowledgebasetests.skipped > true</gatk.knowledgebasetests.skipped>
<gatk.queuetests.run > false</gatk.queuetests.run>
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<scala.maxmemory > 1g</scala.maxmemory>
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<test.maxmemory > 4g</test.maxmemory>
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<java.gc.threads > 4</java.gc.threads>
<java.gc.timeLimit > 50</java.gc.timeLimit>
<java.gc.heapFreeLimit > 10</java.gc.heapFreeLimit>
<test.args > -Xmx${test.maxmemory} -XX:+UseParallelOldGC -XX:ParallelGCThreads=${java.gc.threads} -XX:GCTimeLimit=${java.gc.timeLimit} -XX:GCHeapFreeLimit=${java.gc.heapFreeLimit}</test.args>
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<test.listeners > org.testng.reporters.FailedReporter,org.testng.reporters.JUnitXMLReporter,org.broadinstitute.gatk.utils.TestNGTestTransformer,org.broadinstitute.gatk.utils.GATKTextReporter,org.uncommons.reportng.HTMLReporter</test.listeners>
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<!-- Version numbers for picard and htsjdk -->
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<htsjdk.version > 2.10.0</htsjdk.version>
<picard.version > 2.9.2</picard.version>
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</properties>
<!-- Dependency configuration (versions, etc.) -->
<dependencyManagement >
<dependencies >
<dependency >
<groupId > org.scala-lang</groupId>
<artifactId > scala-compiler</artifactId>
<version > 2.10.2</version>
</dependency>
<dependency >
<groupId > org.scala-lang</groupId>
<artifactId > scala-library</artifactId>
<version > 2.10.2</version>
</dependency>
<dependency >
<groupId > com.google.code.cofoja</groupId>
<artifactId > cofoja</artifactId>
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<version > 1.2-20140817</version>
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</dependency>
<dependency >
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<groupId > com.github.samtools</groupId>
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<artifactId > htsjdk</artifactId>
<version > ${htsjdk.version}</version>
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<exclusions >
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<!-- The jdk15 classfier seems to throw off the normal dependency resolution,
leading to both 6.8 and 5.0-jdk15 on the classpath, then leading to an old
version testng loading, as seen by the super old TestNG4751Configurator.
-->
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<exclusion >
<groupId > org.testng</groupId>
<artifactId > testng</artifactId>
</exclusion>
</exclusions>
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</dependency>
<dependency >
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<groupId > com.github.broadinstitute</groupId>
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<artifactId > picard</artifactId>
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<version > ${picard.version}</version>
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</dependency>
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<dependency >
<groupId > com.intel.gkl</groupId>
<artifactId > gkl</artifactId>
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<version > 0.5.2</version>
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</dependency>
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<dependency >
<groupId > log4j</groupId>
<artifactId > log4j</artifactId>
<version > 1.2.15</version>
<exclusions >
<exclusion >
<groupId > com.sun.jdmk</groupId>
<artifactId > jmxtools</artifactId>
</exclusion>
<exclusion >
<groupId > javax.jms</groupId>
<artifactId > jms</artifactId>
</exclusion>
<exclusion >
<groupId > com.sun.jmx</groupId>
<artifactId > jmxri</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency >
<groupId > javax.mail</groupId>
<artifactId > mail</artifactId>
<version > 1.4.4</version>
</dependency>
<dependency >
<groupId > colt</groupId>
<artifactId > colt</artifactId>
<version > 1.2.0</version>
</dependency>
<dependency >
<groupId > it.unimi.dsi</groupId>
<artifactId > fastutil</artifactId>
<version > 6.5.3</version>
</dependency>
<dependency >
<groupId > org.simpleframework</groupId>
<artifactId > simple-xml</artifactId>
<version > 2.0.4</version>
</dependency>
<dependency >
<groupId > org.reflections</groupId>
<artifactId > reflections</artifactId>
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<version > 0.9.9-RC1</version>
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</dependency>
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<!-- slf4j bindings must only be at the package level: http://www.slf4j.org/manual.html -->
<dependency >
