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>

    <!--
    This pom is the aggregator for all gatk poms
    See also:
      http://maven.apache.org/pom.html#Inheritance_v
      http://maven.apache.org/guides/introduction/introduction-to-the-pom.html#Project_Inheritance_vs_Project_Aggregation
      http://stackoverflow.com/questions/1992213/maven-parent-pom-vs-modules-pom
    -->

    <parent>
        <groupId>org.broadinstitute.gatk</groupId>
        <artifactId>gatk-root</artifactId>
        <version>3.8-1</version>
        <relativePath>public/gatk-root</relativePath>
    </parent>

    <artifactId>gatk-aggregator</artifactId>
    <packaging>pom</packaging>
    <name>GATK Aggregator</name>

    <modules>
        <module>public</module>
        <!-- private & protected optionally enabled as profiles -->
    </modules>

    <properties>
        <gatk.basedir>${project.basedir}</gatk.basedir>
        <resource.bundle.path>GATKText.properties</resource.bundle.path>
        <resource.bundle.skip>false</resource.bundle.skip>
        <!-- TODO: Need a better a way to say "don't include hidden" by default -->
        <gatkdocs.include.hidden>-build-timestamp "${maven.build.timestamp}"</gatkdocs.include.hidden>
        <gatkdocs.extension>html</gatkdocs.extension>
        <gatk.shell.directory>${gatk.basedir}/public/src/main/scripts/shell</gatk.shell.directory>
        <gatk.assembly.directory>${gatk.basedir}/public/src/main/assembly</gatk.assembly.directory>

        <!--
        Phases of the build that may be disabled to speed up compilation.
        -->
        <gatk.jar.phase>package</gatk.jar.phase>
        <gatk.unpack.phase>prepare-package</gatk.unpack.phase>
        <gatk.shade.phase>package</gatk.shade.phase>
        <gatk.generate-resources.phase>generate-resources</gatk.generate-resources.phase>
        <gatk.process-resources.phase>process-resources</gatk.process-resources.phase>
        <gatk.process-test-resources.phase>process-test-resources</gatk.process-test-resources.phase>

        <!--
        Package tests ensure the consistency of the packaged / shaded jars.
        It runs the tests where the monolithic jar is the only dependency on the classpath.
        -->
        <gatk.packagecommittests.skipped>true</gatk.packagecommittests.skipped>
        <gatk.packageunittests.skipped>${gatk.packagecommittests.skipped}</gatk.packageunittests.skipped>
        <gatk.packageintegrationtests.skipped>${gatk.packagecommittests.skipped}</gatk.packageintegrationtests.skipped>
        <gatk.packagequeuetests.skipped>${gatk.packagecommittests.skipped}</gatk.packagequeuetests.skipped>
        <gatk.packagelargescaletests.skipped>true</gatk.packagelargescaletests.skipped>
        <gatk.packageknowledgebasetests.skipped>true</gatk.packageknowledgebasetests.skipped>

        <!--
        Serial tests use the test jars to run tests, such that all tests are run from a single TestNG invocation.
        This is different that the invoker, that runs the test classes from the filesystem, but pointing at the packaged JAR files.
        TODO: Currently, all tests run within each package, since packages already collect dependencies for shading an uber jar.
        TODO: Should there be another level up of tests, possibly running "all tests" via this aggregator level?
        TODO: If that require the aggregator to be dependent on the child dependencies, perhaps a better approach might be another monolithic test project.
        -->
        <gatk.serialcommittests.skipped>true</gatk.serialcommittests.skipped>
        <gatk.serialunittests.skipped>${gatk.serialcommittests.skipped}</gatk.serialunittests.skipped>
        <gatk.serialintegrationtests.skipped>${gatk.serialcommittests.skipped}</gatk.serialintegrationtests.skipped>
        <gatk.serialqueuetests.skipped>${gatk.serialcommittests.skipped}</gatk.serialqueuetests.skipped>
        <gatk.seriallargescaletests.skipped>true</gatk.seriallargescaletests.skipped>
        <gatk.serialknowledgebasetests.skipped>true</gatk.serialknowledgebasetests.skipped>

