740 lines
33 KiB
XML
740 lines
33 KiB
XML
<?xml version="1.0" encoding="UTF-8"?>
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<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">
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<modelVersion>4.0.0</modelVersion>
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<!--
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This pom is parent for all gatk poms
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See also:
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http://maven.apache.org/pom.html#Inheritance_v
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http://maven.apache.org/guides/introduction/introduction-to-the-pom.html#Project_Inheritance_vs_Project_Aggregation
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http://stackoverflow.com/questions/1992213/maven-parent-pom-vs-modules-pom
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-->
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<groupId>org.broadinstitute.gatk</groupId>
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<artifactId>gatk-root</artifactId>
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<version>3.7-SNAPSHOT</version>
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<packaging>pom</packaging>
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<name>GATK Root</name>
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<prerequisites>
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<maven>3.0.4</maven>
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</prerequisites>
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<properties>
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<sourceEncoding>UTF-8</sourceEncoding>
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<project.build.sourceEncoding>${sourceEncoding}</project.build.sourceEncoding>
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<project.reporting.outputEncoding>${sourceEncoding}</project.reporting.outputEncoding>
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<maven.compiler.source>1.8</maven.compiler.source>
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<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>${project.basedir}/../..</gatk.basedir>
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<gatk.committests.skipped>true</gatk.committests.skipped>
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<gatk.unittests.skipped>${gatk.committests.skipped}</gatk.unittests.skipped>
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<gatk.integrationtests.skipped>${gatk.committests.skipped}</gatk.integrationtests.skipped>
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<gatk.queuetests.skipped>${gatk.committests.skipped}</gatk.queuetests.skipped>
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<gatk.largescaletests.skipped>true</gatk.largescaletests.skipped>
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<gatk.knowledgebasetests.skipped>true</gatk.knowledgebasetests.skipped>
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<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>
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<java.gc.timeLimit>50</java.gc.timeLimit>
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<java.gc.heapFreeLimit>10</java.gc.heapFreeLimit>
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<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>2.6.1</htsjdk.version>
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<picard.version>2.6.0</picard.version>
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</properties>
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<!-- Dependency configuration (versions, etc.) -->
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<dependencyManagement>
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<dependencies>
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<dependency>
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<groupId>org.scala-lang</groupId>
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<artifactId>scala-compiler</artifactId>
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<version>2.10.2</version>
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</dependency>
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<dependency>
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<groupId>org.scala-lang</groupId>
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<artifactId>scala-library</artifactId>
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<version>2.10.2</version>
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</dependency>
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<dependency>
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<groupId>com.google.code.cofoja</groupId>
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<artifactId>cofoja</artifactId>
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<version>1.2-20140817</version>
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</dependency>
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<dependency>
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<groupId>com.github.samtools</groupId>
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<artifactId>htsjdk</artifactId>
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<version>${htsjdk.version}</version>
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<exclusions>
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<!-- The jdk15 classfier seems to throw off the normal dependency resolution,
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leading to both 6.8 and 5.0-jdk15 on the classpath, then leading to an old
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version testng loading, as seen by the super old TestNG4751Configurator.
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-->
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<exclusion>
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<groupId>org.testng</groupId>
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<artifactId>testng</artifactId>
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</exclusion>
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</exclusions>
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</dependency>
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<dependency>
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<groupId>com.github.broadinstitute</groupId>
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<artifactId>picard</artifactId>
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<version>${picard.version}</version>
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</dependency>
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<dependency>
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<groupId>log4j</groupId>
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<artifactId>log4j</artifactId>
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<version>1.2.15</version>
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<exclusions>
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<exclusion>
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<groupId>com.sun.jdmk</groupId>
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<artifactId>jmxtools</artifactId>
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</exclusion>
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<exclusion>
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<groupId>javax.jms</groupId>
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<artifactId>jms</artifactId>
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</exclusion>
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<exclusion>
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<groupId>com.sun.jmx</groupId>
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<artifactId>jmxri</artifactId>
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</exclusion>
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</exclusions>
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</dependency>
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<dependency>
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<groupId>javax.mail</groupId>
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<artifactId>mail</artifactId>
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<version>1.4.4</version>
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</dependency>
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<dependency>
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<groupId>colt</groupId>
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<artifactId>colt</artifactId>
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<version>1.2.0</version>
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</dependency>
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<dependency>
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<groupId>it.unimi.dsi</groupId>
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<artifactId>fastutil</artifactId>
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<version>6.5.3</version>
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</dependency>
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<dependency>
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<groupId>org.simpleframework</groupId>
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<artifactId>simple-xml</artifactId>
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<version>2.0.4</version>
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</dependency>
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<dependency>
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<groupId>org.reflections</groupId>
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<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 -->
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<dependency>
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<groupId>org.slf4j</groupId>
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<artifactId>slf4j-api</artifactId>
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<version>1.6.1</version>
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</dependency>
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<dependency>
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<groupId>org.slf4j</groupId>
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<artifactId>slf4j-log4j12</artifactId>
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<version>1.7.5</version>
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</dependency>
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<dependency>