<groupId > org.slf4j</groupId>
<artifactId > slf4j-api</artifactId>
<version > 1.6.1</version>
</dependency>
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<dependency >
<groupId > org.slf4j</groupId>
<artifactId > slf4j-log4j12</artifactId>
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<version > 1.7.5</version>
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</dependency>
<dependency >
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<groupId > gov.nist.math</groupId>
<artifactId > jama</artifactId>
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<version > 1.0.2</version>
</dependency>
<dependency >
<groupId > net.sf.jgrapht</groupId>
<artifactId > jgrapht</artifactId>
<version > 0.8.3</version>
</dependency>
<dependency >
<groupId > org.freemarker</groupId>
<artifactId > freemarker</artifactId>
<version > 2.3.18</version>
</dependency>
<dependency >
<groupId > org.apache.commons</groupId>
<artifactId > commons-email</artifactId>
<version > 1.2</version>
</dependency>
<dependency >
<groupId > org.apache.commons</groupId>
<artifactId > commons-jexl</artifactId>
<version > 2.1.1</version>
</dependency>
<dependency >
<groupId > commons-lang</groupId>
<artifactId > commons-lang</artifactId>
<version > 2.5</version>
</dependency>
<dependency >
<groupId > commons-logging</groupId>
<artifactId > commons-logging</artifactId>
<version > 1.1.1</version>
</dependency>
<dependency >
<groupId > commons-io</groupId>
<artifactId > commons-io</artifactId>
<version > 2.1</version>
</dependency>
<dependency >
<groupId > commons-collections</groupId>
<artifactId > commons-collections</artifactId>
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<version > 3.2.2</version>
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</dependency>
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<dependency >
<groupId > commons-httpclient</groupId>
<artifactId > commons-httpclient</artifactId>
<version > 3.1</version>
</dependency>
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<dependency >
<groupId > org.apache.commons</groupId>
<artifactId > commons-math</artifactId>
<version > 2.2</version>
</dependency>
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<dependency >
<groupId > org.apache.commons</groupId>
<artifactId > commons-math3</artifactId>
<version > 3.5</version>
</dependency>
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<dependency >
<groupId > net.java.dev.jna</groupId>
<artifactId > jna</artifactId>
<version > 3.2.7</version>
</dependency>
<dependency >
<groupId > net.java.dev.jets3t</groupId>
<artifactId > jets3t</artifactId>
<version > 0.8.1</version>
</dependency>
<dependency >
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<groupId > us.levk</groupId>
<artifactId > drmaa-gridengine</artifactId>
<version > 6.2u5</version>
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</dependency>
<dependency >
<groupId > net.sf.snpeff</groupId>
<artifactId > snpeff</artifactId>
<version > 2.0.5</version>
</dependency>
<dependency >
<groupId > org.mongodb</groupId>
<artifactId > mongo-java-driver</artifactId>
<version > 2.7.3</version>
</dependency>
<dependency >
<groupId > com.google.code.gson</groupId>
<artifactId > gson</artifactId>
<version > 2.2.2</version>
</dependency>
<dependency >
<groupId > org.apache.httpcomponents</groupId>
<artifactId > httpclient</artifactId>
<version > 4.1.1</version>
</dependency>
<!--
For com.sun.javadoc
See also: http://sunnytalkstech.blogspot.in/2011/08/maven-dependency-for-toolsjar-in-jdk7.html
-->
<dependency >
<groupId > com.sun</groupId>
<artifactId > tools</artifactId>
<version > 1.4.2</version>
<scope > system</scope>
<systemPath > ${java.home}/../lib/tools.jar</systemPath>
</dependency>
<dependency >
<groupId > org.testng</groupId>
<artifactId > testng</artifactId>
<version > 6.8</version>
<scope > test</scope>
</dependency>
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<dependency >
<groupId > org.uncommons</groupId>
<artifactId > reportng</artifactId>
<version > 1.1.2</version>
<scope > test</scope>
<exclusions >
<exclusion >
<groupId > org.testng</groupId>
<artifactId > testng</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency >
<groupId > com.google.inject</groupId>
<artifactId > guice</artifactId>
<version > 3.0</version>
<scope > test</scope>
</dependency>
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<dependency >
<groupId > com.google.caliper</groupId>
<artifactId > caliper</artifactId>
<version > 0.5-rc1</version>
<scope > test</scope>
<exclusions >
<!--
TODO: After upgrade to caliper 1.0-beta-1 or later, this may need a revisit.
Possibly other modules may need to exclude *their* old guava versions.
