259 lines
10 KiB
XML
259 lines
10 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>2.6-SNAPSHOT</version>
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<relativePath>../..</relativePath>
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</parent>
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<artifactId>queue-framework</artifactId>
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<packaging>jar</packaging>
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<name>Queue Framework</name>
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<properties>
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<sting.basedir>${project.basedir}/../..</sting.basedir>
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<gatk.extensions.sources>${project.build.directory}/generated-sources/gatk-extensions</gatk.extensions.sources>
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<sting.generate-gatk-extensions.skipped>false</sting.generate-gatk-extensions.skipped>
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<sting.packagetests.artifactId>queue-package</sting.packagetests.artifactId>
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<sting.test-utils-jar.phase>${sting.jar.phase}</sting.test-utils-jar.phase>
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</properties>
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<dependencies>
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<dependency>
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<groupId>${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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<dependency>
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<groupId>org.scala-lang</groupId>
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<artifactId>scala-compiler</artifactId>
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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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</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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</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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</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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</dependency>
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<!--
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extgen dependency only applies to the exec:exec,
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not the artifact, but don't know another way to include
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the artifact *only* in the <classpath/> of exec.
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See https://jira.codehaus.org/browse/MEXEC-111
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Perhaps extgen should be wrapped in a maven plugin?
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-->
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<dependency>
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<groupId>${project.groupId}</groupId>
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<artifactId>gatk-queue-extgen</artifactId>
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<version>${project.version}</version>
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<scope>runtime</scope>
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</dependency>
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<dependency>
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<groupId>${project.groupId}</groupId>
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<artifactId>gatk-framework</artifactId>
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<version>${project.version}</version>
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<classifier>test-utils</classifier>
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<type>test-jar</type>
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<scope>test</scope>
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</dependency>
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<dependency>
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<groupId>org.testng</groupId>
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<artifactId>testng</artifactId>
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<scope>test</scope>
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</dependency>
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</dependencies>
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<build>
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<plugins>
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<plugin>
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<groupId>org.codehaus.mojo</groupId>
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<artifactId>exec-maven-plugin</artifactId>
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<executions>
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<execution>
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<id>generate-gatk-extensions</id>
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<goals>
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<goal>exec</goal>
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</goals>
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<phase>generate-sources</phase>
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<configuration>
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<skip>${sting.generate-gatk-extensions.skipped}</skip>
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<executable>java</executable>
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<arguments>
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<argument>-classpath</argument>
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<classpath />
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<argument>org.broadinstitute.sting.queue.extensions.gatk.GATKExtensionsGenerator</argument>
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<argument>-l</argument>
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<argument>WARN</argument>
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<argument>-outDir</argument>
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<argument>${gatk.extensions.sources}</argument>
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</arguments>
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</configuration>
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</execution>
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</executions>
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</plugin>
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<plugin>
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<groupId>org.codehaus.mojo</groupId>
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<artifactId>build-helper-maven-plugin</artifactId>
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<executions>
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<execution>
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<id>add-gatk-extensions</id>
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<goals>
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<goal>add-source</goal>
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</goals>
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<phase>generate-sources</phase>
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<configuration>
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<sources>
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<source>${gatk.extensions.sources}</source>
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</sources>
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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-assembly-plugin</artifactId>
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<executions>
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<execution>
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<id>example-resources</id>
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<phase>generate-resources</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.scala-tools</groupId>
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<artifactId>maven-scala-plugin</artifactId>
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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-public-qscript</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-public-qscript</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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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-resources-plugin</artifactId>
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<executions>
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<execution>
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<id>copy-resource-bundle-log4j</id>
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<phase>prepare-package</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-javadoc-plugin</artifactId>
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<executions>
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<execution>
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<id>extract-resource-bundle</id>
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<phase>prepare-package</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-invoker-plugin</artifactId>
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<executions>
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<execution>
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<id>package-unittests</id>
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</execution>
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<execution>
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<id>package-integrationtests</id>
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</execution>
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<execution>
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<id>package-largescaletests</id>
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</execution>
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<execution>
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<id>package-pipelinetests</id>
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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>${project.version}</version>
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<optional>true</optional>
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</dependency>
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</dependencies>
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</profile>
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<profile>
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<id>private</id>
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<activation>
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<file>
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<exists>${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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</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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<execution>
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<id>link-private-qscript</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-qscript</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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</profiles>
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</project>
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