623 lines
27 KiB
XML
623 lines
27 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 sting/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.sting</groupId>
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<artifactId>sting-root</artifactId>
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<version>3.1-SNAPSHOT</version>
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<packaging>pom</packaging>
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<name>Sting 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>1.7</maven.compiler.source>
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<maven.compiler.target>1.7</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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<sting.basedir>${project.basedir}/../..</sting.basedir>
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<sting.committests.skipped>true</sting.committests.skipped>
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<sting.unittests.skipped>${sting.committests.skipped}</sting.unittests.skipped>
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<sting.integrationtests.skipped>${sting.committests.skipped}</sting.integrationtests.skipped>
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<sting.queuetests.skipped>${sting.committests.skipped}</sting.queuetests.skipped>
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<sting.largescaletests.skipped>true</sting.largescaletests.skipped>
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<sting.knowledgebasetests.skipped>true</sting.knowledgebasetests.skipped>
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<sting.queuetests.run>false</sting.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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<!-- Version numbers for picard sam-jdk. Usually kept in sync. -->
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<picard.public.version>1.107.1683</picard.public.version>
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<sam.version>${picard.public.version}</sam.version>
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<picard.version>${picard.public.version}</picard.version>
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<variant.version>${picard.public.version}</variant.version>
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<tribble.version>${picard.public.version}</tribble.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>1.0-r139</version>
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</dependency>
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<dependency>
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<groupId>net.sf</groupId>
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<artifactId>sam</artifactId>
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<version>${sam.version}</version>
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<exclusions>
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<exclusion>
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<groupId>org.testng</groupId>
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<artifactId>testng</artifactId>
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</exclusion>
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</exclusions>
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</dependency>
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<dependency>
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<groupId>net.sf</groupId>
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<artifactId>picard</artifactId>
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<version>${picard.version}</version>
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</dependency>
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<dependency>
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<groupId>org.broad</groupId>
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<artifactId>tribble</artifactId>
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<version>${tribble.version}</version>
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</dependency>
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<dependency>
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<groupId>org.broadinstitute</groupId>
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<artifactId>variant</artifactId>
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<version>${variant.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>0.9.8</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>1.6.1</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>3.2.1</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>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>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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<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>2.1</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-assembly-plugin</artifactId>
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<version>2.4</version>
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</plugin>
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|
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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>${test.args}</argLine>