-->
<exclusion >
<groupId > com.google.guava</groupId>
<artifactId > guava</artifactId>
</exclusion>
</exclusions>
</dependency>
</dependencies>
</dependencyManagement>
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<dependencies >
<dependency >
<groupId > org.testng</groupId>
<artifactId > testng</artifactId>
<scope > test</scope>
</dependency>
<!-- Dependencies for custom testng reports -->
<dependency >
<groupId > org.uncommons</groupId>
<artifactId > reportng</artifactId>
<scope > test</scope>
</dependency>
<dependency >
<groupId > com.google.inject</groupId>
<artifactId > guice</artifactId>
<scope > test</scope>
</dependency>
</dependencies>
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<build >
<!-- Plugin configuration -->
<pluginManagement >
<plugins >
<plugin >
<groupId > org.codehaus.mojo</groupId>
<artifactId > exec-maven-plugin</artifactId>
<version > 1.2.1</version>
</plugin>
<plugin >
<groupId > com.lukegb.mojo</groupId>
<artifactId > gitdescribe-maven-plugin</artifactId>
<version > 2.0</version>
</plugin>
<plugin >
<groupId > org.codehaus.mojo</groupId>
<artifactId > build-helper-maven-plugin</artifactId>
<version > 1.8</version>
</plugin>
<plugin >
<groupId > org.apache.maven.plugins</groupId>
<artifactId > maven-clean-plugin</artifactId>
<version > 2.5</version>
</plugin>
<plugin >
<groupId > org.apache.maven.plugins</groupId>
<artifactId > maven-dependency-plugin</artifactId>
<version > 2.8</version>
</plugin>
<plugin >
<groupId > org.apache.maven.plugins</groupId>
<artifactId > maven-resources-plugin</artifactId>
<version > 2.6</version>
</plugin>
<plugin >
<groupId > org.apache.maven.plugins</groupId>
<artifactId > maven-javadoc-plugin</artifactId>
<version > 2.9.1</version>
</plugin>
<plugin >
<groupId > org.apache.maven.plugins</groupId>
<artifactId > maven-compiler-plugin</artifactId>
<version > 3.1</version>
</plugin>
<plugin >
<groupId > org.scala-tools</groupId>
<artifactId > maven-scala-plugin</artifactId>
<version > 2.15.2</version>
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<configuration >
<jvmArgs >
<jvmArg > -Xmx${scala.maxmemory}</jvmArg>
</jvmArgs>
</configuration>
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</plugin>
<plugin >
<groupId > org.apache.maven.plugins</groupId>
<artifactId > maven-jar-plugin</artifactId>
<version > 2.4</version>
</plugin>
<plugin >
<groupId > org.apache.maven.plugins</groupId>
<artifactId > maven-shade-plugin</artifactId>
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<version > 2.4.3</version>
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</plugin>
<plugin >
<groupId > org.apache.maven.plugins</groupId>
<artifactId > maven-assembly-plugin</artifactId>
<version > 2.4</version>
</plugin>
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<plugin >
<groupId > org.apache.maven.plugins</groupId>
<artifactId > maven-enforcer-plugin</artifactId>
<version > 1.3.1</version>
</plugin>
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<!--
surefire/failsafe configurations are global, even across poms
not directly aggregated, for example package-tests/pom.xml
-->
<plugin >
<groupId > org.apache.maven.plugins</groupId>
<artifactId > maven-surefire-plugin</artifactId>
<version > 2.16</version>
<configuration >
<!-- See explicit executions below -->
<skip > true</skip>
<failIfNoTests > false</failIfNoTests>
<useFile > false</useFile>
<reportFormat > plain</reportFormat>
<argLine > ${test.args}</argLine>
<properties >
<property >
<name > usedefaultlisteners</name>
<value > false</value>
</property>
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<property >
<name > listener</name>
<value > ${test.listeners}</value>
</property>
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</properties>
<systemPropertyVariables >
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<gatkdir > ${gatk.basedir}</gatkdir>
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<clover.pertest.coverage > diff</clover.pertest.coverage>
<java.awt.headless > true</java.awt.headless>
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<queuetest.run > ${gatk.queuetests.run}</queuetest.run>
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<java.io.tmpdir > ${java.io.tmpdir}</java.io.tmpdir>
</systemPropertyVariables>
</configuration>
<executions >
<execution >
<id > default-test</id>
<phase > none</phase>
</execution>
<execution >
<!-- run all non integration tests -->
<id > unit-tests</id>
<goals >
<goal > test</goal>
</goals>
<configuration >
<!-- TODO: Re - enable unit tests by default? -->
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<skip > ${gatk.unittests.skipped}</skip>
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<reportsDirectory > ${project.build.directory}/surefire-reports/unit/${test}</reportsDirectory>
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<includes >
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<include > **/*UnitTest.class</include>
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</includes>
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<systemPropertyVariables >
<testType > unit</testType>
</systemPropertyVariables>
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</configuration>
</execution>
</executions>
</plugin>
