gatk-3.8/public/external-example/pom.xml

<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>

    <!-- Properties for your assembly -->
    <groupId>org.mycompany.app</groupId>
    <artifactId>external-example</artifactId>
    <packaging>jar</packaging>
    <version>1.0-SNAPSHOT</version>
    <name>External Example</name>

    <properties>
        <gatk.version>3.9-SNAPSHOT</gatk.version>
        <!--
        gatk.basedir property must point to your checkout of GATK/GATK until we can get all the
        dependencies out of the committed gatk repo and into central.
        The installed pom for gatk-root looks for this property.
        Alternatively, one can install all the gatk files into their local ~/.m2/repository repo.
        http://maven.apache.org/plugins/maven-install-plugin/examples/custom-pom-installation.html
        -->
        <gatk.basedir>../..</gatk.basedir>
        <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
        <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
        <maven.build.timestamp.format>yyyy/MM/dd HH:mm:ss</maven.build.timestamp.format>

        <!-- NOTE: Currently the testing infrastructure for walkers does not support running outside the Broad. -->
        <gatk.committests.skipped>true</gatk.committests.skipped>
        <gatk.unittests.skipped>${gatk.committests.skipped}</gatk.unittests.skipped>
        <gatk.integrationtests.skipped>${gatk.committests.skipped}</gatk.integrationtests.skipped>

        <!-- This flag is used by the package tests to disable re-shading -->
        <gatk.unpack.phase>prepare-package</gatk.unpack.phase>
        <gatk.shade.phase>package</gatk.shade.phase>
    </properties>

    <repositories>
        <repository>
            <id>gatk.public.repo.local</id>
            <name>GATK Public Local Repository</name>
            <url>file:${gatk.basedir}/public/repo</url>
        </repository>
    </repositories>

    <dependencies>
        <dependency>
            <groupId>org.broadinstitute.gatk</groupId>
            <artifactId>gatk-tools-public</artifactId>
            <version>${gatk.version}</version>
        </dependency>

        <dependency>
            <groupId>org.broadinstitute.gatk</groupId>
            <artifactId>gatk-utils</artifactId>
            <version>${gatk.version}</version>
            <type>test-jar</type>
            <scope>test</scope>
        </dependency>

        <dependency>
            <groupId>org.broadinstitute.gatk</groupId>
            <artifactId>gatk-engine</artifactId>
            <version>${gatk.version}</version>
            <type>test-jar</type>
            <scope>test</scope>
        </dependency>

        <dependency>
            <groupId>org.testng</groupId>
            <artifactId>testng</artifactId>
            <version>6.8</version>
            <scope>test</scope>
        </dependency>
    </dependencies>

    <build>
        <plugins>

            <!-- Copy test resources to your classes directory -->
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-dependency-plugin</artifactId>
                <version>2.8</version>
                <executions>
                    <execution>
                        <id>unpack</id>
                        <phase>${gatk.unpack.phase}</phase>
                        <goals>
                            <goal>unpack</goal>
                        </goals>
                        <configuration>
                            <artifactItems>
                                <artifactItem>
                                    <groupId>org.broadinstitute.gatk</groupId>
                                    <artifactId>gatk-utils</artifactId>
                                    <version>${gatk.version}</version>
                                    <classifier>example-resources</classifier>
                                    <type>tar.bz2</type>
                                    <outputDirectory>${project.build.outputDirectory}</outputDirectory>
                                </artifactItem>
                            </artifactItems>
                        </configuration>
                    </execution>
                </executions>
            </plugin>

            <!-- Generate help text -->
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-javadoc-plugin</artifactId>
                <version>2.9.1</version>
                <executions>
                    <execution>
                        <id>extract-resource-bundle</id>
                        <goals>
                            <goal>javadoc</goal>
                        </goals>
                        <phase>prepare-package</phase>
                        <configuration>
                            <doclet>org.broadinstitute.gatk.utils.help.ResourceBundleExtractorDoclet</doclet>
                            <!-- Required as doclet uses reflection to access classes for documentation, instead of source java-->
                            <docletPath>${project.build.outputDirectory}</docletPath>
                            <docletArtifact>
                                <groupId>${project.groupId}</groupId>
                                <artifactId>${project.artifactId}</artifactId>
                                <version>${project.version}</version>
                            </docletArtifact>
                            <maxmemory>2g</maxmemory>
                            <useStandardDocletOptions>false</useStandardDocletOptions>
                            <quiet>true</quiet>
                            <additionalparam>-build-timestamp "${maven.build.timestamp}" -absolute-version "${project.version}" -out ${project.build.outputDirectory}/GATKText.properties</additionalparam>
                        </configuration>
                    </execution>
                </executions>
            </plugin>