        <!-- Full path to write the executable MANIFEST.MF only jars, 10 seconds to create at 4KB each, and the accompanying lib directory -->
        <gatk.executable.directory>${gatk.basedir}/target/executable</gatk.executable.directory>
        <!-- Full path to write (symlinks to) the full shaded package jars, 1+ minute to create at 12MB+ each -->
        <gatk.package.directory>${gatk.basedir}/target/package</gatk.package.directory>
        <!--
        Full path to write symlink to either an executable MANIFEST.MF only jar - OR - a fully shaded package jar.
        NOTE: MANIFEST.MF only jars MUST be accompanied by the lib folder, or they will not run.
        -->
        <gatk.shortcut.directory>${gatk.basedir}/target</gatk.shortcut.directory>
    </properties>

    <dependencies>
        <dependency>
            <groupId>com.sun</groupId>
            <artifactId>tools</artifactId>
        </dependency>
    </dependencies>

    <build>
        <!-- Plugin configuration -->
        <pluginManagement>
            <plugins>
                <plugin>
                    <groupId>org.apache.maven.plugins</groupId>
                    <artifactId>maven-clean-plugin</artifactId>
                    <configuration>
                        <filesets>
                            <!--
                            TODO: Once GATKDoclet stops hard coding paths, we remove this and leave
                            TODO: it to the standard maven conventions to clean up for us
                            -->
                            <fileset>
                                <directory>gatkdocs</directory>
                            </fileset>
                            <fileset>
                                <directory>${basedir}</directory>
                                <includes>
                                    <include>javadoc.sh</include>
                                    <include>options</include>
                                    <include>packages</include>
                                </includes>
                            </fileset>
                            <!--
                            Shade dumps this temp file in basedir, with no good way to reconfigure.
                            https://jira.codehaus.org/browse/MSHADE-145
                            -->
                            <fileset>
                                <directory>${basedir}</directory>
                                <includes>
                                    <include>dependency-reduced-pom.xml</include>
                                </includes>
                            </fileset>
                        </filesets>
                    </configuration>
                </plugin>
                <plugin>
                    <groupId>org.apache.maven.plugins</groupId>
                    <artifactId>maven-dependency-plugin</artifactId>
                    <executions>
                        <execution>
                            <id>unpack-direct-dependencies</id>
                            <goals>
                                <goal>unpack-dependencies</goal>
                            </goals>
                            <phase>none</phase>
                            <!--
                            NOTE: Shade include filters do NOT include transient dependencies, only the class directly listed.

                            Thus to fully include all the classes in packages, we must:
                                1) List the artifacts we want shaded as direct dependencies
                                2) Run the unpack direct dependencies into the classes directory
                                3) Shade the classes directory as we normally would.
                            -->
                            <configuration>
                                <excludeTransitive>true</excludeTransitive>
                                <outputDirectory>${project.build.outputDirectory}</outputDirectory>
                                <includeTypes>jar</includeTypes>
                                <includeScope>runtime</includeScope>
                                <!-- Don't unjar the resource bundle, so that shade's AppendingTransformer can merge -->
                                <excludes>${resource.bundle.path}</excludes>
                            </configuration>
                        </execution>
                        <execution>
                            <id>executable-jar-lib</id>
                            <goals>
                                <goal>copy-dependencies</goal>
                            </goals>
                            <phase>none</phase>
                            <configuration>
                                <outputDirectory>${gatk.executable.directory}/lib</outputDirectory>
                                <includeScope>runtime</includeScope>
                                <useBaseVersion>false</useBaseVersion>
                            </configuration>
                        </execution>
                    </executions>
                </plugin>
                <plugin>
                    <groupId>org.apache.maven.plugins</groupId>
                    <artifactId>maven-resources-plugin</artifactId>
                    <executions>
                        <execution>
                            <id>default-resources</id>
                            <goals>
                                <goal>resources</goal>
                            </goals>
                            <phase>${gatk.process-resources.phase}</phase>
                        </execution>
                        <execution>
                            <id>default-testResources</id>
                            <goals>
                                <goal>testResources</goal>
                            </goals>
                            <phase>${gatk.process-test-resources.phase}</phase>
                        </execution>
                    </executions>
                </plugin>
                <plugin>
                    <groupId>org.apache.maven.plugins</groupId>
                    <artifactId>maven-javadoc-plugin</artifactId>
                    <executions>
                        <execution>
                            <id>extract-resource-bundle</id>
                            <goals>
                                <goal>javadoc</goal>
                            </goals>
                            <phase>none</phase>
                            <configuration>
                                <!-- Allow skipping for "fasttest" -->
                                <skip>${resource.bundle.skip}</skip>
                                <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 ${build.version} -out "${project.build.outputDirectory}/${resource.bundle.path}"</additionalparam>
                            </configuration>
                        </execution>
                    </executions>
                </plugin>