<plugin >
<groupId > org.apache.maven.plugins</groupId>
<artifactId > maven-failsafe-plugin</artifactId>
<version > 2.16</version>
<configuration >
<!-- See explicit executions below -->
<skip > true</skip>
<failIfNoTests > false</failIfNoTests>
<useFile > false</useFile>
<reportFormat > plain</reportFormat>
<argLine > ${test.args}</argLine>
<properties >
<property >
<name > usedefaultlisteners</name>
<value > false</value>
</property>
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<property >
<name > listener</name>
<value > ${test.listeners}</value>
</property>
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</properties>
<systemPropertyVariables >
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<gatkdir > ${gatk.basedir}</gatkdir>
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<clover.pertest.coverage > diff</clover.pertest.coverage>
<java.awt.headless > true</java.awt.headless>
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<queuetest.run > ${gatk.queuetests.run}</queuetest.run>
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<java.io.tmpdir > ${java.io.tmpdir}</java.io.tmpdir>
</systemPropertyVariables>
</configuration>
<executions >
<execution >
<id > integration-tests</id>
<goals >
<goal > integration-test</goal>
<goal > verify</goal>
</goals>
<!-- run integration tests -->
<configuration >
<!-- TODO: Re - enable integration tests by default? -->
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<skip > ${gatk.integrationtests.skipped}</skip>
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<reportsDirectory > ${project.build.directory}/failsafe-reports/integration/${it.test}</reportsDirectory>
<summaryFile > ${project.build.directory}/failsafe-reports/integration/failsafe-summary-${it.test}.xml</summaryFile>
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<includes >
<include > **/*IntegrationTest.class</include>
</includes>
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<systemPropertyVariables >
<testType > integration</testType>
</systemPropertyVariables>
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</configuration>
</execution>
<execution >
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<id > queue-tests</id>
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<goals >
<goal > integration-test</goal>
<goal > verify</goal>
</goals>
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<!-- run queue dry run tests -->
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<configuration >
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<!-- TODO: Re - enable queue tests by default? -->
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<skip > ${gatk.queuetests.skipped}</skip>
<reportsDirectory > ${project.build.directory}/failsafe-reports/queue/${it.test}</reportsDirectory>
<summaryFile > ${project.build.directory}/failsafe-reports/queue/failsafe-summary-${it.test}.xml</summaryFile>
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<includes >
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<include > **/*QueueTest.class</include>
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</includes>
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<systemPropertyVariables >
<testType > queue</testType>
</systemPropertyVariables>
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</configuration>
</execution>
<execution >
<id > large-scale-tests</id>
<goals >
<goal > integration-test</goal>
<goal > verify</goal>
</goals>
<!-- run large scale tests -->
<configuration >
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<skip > ${gatk.largescaletests.skipped}</skip>
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<reportsDirectory > ${project.build.directory}/failsafe-reports/largescale/${it.test}</reportsDirectory>
<summaryFile > ${project.build.directory}/failsafe-reports/largescale/failsafe-summary-${it.test}.xml</summaryFile>
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<includes >
<include > **/*LargeScaleTest.class</include>
</includes>
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<systemPropertyVariables >
<testType > largescale</testType>
</systemPropertyVariables>
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</configuration>
</execution>
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<execution >
<id > knowledge-base-tests</id>
<goals >
<goal > integration-test</goal>
<goal > verify</goal>
</goals>
<!-- run knowledge base tests -->
<configuration >
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<skip > ${gatk.knowledgebasetests.skipped}</skip>
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<reportsDirectory > ${project.build.directory}/failsafe-reports/knowledgebasetests/${it.test}</reportsDirectory>
<summaryFile > ${project.build.directory}/failsafe-reports/knowledgebasetests/failsafe-summary-${it.test}.xml</summaryFile>
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<includes >
<include > **/*KnowledgeBaseTest.class</include>
</includes>
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<systemPropertyVariables >
<testType > knowledgebasetests</testType>
</systemPropertyVariables>
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</configuration>
</execution>
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</executions>