            <!-- Create packaged jar, containing only your walker and required classes -->
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-shade-plugin</artifactId>
                <version>2.4.3</version>
                <executions>
                    <execution>
                        <phase>${gatk.shade.phase}</phase>
                        <goals>
                            <goal>shade</goal>
                        </goals>
                        <configuration>
                            <minimizeJar>true</minimizeJar>
                            <createDependencyReducedPom>false</createDependencyReducedPom>
                            <!-- Explicitly include classes loaded via reflection from artifacts below -->
                            <filters>
                                <filter>
                                    <artifact>commons-logging:commons-logging</artifact>
                                    <includes>
                                        <include>**</include>
                                    </includes>
                                </filter>
                                <filter>
                                    <artifact>com.github.samtools:htsjdk</artifact>
                                    <includes>
                                        <include>**</include>
                                    </includes>
                                </filter>
                            </filters>
                            <!-- Stop shade from trying to unzip these indirect dependencies -->
                            <artifactSet>
                                <excludes>
                                    <exclude>org.broadinstitute.gatk:gsalib:tar.gz:*</exclude>
                                    <exclude>org.broadinstitute.gatk:*:tar.bz2:example-resources</exclude>
                                </excludes>
                            </artifactSet>
                            <transformers>
                                <!-- Set the main class to the GATK -->
                                <transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
                                    <mainClass>org.broadinstitute.gatk.engine.CommandLineGATK</mainClass>
                                </transformer>
                                <!-- Include and append to the existing gatk help text in GATKText.properties -->
                                <transformer implementation="org.apache.maven.plugins.shade.resource.AppendingTransformer">
                                    <resource>GATKText.properties</resource>
                                </transformer>
                            </transformers>
                        </configuration>
                    </execution>
                </executions>
            </plugin>

            <!-- surefire runs fast, small (aka unit) tests -->
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-surefire-plugin</artifactId>
                <version>2.16</version>
                <configuration>
                    <!-- See explicit executions below -->
                    <skip>true</skip>
                    <failIfNoTests>false</failIfNoTests>
                    <!-- Pass various system properties -->
                    <systemPropertyVariables>
                        <gatkdir>${gatk.basedir}</gatkdir>
                        <java.io.tmpdir>${java.io.tmpdir}</java.io.tmpdir>
                    </systemPropertyVariables>
                </configuration>
                <executions>
                    <!-- Disable maven default execution -->
                    <execution>
                        <id>default-test</id>
                        <phase>none</phase>
                    </execution>
                    <execution>
                        <id>unit-tests</id>
                        <goals>
                            <goal>test</goal>
                        </goals>
                        <configuration>
                            <skip>${gatk.unittests.skipped}</skip>
                            <includes>
                                <include>**/*UnitTest.class</include>
                            </includes>
                            <systemPropertyVariables>
                                <testType>unit</testType>
                            </systemPropertyVariables>
                        </configuration>
                    </execution>
                </executions>
            </plugin>

            <!-- failsafe runs all other tests that may take longer, and may require pre/post test setup and teardown -->
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-failsafe-plugin</artifactId>
                <version>2.16</version>
                <configuration>
                    <!-- See explicit executions below -->
                    <skip>true</skip>
                    <failIfNoTests>false</failIfNoTests>
                    <!-- Pass various system properties -->
                    <systemPropertyVariables>
                        <gatkdir>${gatk.basedir}</gatkdir>
                        <java.io.tmpdir>${java.io.tmpdir}</java.io.tmpdir>
                    </systemPropertyVariables>
                </configuration>
                <executions>
                    <execution>
                        <id>integration-tests</id>
                        <goals>
                            <goal>integration-test</goal>
                            <goal>verify</goal>
                        </goals>
                        <!-- run integration tests -->
                        <configuration>
                            <skip>${gatk.integrationtests.skipped}</skip>
                            <includes>
                                <include>**/*IntegrationTest.class</include>
                            </includes>
                            <systemPropertyVariables>
                                <testType>integrationtest</testType>
                            </systemPropertyVariables>
                        </configuration>
                    </execution>
                </executions>
            </plugin>
        </plugins>
    </build>

    <reporting>
        <excludeDefaults>true</excludeDefaults>
    </reporting>

    <!-- These profiles are used by the GATK build in a multi-module setting. You do NOT need these profiles. -->
    <profiles>
        <!-- Optionally do not shade/package jars -->
        <!--
        NOTE: Profile id "fast" comes from comments in PR #771.
        The name is meant to be memorable, but is highly non-specific. Users are forewarned that
        behavior of this profile, or the identifier itself, may be heavily modified in the future.
        Hardcode usage in non-VCS controlled scripts at your own risk.
        -->
        <profile>
            <id>fast</id>
            <activation>
                <property>
                    <name>disable.shadepackage</name>
                </property>
            </activation>
            <properties>
                <gatk.unpack.phase>none</gatk.unpack.phase>
                <gatk.shade.phase>none</gatk.shade.phase>
            </properties>
        </profile>
        <!-- Collection of properties for use during package testing -->
        <profile>
            <id>packagetests-enabled</id>
            <activation>
                <property>
                    <name>gatk.packagetests.enabled</name>
                    <value>true</value>
                </property>
            </activation>
            <properties>
                <gatk.jar.phase>none</gatk.jar.phase>
                <gatk.unpack.phase>none</gatk.unpack.phase>
                <gatk.shade.phase>none</gatk.shade.phase>
            </properties>
        </profile>
    </profiles>

</project>