/
pom.xml
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pom.xml
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<?xml version="1.0" encoding="UTF-8"?>
<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">
<modelVersion>4.0.0</modelVersion>
<parent>
<groupId>org.broadinstitute.gatk</groupId>
<artifactId>gatk-aggregator</artifactId>
<version>3.7</version>
<relativePath>../..</relativePath>
</parent>
<artifactId>gatk-queue-extensions-distribution</artifactId>
<packaging>jar</packaging>
<name>GATK Queue Extensions Distribution</name>
<properties>
<gatk.basedir>${project.basedir}/../..</gatk.basedir>
<gatk.extensions.sources>${project.build.directory}/generated-sources/gatk-extensions</gatk.extensions.sources>
<gatk.queue.extensions.public>${gatk.basedir}/public/gatk-queue-extensions-public</gatk.queue.extensions.public>
<gatk.queue.extensions.sources>${gatk.queue.extensions.public}/src/main/scala</gatk.queue.extensions.sources>
<gatk.generate-gatk-extensions.skipped>false</gatk.generate-gatk-extensions.skipped>
<gatk.packagetests.artifactId>gatk-queue-package-distribution</gatk.packagetests.artifactId>
</properties>
<dependencies>
<dependency>
<groupId>${project.groupId}</groupId>
<artifactId>gatk-tools-protected</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>${project.groupId}</groupId>
<artifactId>gatk-queue</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>org.scala-lang</groupId>
<artifactId>scala-compiler</artifactId>
</dependency>
<dependency>
<groupId>log4j</groupId>
<artifactId>log4j</artifactId>
</dependency>
<dependency>
<groupId>com.github.broadinstitute</groupId>
<artifactId>picard</artifactId>
</dependency>
<!--
Extensions generator dependency only applies to the exec:exec,
not the artifact, but don't know another way to include
the artifact *only* in the <classpath/> of exec.
See https://jira.codehaus.org/browse/MEXEC-111
Perhaps extensions-generator should be wrapped in a maven plugin?
-->
<dependency>
<groupId>${project.groupId}</groupId>
<artifactId>gatk-queue-extensions-generator</artifactId>
<version>${project.version}</version>
<scope>runtime</scope>
</dependency>
<!--
NOTE: Because exec-maven-plugin is used, this aggregator dependency
will cause mvn compile to not work. Use mvn test-compile for now.
See:
http://stackoverflow.com/questions/4786881/why-is-test-jar-dependency-required-for-mvn-compile
http://jira.codehaus.org/browse/MEXEC-91
-->
<dependency>
<groupId>${project.groupId}</groupId>
<artifactId>gatk-utils</artifactId>
<version>${project.version}</version>
<type>test-jar</type>
<scope>test</scope>
</dependency>
<dependency>
<groupId>${project.groupId}</groupId>
<artifactId>gatk-queue</artifactId>
<version>${project.version}</version>
<type>test-jar</type>
<scope>test</scope>
</dependency>
</dependencies>
<build>
<plugins>
<!--
See note above about exec plugin breaking mvn compile
-->
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>exec-maven-plugin</artifactId>
<executions>
<execution>
<id>generate-gatk-extensions</id>
<goals>
<goal>exec</goal>
</goals>
<phase>generate-sources</phase>
<configuration>
<skip>${gatk.generate-gatk-extensions.skipped}</skip>
<executable>java</executable>
<arguments>
<argument>-classpath</argument>
<classpath />
<argument>org.broadinstitute.gatk.queue.extensions.gatk.GATKExtensionsGenerator</argument>
<argument>-l</argument>
<argument>WARN</argument>
<argument>-outDir</argument>
<argument>${gatk.extensions.sources}</argument>
</arguments>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>build-helper-maven-plugin</artifactId>
<executions>
<execution>
<id>add-gatk-extensions</id>
<goals>
<goal>add-source</goal>
</goals>
<phase>generate-sources</phase>
<configuration>
<sources>
<source>${gatk.queue.extensions.sources}</source>
<source>${gatk.extensions.sources}</source>
</sources>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.scala-tools</groupId>
<artifactId>maven-scala-plugin</artifactId>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-invoker-plugin</artifactId>
<executions>
<execution>
<id>package-unittests</id>
</execution>
<execution>
<id>package-integrationtests</id>
</execution>
<execution>
<id>package-largescaletests</id>
</execution>
<execution>
<id>package-knowledgebasetests</id>
</execution>
<execution>
<id>package-queuetests</id>
</execution>
</executions>
</plugin>
</plugins>
</build>
</project>