                <plugin>
                    <groupId>org.apache.maven.plugins</groupId>
                    <artifactId>maven-compiler-plugin</artifactId>
                    <configuration>
                        <proc>none</proc>
                        <annotationProcessors>
                            <annotationProcessor>com.google.java.contract.core.apt.AnnotationProcessor</annotationProcessor>
                        </annotationProcessors>
                    </configuration>
                    <executions>
                        <execution>
                            <id>default-compile</id>
                            <phase>none</phase>
                        </execution>
                        <execution>
                            <id>default-testCompile</id>
                            <phase>none</phase>
                        </execution>
                        <!--
                        Explicit package-info creation to match existing ant output.
                        -->
                        <execution>
                            <id>compile-package-info</id>
                            <goals>
                                <goal>compile</goal>
                            </goals>
                            <phase>compile</phase>
                            <configuration>
                                <compilerArgs>
                                    <arg>-Xpkginfo:always</arg>
                                </compilerArgs>
                                <includes>
                                    <include>**/package-info.java</include>
                                </includes>
                            </configuration>
                        </execution>
                        <!--
                        TODO: Currently disabled in build.xml. Here as well.
                        <execution>
                            <id>compile-annotations</id>
                            <phase>compile</phase>
                            <goals>
                                <goal>compile</goal>
                            </goals>
                            <configuration>
                                <proc>only</proc>
                            </configuration>
                        </execution>
                        -->
                        <execution>
                            <id>compile-java</id>
                            <goals>
                                <goal>compile</goal>
                            </goals>
                            <phase>compile</phase>
                            <configuration>
                                <!--
                                Package info is supposed to be in source:
                                    http://maven.apache.org/plugins/maven-javadoc-plugin/examples/javadoc-resources.html
                                But maven-compile-plugin doesn't auto exclude these:
                                    https://jira.codehaus.org/browse/MCOMPILER-205?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=326505#comment-326505
                                So, explicitly exclude them
                                -->
                                <excludes>
                                    <exclude>**/package-info.java</exclude>
                                </excludes>
                            </configuration>
                        </execution>
                        <!--
                        TODO: Currently disabled in build.xml. Here as well.
                        <execution>
                            <id>testCompile-annotations</id>
                            <phase>test-compile</phase>
                            <goals>
                                <goal>testCompile</goal>
                            </goals>
                            <configuration>
                                <proc>only</proc>
                            </configuration>
                        </execution>
                        -->
                        <execution>
                            <id>testCompile-java</id>
                            <goals>
                                <goal>testCompile</goal>
                            </goals>
                            <phase>test-compile</phase>
                        </execution>
                    </executions>
                </plugin>

                <plugin>
                    <groupId>org.scala-tools</groupId>
                    <artifactId>maven-scala-plugin</artifactId>
                    <executions>
                        <execution>
                            <goals>
                                <goal>compile</goal>
                                <goal>testCompile</goal>
                            </goals>
                        </execution>
                    </executions>
                </plugin>

