gatk-3.8/protected/gatk-queue-extensions-distribution/pom.xml

<?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>3.3-SNAPSHOT</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>
        <!--
        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>${project.groupId}</groupId>
            <artifactId>gatk-tools-public</artifactId>
            <version>${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>com.pyx4j</groupId>
                <artifactId>maven-junction-plugin</artifactId>
                <executions>
                    <execution>
                        <id>link-public-qscript</id>
                        <phase>process-test-resources</phase>
                    </execution>
                    <execution>
                        <id>unlink-public-qscript</id>
                        <phase>clean</phase>
                    </execution>
                    <execution>
                        <id>link-extensions-sources</id>
                        <phase>generate-sources</phase>
                    </execution>
                </executions>
            </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>

    <profiles>
        <profile>
            <id>private-testdata</id>
            <activation>
                <file>
                    <exists>${basedir}/../../private/pom.xml</exists>
                </file>
            </activation>
            <build>
                <plugins>
                    <!-- TODO: All tests require access to private. For now. -->
                    <plugin>
                        <groupId>com.pyx4j</groupId>
                        <artifactId>maven-junction-plugin</artifactId>
                        <executions>
                            <execution>
                                <id>link-private-testdata</id>
                                <phase>process-test-resources</phase>
                            </execution>
                            <execution>
                                <id>unlink-private-testdata</id>
                                <phase>clean</phase>
                            </execution>
                            <execution>
                                <id>link-private-qscript</id>
                                <phase>process-test-resources</phase>
                            </execution>
                            <execution>
                                <id>unlink-private-qscript</id>
                                <phase>clean</phase>
                            </execution>
                        </executions>
                    </plugin>
                </plugins>
            </build>
        </profile>
    </profiles>

</project>