gatk-3.8/public/gatk-package/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.sting</groupId>
        <artifactId>sting-aggregator</artifactId>
        <version>2.8-SNAPSHOT</version>
        <relativePath>../..</relativePath>
    </parent>

    <artifactId>gatk-package</artifactId>
    <packaging>jar</packaging>
    <name>GATK Package</name>

    <properties>
        <sting.basedir>${project.basedir}/../..</sting.basedir>
        <sting.unpack.phase>prepare-package</sting.unpack.phase>
        <sting.shade.phase>package</sting.shade.phase>
        <app.main.class>org.broadinstitute.sting.gatk.CommandLineGATK</app.main.class>
        <sting.binary-dist.name>GenomeAnalysisTK</sting.binary-dist.name>
    </properties>

    <dependencies>
        <!-- Package everything in org.broadinstitute.sting -->
        <dependency>
            <groupId>${project.groupId}</groupId>
            <artifactId>gatk-framework</artifactId>
            <version>${project.version}</version>
        </dependency>
        <!-- Tribble codecs -->
        <dependency>
            <groupId>org.broad</groupId>
            <artifactId>tribble</artifactId>
        </dependency>
        <!-- The variant package (VCF, BCF, and VariantContext) -->
        <dependency>
            <groupId>org.broadinstitute</groupId>
            <artifactId>variant</artifactId>
        </dependency>
        <!-- Workaround - depend on the logger impl required by JEXL -->
        <dependency>
            <groupId>commons-logging</groupId>
            <artifactId>commons-logging</artifactId>
        </dependency>
        <!-- Required for binary-dist assembly, excluded by shade -->
        <dependency>
            <groupId>${project.groupId}</groupId>
            <artifactId>gatk-framework</artifactId>
            <version>${project.version}</version>
            <classifier>example-resources</classifier>
            <type>tar.bz2</type>
        </dependency>
    </dependencies>

    <build>
        <plugins>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-dependency-plugin</artifactId>
                <executions>
                    <execution>
                        <id>unpack-direct-dependencies</id>
                        <phase>${sting.unpack.phase}</phase>
                    </execution>
                </executions>
            </plugin>

            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-shade-plugin</artifactId>
                <executions>
                    <execution>
                        <id>sting-executable</id>
                        <phase>${sting.shade.phase}</phase>
                    </execution>
                </executions>
            </plugin>

            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-assembly-plugin</artifactId>
                <executions>
                    <execution>
                        <id>binary-dist</id>
                        <phase>${sting.shade.phase}</phase>
                    </execution>
                </executions>
            </plugin>

            <plugin>
                <groupId>com.pyx4j</groupId>
                <artifactId>maven-junction-plugin</artifactId>
                <executions>
                    <execution>
                        <id>link-git-release</id>
                        <phase>${sting.shade.phase}</phase>
                    </execution>
                </executions>
            </plugin>

            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-install-plugin</artifactId>
                <executions>
                    <execution>
                        <id>default-install</id>
                        <phase>none</phase>
                    </execution>
                    <execution>
                        <id>install-package</id>
                        <phase>install</phase>
                    </execution>
                </executions>
            </plugin>

        </plugins>
    </build>

    <profiles>
        <profile>
            <id>protected</id>
            <activation>
                <file>
                    <exists>${basedir}/../../protected/gatk-protected/pom.xml</exists>
                </file>
            </activation>
            <dependencies>
                <dependency>
                    <groupId>${project.groupId}</groupId>
                    <artifactId>gatk-protected</artifactId>
                    <version>${project.version}</version>
                    <optional>true</optional>
                </dependency>
            </dependencies>
        </profile>
        <profile>
            <id>private</id>
            <activation>
                <file>
                    <exists>${basedir}/../../private/gatk-private/pom.xml</exists>
                </file>
            </activation>
            <dependencies>
                <dependency>
                    <groupId>${project.groupId}</groupId>
                    <artifactId>gatk-private</artifactId>
                    <version>${project.version}</version>
                    <optional>true</optional>
                </dependency>
            </dependencies>
        </profile>
    </profiles>

</project>