                <plugin>
                    <groupId>org.apache.maven.plugins</groupId>
                    <artifactId>maven-jar-plugin</artifactId>
                    <executions>
                        <execution>
                            <id>executable-jar</id>
                            <goals>
                                <goal>jar</goal>
                            </goals>
                            <phase>none</phase>
                            <configuration>
                                <classesDirectory>${project.build.outputDirectory}/ignored_by_executable_jar</classesDirectory>
                                <outputDirectory>${gatk.executable.directory}</outputDirectory>
                                <finalName>${gatk.binary-dist.name}</finalName>
                                <archive>
                                    <manifest>
                                        <mainClass>${app.main.class}</mainClass>
                                        <addClasspath>true</addClasspath>
                                        <classpathPrefix>lib/</classpathPrefix>
                                    </manifest>
                                </archive>
                            </configuration>
                        </execution>
                        <execution>
                            <id>default-jar</id>
                            <phase>${gatk.jar.phase}</phase>
                        </execution>
                        <!--
                        Maven keeps executing default-jar first, even if it's listed AFTER the executable-jar.
                        So while packaging: run executable-jar, disable default-jar, then run unshaded-default-jar.
                        -->
                        <execution>
                            <id>unshaded-default-jar</id>
                            <goals>
                                <goal>jar</goal>
                            </goals>
                            <phase>none</phase>
                        </execution>
                        <execution>
                            <id>test-jar</id>
                            <goals>
                                <goal>test-jar</goal>
                            </goals>
                            <phase>${gatk.jar.phase}</phase>
                            <configuration>
                                <skipIfEmpty>true</skipIfEmpty>
                            </configuration>
                        </execution>
                    </executions>
                </plugin>

                <plugin>
                    <groupId>org.apache.maven.plugins</groupId>
                    <artifactId>maven-shade-plugin</artifactId>
                    <executions>
                        <execution>
                            <id>package-jar</id>
                            <goals>
                                <goal>shade</goal>
                            </goals>
                            <phase>none</phase>
                            <configuration>
                                <minimizeJar>true</minimizeJar>
                                <createDependencyReducedPom>false</createDependencyReducedPom>
                                <artifactSet>
                                    <excludes>
                                        <exclude>org.broadinstitute.gatk:gsalib:tar.gz:*</exclude>
                                        <exclude>org.broadinstitute.gatk:*:tar.bz2:example-resources</exclude>
                                    </excludes>
                                </artifactSet>
                                <filters>
                                    <!--
                                    NOTE: Removing cofoja's annotation service to allow "javac -cp GenomeAnalysisTK.jar ..." without
                                    needing an additional -proc:none argument. Using *:* to catch shaded GATK in Queue package.
                                    -->
                                    <filter>
                                        <artifact>*:*</artifact>
                                        <excludes>
                                            <exclude>META-INF/services/javax.annotation.processing.Processor</exclude>
                                        </excludes>
                                    </filter>
                                </filters>
                                <transformers>
                                    <transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
                                        <manifestEntries>
                                            <Main-Class>${app.main.class}</Main-Class>
                                        </manifestEntries>
                                    </transformer>
                                    <transformer implementation="org.apache.maven.plugins.shade.resource.AppendingTransformer">
                                        <resource>${resource.bundle.path}</resource>
                                    </transformer>
                                </transformers>
                            </configuration>
                        </execution>
                    </executions>
                </plugin>

                <plugin>
                    <groupId>org.apache.maven.plugins</groupId>
                    <artifactId>maven-assembly-plugin</artifactId>
                    <executions>
                        <execution>
                            <id>example-resources</id>
                            <goals>
                                <goal>single</goal>
                            </goals>
                            <phase>none</phase>
                            <configuration>
                                <descriptors>
                                    <descriptor>src/main/assembly/example-resources.xml</descriptor>
                                </descriptors>
                            </configuration>
                        </execution>
                        <execution>
                            <id>binary-dist</id>
                            <goals>
                                <goal>single</goal>
                            </goals>
                            <phase>none</phase>
                            <configuration>
                                <descriptors>
                                    <descriptor>${gatk.assembly.directory}/binary-dist.xml</descriptor>
                                </descriptors>
                            </configuration>
                        </execution>
                    </executions>
                </plugin>

