282 lines
11 KiB
XML
282 lines
11 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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<parent>
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<groupId>org.broadinstitute.sting</groupId>
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<artifactId>sting-aggregator</artifactId>
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<version>2.8-SNAPSHOT</version>
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<relativePath>../..</relativePath>
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</parent>
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<artifactId>gatk-package</artifactId>
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<packaging>jar</packaging>
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<name>GATK Package</name>
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<properties>
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<sting.basedir>${project.basedir}/../..</sting.basedir>
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<sting.unpack.phase>prepare-package</sting.unpack.phase>
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<sting.shade.phase>package</sting.shade.phase>
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<app.main.class>org.broadinstitute.sting.gatk.CommandLineGATK</app.main.class>
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<sting.binary-dist.name>GenomeAnalysisTK</sting.binary-dist.name>
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</properties>
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<dependencies>
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<!-- Package everything in org.broadinstitute.sting -->
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<dependency>
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<groupId>${project.groupId}</groupId>
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<artifactId>gatk-framework</artifactId>
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<version>${project.version}</version>
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</dependency>
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<!-- Tribble codecs -->
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<dependency>
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<groupId>org.broad</groupId>
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<artifactId>tribble</artifactId>
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</dependency>
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<!-- The variant package (VCF, BCF, and VariantContext) -->
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<dependency>
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<groupId>org.broadinstitute</groupId>
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<artifactId>variant</artifactId>
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</dependency>
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<!-- Workaround - depend on the logger impl required by JEXL -->
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<dependency>
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<groupId>commons-logging</groupId>
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<artifactId>commons-logging</artifactId>
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</dependency>
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<!-- Required for binary-dist assembly, excluded by shade -->
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<dependency>
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<groupId>${project.groupId}</groupId>
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<artifactId>gatk-framework</artifactId>
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<version>${project.version}</version>
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<classifier>example-resources</classifier>
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<type>tar.bz2</type>
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</dependency>
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<dependency>
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<groupId>${project.groupId}</groupId>
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<artifactId>gatk-framework</artifactId>
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<version>${project.version}</version>
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<type>test-jar</type>
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</dependency>
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<dependency>
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<groupId>org.testng</groupId>
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<artifactId>testng</artifactId>
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<scope>test</scope>
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</dependency>
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<dependency>
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<groupId>com.google.caliper</groupId>
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<artifactId>caliper</artifactId>
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<scope>test</scope>
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</dependency>
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</dependencies>
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<build>
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<plugins>
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-surefire-plugin</artifactId>
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<executions>
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<execution>
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<id>unit-tests</id>
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<configuration>
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<skip>${sting.serialunittests.skipped}</skip>
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<dependenciesToScan>
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<scan>org.broadinstitute.sting:.*</scan>
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</dependenciesToScan>
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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>
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<executions>
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<execution>
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<id>integration-tests</id>
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<configuration>
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<skip>${sting.serialintegrationtests.skipped}</skip>
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<dependenciesToScan>
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<scan>org.broadinstitute.sting:.*</scan>
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</dependenciesToScan>
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</configuration>
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</execution>
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<execution>
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<id>pipeline-tests</id>
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<configuration>
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<skip>${sting.serialpipelinetests.skipped}</skip>
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<dependenciesToScan>
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<scan>org.broadinstitute.sting:.*</scan>
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</dependenciesToScan>
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</configuration>
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</execution>
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<execution>
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<id>large-scale-tests</id>
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<configuration>
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<skip>${sting.seriallargescaletests.skipped}</skip>
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<dependenciesToScan>
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<scan>org.broadinstitute.sting:.*</scan>
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</dependenciesToScan>
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</configuration>
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</execution>
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<execution>
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<id>knowledge-base-tests</id>
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<configuration>
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<skip>${sting.serialknowledgebasetests.skipped}</skip>
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<dependenciesToScan>
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<scan>org.broadinstitute.sting:.*</scan>
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</dependenciesToScan>
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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-dependency-plugin</artifactId>
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<executions>
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<execution>
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<id>unpack-direct-dependencies</id>
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<phase>${sting.unpack.phase}</phase>
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</execution>
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</executions>
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</plugin>
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-shade-plugin</artifactId>
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<executions>
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<execution>
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<id>sting-executable</id>
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<phase>${sting.shade.phase}</phase>
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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-assembly-plugin</artifactId>
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<executions>
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<execution>
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<id>binary-dist</id>
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<phase>${sting.shade.phase}</phase>
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</execution>
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</executions>
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</plugin>
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<plugin>
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<groupId>com.pyx4j</groupId>
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<artifactId>maven-junction-plugin</artifactId>
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<executions>
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<execution>
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<id>link-git-release</id>
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<phase>${sting.shade.phase}</phase>
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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-install-plugin</artifactId>
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<executions>
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<execution>
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<id>default-install</id>
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<phase>none</phase>
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</execution>
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<execution>
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<id>install-package</id>
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<phase>install</phase>
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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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<profiles>
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<profile>
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<id>protected</id>
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<activation>
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<file>
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<exists>${basedir}/../../protected/gatk-protected/pom.xml</exists>
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</file>
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</activation>
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<dependencies>
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<dependency>
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<groupId>${project.groupId}</groupId>
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<artifactId>gatk-protected</artifactId>
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<version>${project.version}</version>
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<optional>true</optional>
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</dependency>
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<dependency>
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<groupId>${project.groupId}</groupId>
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<artifactId>gatk-protected</artifactId>
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<version>${project.version}</version>
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<type>test-jar</type>
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<scope>test</scope>
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<optional>true</optional>
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</dependency>
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</dependencies>
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</profile>
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<profile>
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<id>private</id>
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<activation>
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<file>
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<exists>${basedir}/../../private/gatk-private/pom.xml</exists>
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</file>
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</activation>
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<dependencies>
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<dependency>
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<groupId>${project.groupId}</groupId>
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<artifactId>gatk-private</artifactId>
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<version>${project.version}</version>
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<optional>true</optional>
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</dependency>
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<dependency>
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<groupId>${project.groupId}</groupId>
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<artifactId>gatk-private</artifactId>
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<version>${project.version}</version>
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<type>test-jar</type>
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<scope>test</scope>
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<optional>true</optional>
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</dependency>
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</dependencies>
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<build>
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<plugins>
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<!-- TODO: All tests require access to private. For now. -->
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<plugin>
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<groupId>com.pyx4j</groupId>
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<artifactId>maven-junction-plugin</artifactId>
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<executions>
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<execution>
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<id>link-private-testdata</id>
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<phase>process-test-resources</phase>
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</execution>
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<execution>
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<id>unlink-private-testdata</id>
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<phase>clean</phase>
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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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</profile>
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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>sting.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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<sting.unpack.phase>none</sting.unpack.phase>
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<sting.shade.phase>none</sting.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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