gatk-3.8/public/gatk-utils/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>3.4-SNAPSHOT</version>
        <relativePath>../..</relativePath>
    </parent>

    <artifactId>gatk-utils</artifactId>
    <packaging>jar</packaging>
    <name>GATK Utils</name>

    <properties>
        <gatk.basedir>${project.basedir}/../..</gatk.basedir>
        <gatk.packagetests.artifactId>gatk-package-distribution</gatk.packagetests.artifactId>
        <gsalib.packagedir>org/broadinstitute/gatk/utils/R</gsalib.packagedir>
        <gsalib.filename>gsalib.tar.gz</gsalib.filename>
    </properties>

    <dependencies>
        <dependency>
            <groupId>samtools</groupId>
            <artifactId>htsjdk</artifactId>
        </dependency>
        <dependency>
            <groupId>picard</groupId>
            <artifactId>picard</artifactId>
        </dependency>
        <dependency>
            <groupId>log4j</groupId>
            <artifactId>log4j</artifactId>
        </dependency>
        <dependency>
            <groupId>colt</groupId>
            <artifactId>colt</artifactId>
        </dependency>
        <dependency>
            <groupId>it.unimi.dsi</groupId>
            <artifactId>fastutil</artifactId>
        </dependency>
        <dependency>
            <groupId>org.simpleframework</groupId>
            <artifactId>simple-xml</artifactId>
        </dependency>
        <dependency>
            <groupId>org.reflections</groupId>
            <artifactId>reflections</artifactId>
        </dependency>
        <dependency>
            <groupId>org.slf4j</groupId>
            <artifactId>slf4j-log4j12</artifactId>
        </dependency>
        <dependency>
            <groupId>org.freemarker</groupId>
            <artifactId>freemarker</artifactId>
        </dependency>
        <dependency>
            <groupId>org.apache.commons</groupId>
            <artifactId>commons-jexl</artifactId>
        </dependency>
        <dependency>
            <groupId>commons-lang</groupId>
            <artifactId>commons-lang</artifactId>
        </dependency>
        <dependency>
            <groupId>commons-io</groupId>
            <artifactId>commons-io</artifactId>
        </dependency>
        <dependency>
            <groupId>commons-collections</groupId>
            <artifactId>commons-collections</artifactId>
        </dependency>
        <dependency>
            <groupId>org.apache.commons</groupId>
            <artifactId>commons-math</artifactId>
        </dependency>
        <dependency>
            <groupId>net.java.dev.jna</groupId>
            <artifactId>jna</artifactId>
        </dependency>
        <dependency>
            <groupId>net.java.dev.jets3t</groupId>
            <artifactId>jets3t</artifactId>
        </dependency>
        <dependency>
            <groupId>us.levk</groupId>
            <artifactId>drmaa-gridengine</artifactId>
        </dependency>
        <dependency>
            <groupId>com.google.code.gson</groupId>
            <artifactId>gson</artifactId>
        </dependency>
        <dependency>
            <groupId>org.apache.httpcomponents</groupId>
            <artifactId>httpclient</artifactId>
        </dependency>
        <dependency>
            <groupId>com.google.code.cofoja</groupId>
            <artifactId>cofoja</artifactId>
        </dependency>
        <dependency>
            <groupId>${project.groupId}</groupId>
            <artifactId>gsalib</artifactId>
            <version>${project.version}</version>
            <type>tar.gz</type>
        </dependency>

        <dependency>
            <groupId>com.google.caliper</groupId>
            <artifactId>caliper</artifactId>
            <scope>test</scope>
        </dependency>
    </dependencies>

    <build>
        <plugins>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-dependency-plugin</artifactId>
                <executions>
                    <execution>
                        <id>copy-gsalib</id>
                        <goals>
                            <goal>copy</goal>
                        </goals>
                        <phase>process-resources</phase>
                        <configuration>
                            <artifactItems>
                                <artifactItem>
                                    <groupId>${project.groupId}</groupId>
                                    <artifactId>gsalib</artifactId>
                                    <version>${project.version}</version>
                                    <type>tar.gz</type>
                                    <outputDirectory>${project.build.outputDirectory}/${gsalib.packagedir}</outputDirectory>
                                    <destFileName>${gsalib.filename}</destFileName>
                                </artifactItem>
                            </artifactItems>
                        </configuration>
                    </execution>
                </executions>
            </plugin>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-resources-plugin</artifactId>
                <executions>
                    <execution>
                        <id>copy-resource-bundle-log4j</id>
                        <phase>prepare-package</phase>
                    </execution>
                </executions>
            </plugin>
            <!--
            TODO: Refactor ResourceBundleExtractorDoclet.isWalker() and move the RBED to utils.
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-javadoc-plugin</artifactId>
                <executions>
                    <execution>
                        <id>extract-resource-bundle</id>
                        <phase>prepare-package</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>

</project>