                <plugin>
                    <groupId>com.pyx4j</groupId>
                    <artifactId>maven-junction-plugin</artifactId>
                    <executions>
                        <!--
                        HACK: Adding the source directory via build-helper-maven-plugin doesn't work with IntelliJ.
                        Add compatibility link from public's extensions source code to target/generated-sources.
                        see: http://wiki.jetbrains.net/intellij/Maven_FAQ
                        -->
                        <execution>
                            <id>link-extensions-sources</id>
                            <goals>
                                <goal>link</goal>
                            </goals>
                            <phase>none</phase>
                            <configuration>
                                <links>
                                    <link>
                                        <dst>${project.build.directory}/generated-sources/gatk-queue-extensions-public-src-main-scala</dst>
                                        <src>${gatk.basedir}/public/gatk-queue-extensions-public/src/main/scala</src>
                                    </link>
                                </links>
                            </configuration>
                        </execution>
                        <execution>
                            <id>link-executable-jar</id>
                            <goals>
                                <goal>link</goal>
                            </goals>
                            <phase>none</phase>
                            <configuration>
                                <links>
                                    <link>
                                        <dst>${gatk.shortcut.directory}/${gatk.binary-dist.name}.${project.packaging}</dst>
                                        <src>${gatk.executable.directory}/${gatk.binary-dist.name}.${project.packaging}</src>
                                    </link>
                                </links>
                            </configuration>
                        </execution>
                        <execution>
                            <id>link-package-jar</id>
                            <goals>
                                <goal>link</goal>
                            </goals>
                            <phase>none</phase>
                            <configuration>
                                <links>
                                    <link>
                                        <dst>${gatk.package.directory}/${gatk.binary-dist.name}.${project.packaging}</dst>
                                        <src>${project.build.directory}/${project.build.finalName}.${project.packaging}</src>
                                    </link>
                                    <link>
                                        <dst>${gatk.shortcut.directory}/${gatk.binary-dist.name}.${project.packaging}</dst>
                                        <src>${project.build.directory}/${project.build.finalName}.${project.packaging}</src>
                                    </link>
                                </links>
                            </configuration>
                        </execution>
                        <execution>
                            <id>link-git-release</id>
                            <goals>
                                <goal>link</goal>
                            </goals>
                            <phase>none</phase>
                            <configuration>
                                <links>
                                    <link>
                                        <dst>${project.build.directory}/${gatk.binary-dist.name}-${build.version}.tar.bz2</dst>
                                        <src>${project.build.directory}/${project.build.finalName}-binary-dist.tar.bz2</src>
                                    </link>
                                </links>
                            </configuration>
                        </execution>
                    </executions>
                </plugin>
                <plugin>
                    <groupId>org.apache.maven.plugins</groupId>
                    <artifactId>maven-invoker-plugin</artifactId>
                    <configuration>
                        <skipInvocation>true</skipInvocation>
                        <debug>false</debug>
                        <pom>${gatk.basedir}/public/package-tests/pom.xml</pom>
                        <noLog>true</noLog>
                        <streamLogs>true</streamLogs>
                        <localRepositoryPath>${gatk.basedir}/${maven.repo.local}</localRepositoryPath>
                        <properties>
                            <test>${test}</test>
                            <it.test>${it.test}</it.test>
                            <skip>false</skip>
                            <maven.test.skip>false</maven.test.skip>
                            <gatk.packagetests.artifactId>${gatk.packagetests.artifactId}</gatk.packagetests.artifactId>
                            <gatk.packagetests.testClasses>${project.build.testOutputDirectory}</gatk.packagetests.testClasses>
                            <gatk.packagetests.basedir>${project.basedir}</gatk.packagetests.basedir>
                            <gatk.queuetests.run>${gatk.queuetests.run}</gatk.queuetests.run>
                            <maven.surefire.debug>${maven.surefire.debug}</maven.surefire.debug>
                            <maven.failsafe.debug>${maven.failsafe.debug}</maven.failsafe.debug>
                        </properties>
                        <!--
                        To allow using separated integration-test and verify, each execution must use a separate reportsDirectory.

                        Otherwise, when an empty "pipeline test" later runs on an IntegrationTest class,
                        it overwrites the results of the previous invocation always with a zero exit status.

                        Mixing in the test name into the reportsDirectory also avoids collisions, when different maven jobs run tests in parallel.

