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/xsd/maven-4.0.0.xsd">
    <modelVersion>4.0.0</modelVersion>
    <groupId>org.justinpaschall</groupId>
    <artifactId>Spark_eQTL_assoc</artifactId>
    <version>0.1-SNAPSHOT</version>
    <properties>
        <spark.version>1.2.0</spark.version>
        <adam.version>0.17.0</adam.version>
    </properties>
    <pluginRepositories>
        <pluginRepository>
            <id>scala-tools.org</id>
            <name>Scala-tools Maven2 Repository</name>
            <url>http://scala-tools.org/repo-releases</url>
        </pluginRepository>
    </pluginRepositories>
    <dependencies>
        <dependency>
            <groupId>org.apache.spark</groupId>
            <artifactId>spark-core_2.10</artifactId>
            <version>${spark.version}</version>
        </dependency>
        <dependency>
            <groupId>org.bdgenomics.adam</groupId>
            <artifactId>adam-core_2.10</artifactId>
            <version>${adam.version}</version>
        </dependency>
        <dependency>
            <groupId>org.bdgenomics.adam</groupId>
            <artifactId>adam-apis_2.10</artifactId>
            <version>${adam.version}</version>
        </dependency>
        <dependency>
            <groupId>org.apache.commons</groupId>
            <artifactId>commons-math3</artifactId>
            <version>3.2</version>
        </dependency>

    </dependencies>
    <build>
        <sourceDirectory>src/main/scala</sourceDirectory>
        <plugins>
            <plugin>
                <groupId>org.scala-tools</groupId>
                <artifactId>maven-scala-plugin</artifactId>
                <version>2.14.1</version>
                <executions>
                    <execution>
                        <goals>
                            <goal>compile</goal>
                        </goals>
                    </execution>
                </executions>
            </plugin>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-compiler-plugin</artifactId>
                <version>2.3.2</version>
                <configuration>
                    <source>1.8</source>
                    <target>1.8</target>
                </configuration>
            </plugin>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-shade-plugin</artifactId>
                <version>2.3</version>
                <executions>
                    <execution>
                        <phase>package</phase>
                        <goals>
                            <goal>shade</goal>
                        </goals>
                    </execution>
                </executions>
                <configuration>
                    <filters>
                        <filter>
                            <artifact>*:*</artifact>
                            <excludes>
                                <exclude>META-INF/*.SF</exclude>
                                <exclude>META-INF/*.DSA</exclude>
                                <exclude>META-INF/*.RSA</exclude>
                            </excludes>
                        </filter>
                    </filters>
                    <finalName>uberScalajar-${project.artifactId}-${project.version}</finalName>
                </configuration>
            </plugin>
        </plugins>
    </build>
</project>