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/xsd/maven-4.0.0.xsd">
    <modelVersion>4.0.0</modelVersion>

    <groupId>edu.berkeley.amplab</groupId>
    <artifactId>adam</artifactId>
    <version>0.1-SNAPSHOT</version>
    <packaging>jar</packaging>

    <properties>
        <avro.version>1.7.4</avro.version>
        <hadoop.version>1.1.2</hadoop.version>
    </properties>

    <build>
        <plugins>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-compiler-plugin</artifactId>
                <version>3.1</version>
                <configuration>
                    <source>1.6</source>
                    <target>1.6</target>
                </configuration>
            </plugin>
            <plugin>
                <groupId>org.apache.avro</groupId>
                <artifactId>avro-maven-plugin</artifactId>
                <version>${avro.version}</version>
                <executions>
                    <execution>
                        <id>schemas</id>
                        <phase>generate-sources</phase>
                        <goals>
                            <goal>schema</goal>
                            <goal>protocol</goal>
                            <goal>idl-protocol</goal>
                        </goals>
                        <configuration>
                            <sourceDirectory>${project.basedir}/src/main/resources/avro
                            </sourceDirectory>
                            <outputDirectory>${project.basedir}/src/main/java</outputDirectory>
                            <!--
                            <testSourceDirectory>${project.basedir}/src/test/avro/</testSourceDirectory>
                            <testOutputDirectory>${project.basedir}/src/test/java/</testOutputDirectory>
                            -->
                        </configuration>
                    </execution>
                </executions>
            </plugin>
            <plugin>
                <artifactId>maven-assembly-plugin</artifactId>
                <version>2.2.1</version>
                <executions>
                    <execution>
                        <id>job</id>
                        <phase>package</phase>
                        <goals>
                            <goal>single</goal>
                        </goals>
                        <configuration>
                            <descriptors>
                                <descriptor>src/main/assembly/job.xml</descriptor>
                            </descriptors>
                            <finalName>adam-${project.version}</finalName>
                            <outputDirectory>${project.build.directory}/../</outputDirectory>
                            <appendAssemblyId>false</appendAssemblyId>
			    <attach>false</attach>
                            <archive>
                                <manifest>
                                    <mainClass>edu.berkeley.amplab.adam.AdamMain</mainClass>
                                </manifest>
                            </archive>
                        </configuration>
                    </execution>
                </executions>
            </plugin>
        </plugins>
    </build>

    <repositories><repository>
    <id>LocalLibs</id>
    <name>LocalLibs></name>
    <url>file://${project.basedir}/libs</url>
    </repository></repositories>

    <dependencies>
        <!-- Picard -->
        <dependency>
            <!-- <groupId>org.utgenome.thirdparty</groupId>-->
	    <groupId>samtools</groupId>
            <artifactId>picard</artifactId>
            <version>1.76.0</version>
        </dependency>
        <dependency>
            <!-- <groupId>org.utgenome.thirdparty</groupId>-->
            <groupId>samtools</groupId>
            <artifactId>sam</artifactId>
            <version>1.76.0</version>
        </dependency>
        <!-- Avro -->
        <dependency>
            <groupId>org.apache.avro</groupId>
            <artifactId>avro</artifactId>
            <version>${avro.version}</version>
        </dependency>
        <dependency>
            <groupId>org.apache.avro</groupId>
            <artifactId>avro-mapred</artifactId>
            <version>${avro.version}</version>
        </dependency>
        <dependency>
            <groupId>org.apache.hadoop</groupId>
            <artifactId>hadoop-core</artifactId>
            <version>1.1.0</version>
        </dependency>
<dependency>
	<groupId>args4j</groupId>
	<artifactId>args4j</artifactId>
	<version>2.0.23</version>
</dependency>

<!--
        <dependency>
            <groupId>commons-cli</groupId>
            <artifactId>commons-cli</artifactId>
            <version>1.2</version>
        </dependency>
-->
    </dependencies>

</project>