                        Similarly generating unique failsafe summary reports to avoid collisions.
                        -->
                    </configuration>
                    <executions>
                        <execution>
                            <id>package-unittests</id>
                            <goals>
                                <goal>run</goal>
                            </goals>
                            <configuration>
                                <goals>
                                    <goal>test</goal>
                                </goals>
                                <reportsDirectory>${project.build.directory}/invoker-reports/unit/${test}</reportsDirectory>
                                <skipInvocation>${gatk.packageunittests.skipped}</skipInvocation>
                                <properties>
                                    <unittests.profile.enabled>true</unittests.profile.enabled>
                                    <gatk.packageunittests.skipped>${gatk.packageunittests.skipped}</gatk.packageunittests.skipped>
                                </properties>
                            </configuration>
                        </execution>
                        <execution>
                            <id>package-integrationtests</id>
                            <goals>
                                <goal>integration-test</goal>
                                <goal>verify</goal>
                            </goals>
                            <configuration>
                                <goals>
                                    <goal>verify</goal>
                                </goals>
                                <reportsDirectory>${project.build.directory}/invoker-reports/integration/${it.test}</reportsDirectory>
                                <skipInvocation>${gatk.packageintegrationtests.skipped}</skipInvocation>
                                <properties>
                                    <integrationtests.profile.enabled>true</integrationtests.profile.enabled>
                                    <gatk.packageintegrationtests.skipped>${gatk.packageintegrationtests.skipped}</gatk.packageintegrationtests.skipped>
                                </properties>
                            </configuration>
                        </execution>
                        <execution>
                            <id>package-queuetests</id>
                            <goals>
                                <goal>integration-test</goal>
                                <goal>verify</goal>
                            </goals>
                            <configuration>
                                <goals>
                                    <goal>verify</goal>
                                </goals>
                                <reportsDirectory>${project.build.directory}/invoker-reports/queuetest/${it.test}</reportsDirectory>
                                <skipInvocation>${gatk.packagequeuetests.skipped}</skipInvocation>
                                <properties>
                                    <integrationtests.profile.enabled>true</integrationtests.profile.enabled>
                                    <gatk.packagequeuetests.skipped>${gatk.packagequeuetests.skipped}</gatk.packagequeuetests.skipped>
                                </properties>
                            </configuration>
                        </execution>
                        <execution>
                            <id>package-largescaletests</id>
                            <goals>
                                <goal>integration-test</goal>
                                <goal>verify</goal>
                            </goals>
                            <configuration>
                                <goals>
                                    <goal>verify</goal>
                                </goals>
                                <reportsDirectory>${project.build.directory}/invoker-reports/largescale/${it.test}</reportsDirectory>
                                <skipInvocation>${gatk.packagelargescaletests.skipped}</skipInvocation>
                                <properties>
                                    <integrationtests.profile.enabled>true</integrationtests.profile.enabled>
                                    <gatk.packagelargescaletests.skipped>${gatk.packagelargescaletests.skipped}</gatk.packagelargescaletests.skipped>
                                </properties>
                            </configuration>
                        </execution>
                        <execution>
                            <id>package-knowledgebasetests</id>
                            <goals>
                                <goal>integration-test</goal>
                                <goal>verify</goal>
                            </goals>
                            <configuration>
                                <goals>
                                    <goal>verify</goal>
                                </goals>
                                <reportsDirectory>${project.build.directory}/invoker-reports/knowledgebase/${it.test}</reportsDirectory>
                                <skipInvocation>${gatk.packageknowledgebasetests.skipped}</skipInvocation>
                                <properties>
                                    <integrationtests.profile.enabled>true</integrationtests.profile.enabled>
                                    <gatk.packageknowledgebasetests.skipped>${gatk.packageknowledgebasetests.skipped}</gatk.packageknowledgebasetests.skipped>
                                </properties>
                            </configuration>
                        </execution>
                    </executions>
                </plugin>
                <plugin>
                    <groupId>org.apache.maven.plugins</groupId>
                    <artifactId>maven-install-plugin</artifactId>
                    <version>2.5</version>
                    <executions>
                        <execution>
                            <id>install-package</id>
                            <goals>
                                <goal>install-file</goal>
                            </goals>
                            <phase>none</phase>
                            <configuration>
                                <generatePom>true</generatePom>
                                <groupId>${project.groupId}</groupId>
                                <artifactId>${project.artifactId}</artifactId>
                                <version>${project.version}</version>
                                <packaging>${project.packaging}</packaging>
                                <file>${project.build.directory}/${project.build.finalName}.${project.packaging}</file>
                            </configuration>
                        </execution>
                    </executions>
                </plugin>
            </plugins>
        </pluginManagement>