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<properties>
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<property>
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<name>usedefaultlisteners</name>
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<value>false</value>
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</property>
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</properties>
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<systemPropertyVariables>
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<clover.pertest.coverage>diff</clover.pertest.coverage>
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<java.awt.headless>true</java.awt.headless>
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<java.io.tmpdir>${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>${sting.unittests.skipped}</skip>
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<reportsDirectory>${project.build.directory}/surefire-reports/unit/${test}</reportsDirectory>
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<includes>
|
|
<include>**/*UnitTest.class</include>
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</includes>
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</configuration>
|
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</execution>
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</executions>
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</plugin>
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-failsafe-plugin</artifactId>
|
|
<version>2.16</version>
|
|
<configuration>
|
|
<!-- See explicit executions below -->
|
|
<skip>true</skip>
|
|
<failIfNoTests>false</failIfNoTests>
|
|
<useFile>false</useFile>
|
|
<reportFormat>plain</reportFormat>
|
|
<argLine>${test.args}</argLine>
|
|
<properties>
|
|
<property>
|
|
<name>usedefaultlisteners</name>
|
|
<value>false</value>
|
|
</property>
|
|
</properties>
|
|
<systemPropertyVariables>
|
|
<clover.pertest.coverage>diff</clover.pertest.coverage>
|
|
<java.awt.headless>true</java.awt.headless>
|
|
<!-- TODO: Fix BaseTest to not error out if this property is missing. -->
|
|
<queuetest.run>${sting.queuetests.run}</queuetest.run>
|
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<java.io.tmpdir>${java.io.tmpdir}</java.io.tmpdir>
|
|
</systemPropertyVariables>
|
|
</configuration>
|
|
<executions>
|
|
<execution>
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|
<id>integration-tests</id>
|
|
<goals>
|
|
<goal>integration-test</goal>
|
|
<goal>verify</goal>
|
|
</goals>
|
|
<!-- run integration tests -->
|
|
<configuration>
|
|
<!-- TODO: Re-enable integration tests by default? -->
|
|
<skip>${sting.integrationtests.skipped}</skip>
|
|
<reportsDirectory>${project.build.directory}/failsafe-reports/integration/${it.test}</reportsDirectory>
|
|
<summaryFile>${project.build.directory}/failsafe-reports/integration/failsafe-summary-${it.test}.xml</summaryFile>
|
|
<includes>
|
|
<include>**/*IntegrationTest.class</include>
|
|
</includes>
|
|
</configuration>
|
|
</execution>
|
|
<execution>
|
|
<id>queue-tests</id>
|
|
<goals>
|
|
<goal>integration-test</goal>
|
|
<goal>verify</goal>
|
|
</goals>
|
|
<!-- run queue dry run tests -->
|
|
<configuration>
|
|
<!-- TODO: Re-enable queue tests by default? -->
|
|
<skip>${sting.queuetests.skipped}</skip>
|
|
<reportsDirectory>${project.build.directory}/failsafe-reports/queuetest/${it.test}</reportsDirectory>
|
|
<summaryFile>${project.build.directory}/failsafe-reports/queuetest/failsafe-summary-${it.test}.xml</summaryFile>
|
|
<includes>
|
|
<include>**/*QueueTest.class</include>
|
|
</includes>
|
|
</configuration>
|
|
</execution>
|
|
<execution>
|
|
<id>large-scale-tests</id>
|
|
<goals>
|
|
<goal>integration-test</goal>
|
|
<goal>verify</goal>
|
|
</goals>
|
|
<!-- run large scale tests -->
|
|
<configuration>
|
|
<skip>${sting.largescaletests.skipped}</skip>
|
|
<reportsDirectory>${project.build.directory}/failsafe-reports/largescale/${it.test}</reportsDirectory>
|
|
<summaryFile>${project.build.directory}/failsafe-reports/largescale/failsafe-summary-${it.test}.xml</summaryFile>
|
|
<includes>
|
|
<include>**/*LargeScaleTest.class</include>
|
|
</includes>
|
|
</configuration>
|
|
</execution>
|
|
<execution>
|
|
<id>knowledge-base-tests</id>
|
|
<goals>
|
|
<goal>integration-test</goal>
|
|
<goal>verify</goal>
|
|
</goals>
|
|
<!-- run knowledge base tests -->
|
|
<configuration>
|
|
<skip>${sting.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>
|
|
</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>${git.version}</value>
|
|
<regex>git-</regex>
|
|
</configuration>
|
|
</execution>
|
|
</executions>
|
|
</plugin>
|
|
<plugin>
|
|
<groupId>com.google.code.sortpom</groupId>
|
|
<artifactId>maven-sortpom-plugin</artifactId>
|
|
<executions>
|
|
<execution>
|
|
<id>default</id>
|
|
<goals>
|
|
<goal>sort</goal>
|
|
</goals>
|
|
<phase>verify</phase>
|
|
</execution>
|
|
</executions>
|
|
</plugin>
|
|
</plugins>
|
|
</build>
|
|
|
|
<reporting>
|
|
<excludeDefaults>true</excludeDefaults>
|
|
</reporting>
|
|
|
|
<repositories>
|
|
<repository>
|
|
<id>sting.public.repo.local</id>
|
|
<name>Sting Public Local Repository</name>
|
|
<url>file:${sting.basedir}/public/repo</url>
|
|
</repository>
|
|
</repositories>
|
|
|
|
</project>
|