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<groupId>gov.nist.math</groupId>
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<artifactId>jama</artifactId>
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<version>1.0.2</version>
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</dependency>
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<dependency>
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<groupId>net.sf.jgrapht</groupId>
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<artifactId>jgrapht</artifactId>
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<version>0.8.3</version>
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</dependency>
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<dependency>
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<groupId>org.freemarker</groupId>
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<artifactId>freemarker</artifactId>
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<version>2.3.18</version>
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</dependency>
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<dependency>
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<groupId>org.apache.commons</groupId>
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<artifactId>commons-email</artifactId>
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<version>1.2</version>
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</dependency>
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<dependency>
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<groupId>org.apache.commons</groupId>
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<artifactId>commons-jexl</artifactId>
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<version>2.1.1</version>
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</dependency>
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<dependency>
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<groupId>commons-lang</groupId>
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<artifactId>commons-lang</artifactId>
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<version>2.5</version>
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</dependency>
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<dependency>
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<groupId>commons-logging</groupId>
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<artifactId>commons-logging</artifactId>
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<version>1.1.1</version>
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</dependency>
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<dependency>
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<groupId>commons-io</groupId>
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<artifactId>commons-io</artifactId>
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<version>2.1</version>
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</dependency>
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<dependency>
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<groupId>commons-collections</groupId>
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<artifactId>commons-collections</artifactId>
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<version>3.2.2</version>
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</dependency>
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<dependency>
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<groupId>commons-httpclient</groupId>
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<artifactId>commons-httpclient</artifactId>
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<version>3.1</version>
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</dependency>
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<dependency>
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<groupId>org.apache.commons</groupId>
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<artifactId>commons-math</artifactId>
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<version>2.2</version>
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</dependency>
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<dependency>
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<groupId>org.apache.commons</groupId>
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<artifactId>commons-math3</artifactId>
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<version>3.5</version>
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</dependency>
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<dependency>
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<groupId>net.java.dev.jna</groupId>
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<artifactId>jna</artifactId>
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<version>3.2.7</version>
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</dependency>
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<dependency>
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<groupId>net.java.dev.jets3t</groupId>
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<artifactId>jets3t</artifactId>
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<version>0.8.1</version>
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</dependency>
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<dependency>
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<groupId>us.levk</groupId>
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<artifactId>drmaa-gridengine</artifactId>
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<version>6.2u5</version>
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</dependency>
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<dependency>
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<groupId>net.sf.snpeff</groupId>
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<artifactId>snpeff</artifactId>
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<version>2.0.5</version>
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</dependency>
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<dependency>
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<groupId>org.mongodb</groupId>
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<artifactId>mongo-java-driver</artifactId>
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<version>2.7.3</version>
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</dependency>
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<dependency>
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<groupId>com.google.code.gson</groupId>
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<artifactId>gson</artifactId>
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<version>2.2.2</version>
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</dependency>
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<dependency>
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<groupId>org.apache.httpcomponents</groupId>
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<artifactId>httpclient</artifactId>
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<version>4.1.1</version>
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</dependency>
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<!--
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For com.sun.javadoc
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See also: http://sunnytalkstech.blogspot.in/2011/08/maven-dependency-for-toolsjar-in-jdk7.html
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-->
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<dependency>
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<groupId>com.sun</groupId>
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<artifactId>tools</artifactId>
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<version>1.4.2</version>
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<scope>system</scope>
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<systemPath>${java.home}/../lib/tools.jar</systemPath>
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</dependency>
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<dependency>
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<groupId>org.testng</groupId>
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<artifactId>testng</artifactId>
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<version>6.8</version>
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<scope>test</scope>
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</dependency>
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<dependency>
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<groupId>org.uncommons</groupId>
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<artifactId>reportng</artifactId>
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<version>1.1.2</version>
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<scope>test</scope>
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<exclusions>
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<exclusion>
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<groupId>org.testng</groupId>
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<artifactId>testng</artifactId>
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</exclusion>
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</exclusions>
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</dependency>
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<dependency>
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<groupId>com.google.inject</groupId>
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<artifactId>guice</artifactId>
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<version>3.0</version>
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<scope>test</scope>
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</dependency>
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<dependency>
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<groupId>com.google.caliper</groupId>
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<artifactId>caliper</artifactId>
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<version>0.5-rc1</version>
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<scope>test</scope>
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<exclusions>
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<!--
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TODO: After upgrade to caliper 1.0-beta-1 or later, this may need a revisit.
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Possibly other modules may need to exclude *their* old guava versions.
