282 lines
10 KiB
XML
282 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.gatk</groupId>
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<artifactId>gatk-aggregator</artifactId>
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<version>3.4-SNAPSHOT</version>
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<relativePath>../..</relativePath>
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</parent>
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<artifactId>gatk-queue-package-distribution</artifactId>
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<packaging>jar</packaging>
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<name>GATK Queue Package Distribution</name>
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<properties>
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<gatk.basedir>${project.basedir}/../..</gatk.basedir>
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<gatk.binary-dist.name>Queue</gatk.binary-dist.name>
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<app.main.class>org.broadinstitute.gatk.queue.QCommandLine</app.main.class>
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</properties>
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<dependencies>
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<!-- Queue -->
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<dependency>
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<groupId>${project.groupId}</groupId>
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<artifactId>gatk-queue</artifactId>
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<version>${project.version}</version>
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</dependency>
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<dependency>
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<groupId>${project.groupId}</groupId>
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<artifactId>gatk-package-distribution</artifactId>
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<version>${project.version}</version>
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</dependency>
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<dependency>
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<groupId>${project.groupId}</groupId>
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<artifactId>gatk-queue-extensions-distribution</artifactId>
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<version>${project.version}</version>
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</dependency>
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<!-- Scala -->
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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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</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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<!-- Picard -->
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<dependency>
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<groupId>picard</groupId>
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<artifactId>picard</artifactId>
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</dependency>
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<!-- JavaMail -->
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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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<!-- JNA, including embedded native libraries -->
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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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</dependency>
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<!-- Contracts for Java -->
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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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</dependency>
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<!-- snpEff -->
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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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</dependency>
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<!-- Workaround - depend on commons-httpclient to prevent shade from eliminating IgnoreCookiesSpec class -->
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<dependency>
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<groupId>commons-httpclient</groupId>
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<artifactId>commons-httpclient</artifactId>
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</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-utils</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-queue-extensions-public</artifactId>
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<version>${project.version}</version>
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<classifier>example-resources</classifier>
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<type>tar.bz2</type>
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</dependency>
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<!-- Test dependencies to run for for serial tests -->
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<dependency>
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<groupId>${project.groupId}</groupId>
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<artifactId>gatk-queue</artifactId>
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<version>${project.version}</version>
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<type>test-jar</type>
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<scope>test</scope>
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</dependency>
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<!-- Transitive dependencies for the serial test artifacts above -->
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<dependency>
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<groupId>com.google.caliper</groupId>
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<artifactId>caliper</artifactId>
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<scope>test</scope>
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</dependency>
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</dependencies>
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<build>
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<plugins>
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-surefire-plugin</artifactId>
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<executions>
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<execution>
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<id>unit-tests</id>
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<configuration>
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<skip>${gatk.serialunittests.skipped}</skip>
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<dependenciesToScan>
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<scan>org.broadinstitute.gatk:.*</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>${gatk.serialintegrationtests.skipped}</skip>
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<dependenciesToScan>
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<scan>org.broadinstitute.gatk:.*</scan>
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</dependenciesToScan>
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</configuration>
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</execution>
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<execution>
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<id>queue-tests</id>
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<configuration>
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<skip>${gatk.serialqueuetests.skipped}</skip>
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<dependenciesToScan>
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<scan>org.broadinstitute.gatk:.*</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>${gatk.seriallargescaletests.skipped}</skip>
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<dependenciesToScan>
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<scan>org.broadinstitute.gatk:.*</scan>
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</dependenciesToScan>
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</configuration>
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</execution>
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<execution>
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<id>knowledge-base-tests</id>
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<configuration>
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<skip>${gatk.serialknowledgebasetests.skipped}</skip>
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<dependenciesToScan>
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<scan>org.broadinstitute.gatk:.*</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-jar-plugin</artifactId>
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<executions>
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<execution>
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<id>executable-jar</id>
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<phase>${gatk.jar.phase}</phase>
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</execution>
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<execution>
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<id>default-jar</id>
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<phase>none</phase>
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</execution>
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<execution>
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<id>unshaded-default-jar</id>
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<phase>${gatk.jar.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-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>${gatk.unpack.phase}</phase>
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</execution>
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<execution>
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<id>executable-jar-lib</id>
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<phase>${gatk.jar.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>package-jar</id>
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<phase>${gatk.shade.phase}</phase>
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</execution>
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</executions>
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</plugin>
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-assembly-plugin</artifactId>
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<executions>
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<execution>
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<id>binary-dist</id>
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<phase>${gatk.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-executable-jar</id>
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<phase>${gatk.jar.phase}</phase>
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</execution>
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<execution>
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<id>link-package-jar</id>
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<phase>${gatk.shade.phase}</phase>
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</execution>
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<execution>
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<id>link-git-release</id>
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<phase>${gatk.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>gsadev</id>
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<activation>
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<property>
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<name>gsadev</name>
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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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