306 lines
14 KiB
XML
306 lines
14 KiB
XML
<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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<!-- Properties for your assembly -->
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<groupId>org.mycompany.app</groupId>
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<artifactId>external-example</artifactId>
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<packaging>jar</packaging>
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<version>1.0-SNAPSHOT</version>
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<name>External Example</name>
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<properties>
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<gatk.version>3.4-SNAPSHOT</gatk.version>
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<!--
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gatk.basedir property must point to your checkout of GATK/GATK until we can get all the
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dependencies out of the committed gatk repo and into central.
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The installed pom for gatk-root looks for this property.
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Alternatively, one can install all the gatk files into their local ~/.m2/repository repo.
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http://maven.apache.org/plugins/maven-install-plugin/examples/custom-pom-installation.html
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-->
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<gatk.basedir>../..</gatk.basedir>
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<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
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<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
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<maven.build.timestamp.format>yyyy/MM/dd HH:mm:ss</maven.build.timestamp.format>
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<!-- NOTE: Currently the testing infrastructure for walkers does not support running outside the Broad. -->
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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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<!-- This flag is used by the package tests to disable re-shading -->
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<gatk.unpack.phase>prepare-package</gatk.unpack.phase>
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<gatk.shade.phase>package</gatk.shade.phase>
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</properties>
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<repositories>
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<repository>
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<id>gatk.public.repo.local</id>
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<name>GATK Public Local Repository</name>
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<url>file:${gatk.basedir}/public/repo</url>
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</repository>
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</repositories>
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<dependencies>
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<dependency>
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<groupId>org.broadinstitute.gatk</groupId>
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<artifactId>gatk-tools-public</artifactId>
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<version>${gatk.version}</version>
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</dependency>
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<dependency>
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<groupId>org.broadinstitute.gatk</groupId>
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<artifactId>gatk-utils</artifactId>
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<version>${gatk.version}</version>
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<type>test-jar</type>
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<scope>test</scope>
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</dependency>
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<dependency>
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<groupId>org.broadinstitute.gatk</groupId>
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<artifactId>gatk-engine</artifactId>
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<version>${gatk.version}</version>
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<type>test-jar</type>
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<scope>test</scope>
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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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</dependencies>
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<build>
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<plugins>
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<!-- Copy test resources to your classes directory -->
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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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<executions>
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<execution>
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<id>unpack</id>
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<phase>${gatk.unpack.phase}</phase>
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<goals>
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<goal>unpack</goal>
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</goals>
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<configuration>
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<artifactItems>
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<artifactItem>
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<groupId>org.broadinstitute.gatk</groupId>
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<artifactId>gatk-utils</artifactId>
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<version>${gatk.version}</version>
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<classifier>example-resources</classifier>
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<type>tar.bz2</type>
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<outputDirectory>${project.build.outputDirectory}</outputDirectory>
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</artifactItem>
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</artifactItems>
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</configuration>
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</execution>
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</executions>
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</plugin>
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<!-- Generate help text -->
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-javadoc-plugin</artifactId>
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<version>2.9.1</version>
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<executions>
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<execution>
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<id>extract-resource-bundle</id>
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<goals>
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<goal>javadoc</goal>
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</goals>
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<phase>prepare-package</phase>
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<configuration>
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<doclet>org.broadinstitute.gatk.utils.help.ResourceBundleExtractorDoclet</doclet>
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<!-- Required as doclet uses reflection to access classes for documentation, instead of source java-->
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<docletPath>${project.build.outputDirectory}</docletPath>
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<docletArtifact>
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<groupId>${project.groupId}</groupId>
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<artifactId>${project.artifactId}</artifactId>
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<version>${project.version}</version>
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</docletArtifact>
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<maxmemory>2g</maxmemory>
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<useStandardDocletOptions>false</useStandardDocletOptions>
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<quiet>true</quiet>
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<additionalparam>-build-timestamp "${maven.build.timestamp}" -absolute-version "${project.version}" -out ${project.build.outputDirectory}/GATKText.properties</additionalparam>
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</configuration>
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</execution>
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</executions>
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</plugin>
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<!-- Create packaged jar, containing only your walker and required classes -->
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-shade-plugin</artifactId>
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<version>2.1</version>
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<executions>
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<execution>
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<phase>${gatk.shade.phase}</phase>
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<goals>
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<goal>shade</goal>
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</goals>
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<configuration>
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<minimizeJar>true</minimizeJar>
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<createDependencyReducedPom>false</createDependencyReducedPom>
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<!-- Explicitly include classes loaded via reflection from artifacts below -->