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-->
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<exclusion>
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<groupId>com.google.guava</groupId>
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<artifactId>guava</artifactId>
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</exclusion>
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</exclusions>
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</dependency>
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</dependencies>
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</dependencyManagement>
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<dependencies>
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<dependency>
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<groupId>org.testng</groupId>
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<artifactId>testng</artifactId>
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<scope>test</scope>
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</dependency>
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<!-- Dependencies for custom testng reports -->
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<dependency>
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<groupId>org.uncommons</groupId>
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<artifactId>reportng</artifactId>
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<scope>test</scope>
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</dependency>
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<dependency>
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<groupId>com.google.inject</groupId>
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<artifactId>guice</artifactId>
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<scope>test</scope>
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</dependency>
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</dependencies>
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<build>
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<!-- Plugin configuration -->
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<pluginManagement>
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<plugins>
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<plugin>
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<groupId>org.codehaus.mojo</groupId>
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<artifactId>exec-maven-plugin</artifactId>
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<version>1.2.1</version>
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</plugin>
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<plugin>
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<groupId>com.lukegb.mojo</groupId>
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<artifactId>gitdescribe-maven-plugin</artifactId>
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<version>2.0</version>
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</plugin>
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<plugin>
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<groupId>org.codehaus.mojo</groupId>
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<artifactId>build-helper-maven-plugin</artifactId>
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<version>1.8</version>
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</plugin>
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-clean-plugin</artifactId>
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<version>2.5</version>
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</plugin>
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-dependency-plugin</artifactId>
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<version>2.8</version>
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</plugin>
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-resources-plugin</artifactId>
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<version>2.6</version>
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</plugin>
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-javadoc-plugin</artifactId>
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<version>2.9.1</version>
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</plugin>
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-compiler-plugin</artifactId>
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<version>3.1</version>
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</plugin>
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<plugin>
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<groupId>org.scala-tools</groupId>
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<artifactId>maven-scala-plugin</artifactId>
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<version>2.15.2</version>
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<configuration>
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<jvmArgs>
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<jvmArg>-Xmx${scala.maxmemory}</jvmArg>
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</jvmArgs>
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</configuration>
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</plugin>
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-jar-plugin</artifactId>
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<version>2.4</version>
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</plugin>
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-shade-plugin</artifactId>
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<version>2.4.3</version>
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</plugin>
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-assembly-plugin</artifactId>
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<version>2.4</version>
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</plugin>
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-enforcer-plugin</artifactId>
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<version>1.3.1</version>
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</plugin>
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<!--
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surefire/failsafe configurations are global, even across poms
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not directly aggregated, for example package-tests/pom.xml
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-->
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-surefire-plugin</artifactId>
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<version>2.16</version>
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<configuration>
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<!-- See explicit executions below -->
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<skip>true</skip>
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<failIfNoTests>false</failIfNoTests>
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<useFile>false</useFile>
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<reportFormat>plain</reportFormat>
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<argLine>${test.args}</argLine>
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<properties>
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<property>
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<name>usedefaultlisteners</name>
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<value>false</value>
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</property>
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<property>
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<name>listener</name>
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<value>${test.listeners}</value>
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</property>
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</properties>
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<systemPropertyVariables>
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<gatkdir>${gatk.basedir}</gatkdir>
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<clover.pertest.coverage>diff</clover.pertest.coverage>