</plugin>
<plugin >
<groupId > com.google.code.sortpom</groupId>
<artifactId > maven-sortpom-plugin</artifactId>
<version > 2.2</version>
<configuration >
<createBackupFile > false</createBackupFile>
<predefinedSortOrder > custom_1</predefinedSortOrder>
<lineSeparator > \n</lineSeparator>
<encoding > ${sourceEncoding}</encoding>
<keepBlankLines > true</keepBlankLines>
<sortDependencies > scope</sortDependencies>
<nrOfIndentSpace > 4</nrOfIndentSpace>
<expandEmptyElements > false</expandEmptyElements>
</configuration>
<executions >
<execution >
<goals >
<goal > sort</goal>
</goals>
<phase > verify</phase>
</execution>
</executions>
</plugin>
<!-- TODO: Remove temporary symbolic link creation, after fixing test paths to use local resources. -->
<plugin >
<groupId > com.pyx4j</groupId>
<artifactId > maven-junction-plugin</artifactId>
<version > 1.0.3</version>
</plugin>
<plugin >
<groupId > org.apache.maven.plugins</groupId>
<artifactId > maven-invoker-plugin</artifactId>
<version > 1.8</version>
</plugin>
<plugin >
<groupId > org.apache.maven.plugins</groupId>
<artifactId > maven-install-plugin</artifactId>
<version > 2.5</version>
</plugin>
<plugin >
<groupId > org.apache.maven.plugins</groupId>
<artifactId > maven-site-plugin</artifactId>
<version > 3.3</version>
</plugin>
</plugins>
</pluginManagement>
<!-- Invoke plugins that always run -->
<plugins >
<plugin >
<groupId > com.lukegb.mojo</groupId>
<artifactId > gitdescribe-maven-plugin</artifactId>
<configuration >
<extraArguments >
<param > --long</param>
</extraArguments>
<setReactorProjectsProperties > true</setReactorProjectsProperties>
<descriptionProperty > git.version</descriptionProperty>
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<failOutput > exported</failOutput>
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</configuration>
<executions >
<execution >
<id > gitdescribe-initialize</id>
<goals >
<goal > gitdescribe</goal>
</goals>
<phase > initialize</phase>
</execution>
<execution >
<id > gitdescribe-presite</id>
<goals >
<goal > gitdescribe</goal>
</goals>
<phase > pre-site</phase>
</execution>
</executions>
</plugin>
<plugin >
<groupId > org.codehaus.mojo</groupId>
<artifactId > build-helper-maven-plugin</artifactId>
<!-- TODO: gitdescribe plugin doesn't allow null prefixes -->
<executions >
<execution >
<id > fix-version-initialize</id>
<goals >
<goal > regex-property</goal>
</goals>
<phase > initialize</phase>
<configuration >
<name > build.version</name>
<value > ${git.version}</value>
<regex > git-</regex>
</configuration>
</execution>
<execution >
<id > fix-version-pre-site</id>
<goals >
<goal > regex-property</goal>
</goals>
<phase > pre-site</phase>
<configuration >
<name > build.version</name>
<value > ${git.version}</value>
<regex > git-</regex>
</configuration>
</execution>
</executions>
</plugin>
<plugin >
<groupId > com.google.code.sortpom</groupId>
<artifactId > maven-sortpom-plugin</artifactId>
<executions >
<execution >
<id > default</id>
<goals >
<goal > sort</goal>
</goals>
<phase > verify</phase>
</execution>
</executions>
</plugin>
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<plugin >
<groupId > org.apache.maven.plugins</groupId>
<artifactId > maven-install-plugin</artifactId>
<executions >
<!--
The pom for com.pyx4j:maven-junction-plugin:1.0.3 points to
sysinternals:junction:1.04:exe. This file is only hosted in the repo
http://www.pyx4me.com/maven2, and the website keeps going down.
This file is only used on windows, but the maven-plugin devs never finished
implementing *plugin* dependency exclusions: http://jira.codehaus.org/browse/MNG-2163
Until someone updates or replaces this 2007 plugin with a new plugin using Java 7's Files class,
for now we copy over the artifact just in case the website is unavailable.
See also: http://docs.oracle.com/javase/7/docs/api/java/nio/file/Files.html#createSymbolicLink(java.nio.file.Path,%20java.nio.file.Path,%20java.nio.file.attribute.FileAttribute...)
-->
<execution >
<id > install-sysinternals-junction</id>
<goals >
<goal > install-file</goal>
</goals>
<phase > initialize</phase>
<inherited > false</inherited>
<configuration >
<file > ${gatk.basedir}/public/repo/sysinternals/junction/1.04/junction-1.04.exe</file>
<pomFile > ${gatk.basedir}/public/repo/sysinternals/junction/1.04/junction-1.04.pom</pomFile>
<packaging > exe</packaging>
</configuration>
</execution>
</executions>
</plugin>
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</plugins>
</build>
<reporting >
<excludeDefaults > true</excludeDefaults>
</reporting>
<repositories >
<repository >
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<id > gatk.public.repo.local</id>
<name > GATK Public Local Repository</name>
<url > file:${gatk.basedir}/public/repo</url>
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</repository>
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<repository >
<releases >
<enabled > false</enabled>
</releases>
<snapshots >
<enabled > true</enabled>
</snapshots>
<id > broad.artifactory.snapshots</id>
<name > Broad Institute Artifactory SNAPSHOTs</name>
<url > https://artifactory.broadinstitute.org/artifactory/libs-snapshot</url>
</repository>
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</repositories>
</project>