        <!-- Invoke plugins that always run -->
        <plugins>
            <plugin>
                <groupId>org.codehaus.mojo</groupId>
                <artifactId>exec-maven-plugin</artifactId>
                <executions>
                    <execution>
                        <!--
                        TODO: Separate maven modules into separate git repos?
                        Until then, keep devs from accidentally mixing utils/engine/tools.
                        -->
                        <id>check-utils-engine-tools</id>
                        <goals>
                            <goal>exec</goal>
                        </goals>
                        <phase>process-sources</phase>
                        <inherited>false</inherited>
                        <configuration>
                            <executable>${gatk.shell.directory}/check_utils_engine_tools.sh</executable>
                        </configuration>
                    </execution>
                    <execution>
                        <!--
                        TODO: Remove after 3.3+ release.
                        Until then, will clean out symbolic links from users who download public/protected.
                        Perhaps leave the script even longer.
                        -->
                        <id>delete-mavens-links</id>
                        <goals>
                            <goal>exec</goal>
                        </goals>
                        <phase>process-test-resources</phase>
                        <inherited>false</inherited>
                        <configuration>
                            <executable>${gatk.shell.directory}/delete_maven_links.sh</executable>
                        </configuration>
                    </execution>
                </executions>
            </plugin>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-failsafe-plugin</artifactId>
            </plugin>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-clean-plugin</artifactId>
            </plugin>
            <plugin>
                <groupId>com.google.code.sortpom</groupId>
                <artifactId>maven-sortpom-plugin</artifactId>
                <executions>
                    <execution>
                        <id>package-tests</id>
                        <goals>
                            <goal>sort</goal>
                        </goals>
                        <phase>verify</phase>
                        <inherited>false</inherited>
                        <configuration>
                            <pomFile>public/package-tests/pom.xml</pomFile>
                        </configuration>
                    </execution>
                </executions>
            </plugin>
        </plugins>
    </build>

    <reporting>
        <plugins>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-javadoc-plugin</artifactId>
                <version>2.9.1</version>
                <reportSets>
                    <!-- By not specifying an id, shut off all default javadocs from mvn site -->
                    <reportSet>
                        <reports />
                    </reportSet>
                    <reportSet>
                        <id>generate-gatk-docs</id>
                        <reports>
                            <report>aggregate</report>
                        </reports>
                        <!-- Only generate the GATK Docs across the parent aggregation, not the children too. -->
                        <inherited>false</inherited>
                        <configuration>
                            <doclet>org.broadinstitute.gatk.tools.walkers.help.WalkerDoclet</doclet>
                            <docletArtifact>
                                <groupId>${project.groupId}</groupId>
                                <artifactId>gatk-package-distribution</artifactId>
                                <version>${project.version}</version>
                            </docletArtifact>
                            <useStandardDocletOptions>false</useStandardDocletOptions>
                            <quiet>true</quiet>
                            <show>private</show>
                            <additionalparam>-build-timestamp "${maven.build.timestamp}" -absolute-version ${build.version} ${gatkdocs.include.hidden} -settings-dir ${gatk.basedir}/settings/helpTemplates -destination-dir ${project.build.directory}/gatkdocs -output-file-extension ${gatkdocs.extension}</additionalparam>
                        </configuration>
                    </reportSet>
                </reportSets>
            </plugin>
        </plugins>
    </reporting>

    <profiles>
        <!-- Optionally include protected -->
        <profile>
            <id>protected</id>
            <activation>
                <file>
                    <exists>${basedir}/protected/pom.xml</exists>
                </file>
            </activation>
            <modules>
                <module>protected</module>
            </modules>
        </profile>

        <!-- Optionally include private -->
        <profile>
            <id>private</id>
            <activation>
                <file>
                    <exists>${basedir}/private/pom.xml</exists>
                </file>
            </activation>
            <modules>
                <module>private</module>
            </modules>
        </profile>

        <!-- 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>
                <maven.javadoc.skip>true</maven.javadoc.skip>
                <gatk.generate-gatk-extensions.skipped>true</gatk.generate-gatk-extensions.skipped>
                <gatk.jar.phase>none</gatk.jar.phase>
                <gatk.unpack.phase>none</gatk.unpack.phase>
                <gatk.shade.phase>none</gatk.shade.phase>
                <gatk.generate-resources.phase>none</gatk.generate-resources.phase>
                <gatk.process-resources.phase>none</gatk.process-resources.phase>
                <gatk.process-test-resources.phase>none</gatk.process-test-resources.phase>
            </properties>
        </profile>
    </profiles>

</project>