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<java.awt.headless>true</java.awt.headless>
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<queuetest.run>${gatk.queuetests.run}</queuetest.run>
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<java.io.tmpdir>${java.io.tmpdir}</java.io.tmpdir>
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</systemPropertyVariables>
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</configuration>
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<executions>
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<execution>
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<id>default-test</id>
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<phase>none</phase>
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</execution>
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<execution>
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<!-- run all non integration tests -->
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<id>unit-tests</id>
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<goals>
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<goal>test</goal>
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</goals>
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<configuration>
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<!-- TODO: Re-enable unit tests by default? -->
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<skip>${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>
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<testType>unit</testType>
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</systemPropertyVariables>
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</configuration>
|
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</execution>
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</executions>
|
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</plugin>
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|
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<plugin>
|
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-failsafe-plugin</artifactId>
|
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<version>2.16</version>
|
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<configuration>
|
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<!-- See explicit executions below -->
|
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<skip>true</skip>
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<failIfNoTests>false</failIfNoTests>
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<useFile>false</useFile>
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<reportFormat>plain</reportFormat>
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<argLine>${test.args}</argLine>
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<properties>
|
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<property>
|
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<name>usedefaultlisteners</name>
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<value>false</value>
|
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</property>
|
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<property>
|
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<name>listener</name>
|
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<value>${test.listeners}</value>
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</property>
|
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</properties>
|
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<systemPropertyVariables>
|
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<gatkdir>${gatk.basedir}</gatkdir>
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<clover.pertest.coverage>diff</clover.pertest.coverage>
|
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<java.awt.headless>true</java.awt.headless>
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<queuetest.run>${gatk.queuetests.run}</queuetest.run>
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<java.io.tmpdir>${java.io.tmpdir}</java.io.tmpdir>
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</systemPropertyVariables>
|
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</configuration>
|
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<executions>
|
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<execution>
|
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<id>integration-tests</id>
|
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<goals>
|
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<goal>integration-test</goal>
|
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<goal>verify</goal>
|
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</goals>
|
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<!-- run integration tests -->
|
|
<configuration>
|
|
<!-- TODO: Re-enable integration tests by default? -->
|
|
<skip>${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>
|
|
<includes>
|
|
<include>**/*IntegrationTest.class</include>
|
|
</includes>
|
|
<systemPropertyVariables>
|
|
<testType>integration</testType>
|
|
</systemPropertyVariables>
|
|
</configuration>
|
|
</execution>
|
|
<execution>
|
|
<id>queue-tests</id>
|
|
<goals>
|
|
<goal>integration-test</goal>
|
|
<goal>verify</goal>
|
|
</goals>
|
|
<!-- run queue dry run tests -->
|
|
<configuration>
|
|
<!-- TODO: Re-enable queue tests by default? -->
|
|
<skip>${gatk.queuetests.skipped}</skip>
|
|
<reportsDirectory>${project.build.directory}/failsafe-reports/queue/${it.test}</reportsDirectory>
|
|
<summaryFile>${project.build.directory}/failsafe-reports/queue/failsafe-summary-${it.test}.xml</summaryFile>
|
|
<includes>
|
|
<include>**/*QueueTest.class</include>
|
|
</includes>
|
|
<systemPropertyVariables>
|
|
<testType>queue</testType>
|
|
</systemPropertyVariables>
|
|
</configuration>
|
|
</execution>
|
|
<execution>
|
|
<id>large-scale-tests</id>
|
|
<goals>
|
|
<goal>integration-test</goal>
|
|
<goal>verify</goal>
|
|
</goals>
|
|
<!-- run large scale tests -->
|
|
<configuration>
|
|
<skip>${gatk.largescaletests.skipped}</skip>
|
|
<reportsDirectory>${project.build.directory}/failsafe-reports/largescale/${it.test}</reportsDirectory>
|
|
<summaryFile>${project.build.directory}/failsafe-reports/largescale/failsafe-summary-${it.test}.xml</summaryFile>
|
|
<includes>
|
|
<include>**/*LargeScaleTest.class</include>
|
|
</includes>
|
|
<systemPropertyVariables>
|
|
<testType>largescale</testType>
|
|
</systemPropertyVariables>
|
|
</configuration>
|
|
</execution>
|
|
<execution>
|
|
<id>knowledge-base-tests</id>
|
|
<goals>
|
|
<goal>integration-test</goal>
|
|
<goal>verify</goal>
|
|
</goals>
|
|
<!-- run knowledge base tests -->
|
|
<configuration>
|
|
<skip>${gatk.knowledgebasetests.skipped}</skip>
|
|
<reportsDirectory>${project.build.directory}/failsafe-reports/knowledgebasetests/${it.test}</reportsDirectory>
|
|
<summaryFile>${project.build.directory}/failsafe-reports/knowledgebasetests/failsafe-summary-${it.test}.xml</summaryFile>
|
|
<includes>
|
|
<include>**/*KnowledgeBaseTest.class</include>
|
|
</includes>
|
|
<systemPropertyVariables>
|
|
<testType>knowledgebasetests</testType>
|
|
</systemPropertyVariables>
|
|
</configuration>
|
|
</execution>
|
|
</executions>
|
|
</plugin>
|
|
|
|
<plugin>
|
|
<groupId>com.google.code.sortpom</groupId>
|
|
<artifactId>maven-sortpom-plugin</artifactId>
|
|
<version>2.2</version>
|
|
<configuration>
|
|
<createBackupFile>false</createBackupFile>
|
|
<predefinedSortOrder>custom_1</predefinedSortOrder>
|
|
<lineSeparator>\n</lineSeparator>
|
|
<encoding>${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>
|
|
<failOutput>exported</failOutput>
|
|
</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>
|
|
<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>
|
|
</plugins>
|
|
</build>
|
|
|
|
<reporting>
|
|
<excludeDefaults>true</excludeDefaults>
|
|
</reporting>
|
|
|
|
<repositories>
|
|
<repository>
|
|
<id>gatk.public.repo.local</id>
|
|
<name>GATK Public Local Repository</name>
|
|
<url>file:${gatk.basedir}/public/repo</url>
|
|
</repository>
|
|
<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>
|
|
</repositories>
|
|
|
|
</project>
|