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<filters>
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<filter>
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<artifact>commons-logging:commons-logging</artifact>
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<includes>
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<include>**</include>
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</includes>
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</filter>
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<filter>
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<artifact>com.github.samtools:htsjdk</artifact>
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<includes>
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<include>**</include>
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</includes>
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</filter>
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</filters>
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<!-- Stop shade from trying to unzip these indirect dependencies -->
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<artifactSet>
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<excludes>
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<exclude>org.broadinstitute.gatk:gsalib:tar.gz:*</exclude>
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<exclude>org.broadinstitute.gatk:*:tar.bz2:example-resources</exclude>
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</excludes>
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</artifactSet>
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<transformers>
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<!-- Set the main class to the GATK -->
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<transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
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<mainClass>org.broadinstitute.gatk.engine.CommandLineGATK</mainClass>
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</transformer>
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<!-- Include and append to the existing gatk help text in GATKText.properties -->
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<transformer implementation="org.apache.maven.plugins.shade.resource.AppendingTransformer">
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<resource>GATKText.properties</resource>
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</transformer>
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</transformers>
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</configuration>
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</execution>
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</executions>
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</plugin>
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<!-- surefire runs fast, small (aka unit) tests -->
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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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<!-- Pass various system properties -->
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<systemPropertyVariables>
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<gatkdir>${gatk.basedir}</gatkdir>
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<java.io.tmpdir>${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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<!-- Disable maven default execution -->
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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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<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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<skip>${gatk.unittests.skipped}</skip>
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<includes>
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<include>**/*UnitTest.class</include>
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</includes>
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<systemPropertyVariables>
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<testType>unit</testType>
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</systemPropertyVariables>
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</configuration>
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</execution>
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</executions>
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</plugin>
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<!-- failsafe runs all other tests that may take longer, and may require pre/post test setup and teardown -->
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-failsafe-plugin</artifactId>
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<version>2.16</version>
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<configuration>
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<!-- See explicit executions below -->
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<skip>true</skip>
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<failIfNoTests>false</failIfNoTests>
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<!-- Pass various system properties -->
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<systemPropertyVariables>
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<gatkdir>${gatk.basedir}</gatkdir>
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<java.io.tmpdir>${java.io.tmpdir}</java.io.tmpdir>
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</systemPropertyVariables>
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</configuration>
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<executions>
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<execution>
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<id>integration-tests</id>
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<goals>
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<goal>integration-test</goal>
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<goal>verify</goal>
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</goals>
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<!-- run integration tests -->
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<configuration>
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<skip>${gatk.integrationtests.skipped}</skip>
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<includes>
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<include>**/*IntegrationTest.class</include>
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</includes>
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<systemPropertyVariables>
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<testType>integrationtest</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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</plugins>
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</build>
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<reporting>
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<excludeDefaults>true</excludeDefaults>
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</reporting>
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<!-- These profiles are used by the GATK build in a multi-module setting. You do NOT need these profiles. -->
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<profiles>
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<!-- Optionally do not shade/package jars -->
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<!--
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NOTE: Profile id "fast" comes from comments in PR #771.
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The name is meant to be memorable, but is highly non-specific. Users are forewarned that
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behavior of this profile, or the identifier itself, may be heavily modified in the future.
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Hardcode usage in non-VCS controlled scripts at your own risk.
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-->
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<profile>
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<id>fast</id>
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<activation>
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<property>
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<name>disable.shadepackage</name>
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</property>
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</activation>
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<properties>
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<gatk.unpack.phase>none</gatk.unpack.phase>
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<gatk.shade.phase>none</gatk.shade.phase>
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</properties>
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</profile>
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<!-- Collection of properties for use during package testing -->
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<profile>
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<id>packagetests-enabled</id>
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<activation>
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<property>
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<name>gatk.packagetests.enabled</name>
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<value>true</value>
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</property>
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</activation>
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<properties>
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<gatk.jar.phase>none</gatk.jar.phase>
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<gatk.unpack.phase>none</gatk.unpack.phase>
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<gatk.shade.phase>none</gatk.shade.phase>
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</properties>
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</profile>
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</profiles>
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</project>
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