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>fi.aalto</groupId>
    <artifactId>seqpig</artifactId>
    <version>0.6-SNAPSHOT</version>

    <properties>
        <java.version>1.8</java.version>
        <hadoop.version>2.6.0-cdh5.6.0</hadoop.version>
        <hadoopbam.version>7.4.0</hadoopbam.version>
        <htsjdk.version>2.1.0</htsjdk.version>
        <seal.version>0.4.0-with-hadoop-bam-7.4.0</seal.version>
        <pig.version>0.12.0-cdh5.6.0</pig.version>
        <piggybank.version>0.12.0-cdh5.6.0</piggybank.version>

        <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
        <github.global.server>github</github.global.server>

    </properties>
    <repositories>
        <repository>
            <id>cloudera</id>
            <url>https://repository.cloudera.com/artifactory/cloudera-repos/</url>
        </repository>
    </repositories>

      <dependencies>
        <dependency>
            <groupId>org.apache.pig</groupId>
            <artifactId>pig</artifactId>
            <version>${pig.version}</version>
        </dependency>
        <dependency>
            <groupId>org.apache.pig</groupId>
            <artifactId>piggybank</artifactId>
            <version>${piggybank.version}</version>
        </dependency>
        <dependency>
            <groupId>org.apache.hadoop</groupId>
            <artifactId>hadoop-client</artifactId>
            <version>${hadoop.version}</version>
        </dependency>
        <dependency>
            <groupId>org.seqdoop</groupId>
            <artifactId>hadoop-bam</artifactId>
            <version>${hadoopbam.version}</version>
            <exclusions>
                <exclusion>
                    <groupId>org.testng</groupId>
                    <artifactId>testng</artifactId>
                </exclusion>
            </exclusions>
        </dependency>

          <dependency>
              <groupId>com.github.samtools</groupId>
              <artifactId>htsjdk</artifactId>
              <version>${htsjdk.version}</version>
          </dependency>

          <dependency>
              <groupId>it.crs4</groupId>
              <artifactId>seal</artifactId>
              <version>${seal.version}</version>
          </dependency>
          <dependency>
              <groupId>org.apache.hadoop</groupId>
              <artifactId>hadoop-mapreduce-client-core</artifactId>
              <version>${hadoop.version}</version>
          </dependency>

    </dependencies>

    <build>
        <plugins>

            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-assembly-plugin</artifactId>
                <configuration>
                    <descriptorRefs>
                        <descriptorRef>jar-with-dependencies</descriptorRef>
                    </descriptorRefs>
                    <archive>
                        <index>true</index>
                        <manifest>
                            <addClasspath>true</addClasspath>
                            <mainClass>fi.aalto.seqpig.BamUDFTest</mainClass>
                        </manifest>
                    </archive>
                    <attach>false</attach>
                </configuration>
                <executions>
                    <execution>
                        <phase>package</phase>
                        <goals>
                            <goal>single</goal>
                        </goals>
                    </execution>
                </executions>
            </plugin>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-compiler-plugin</artifactId>
                <configuration>
                    <source>1.8</source>
                    <target>1.8</target>
                </configuration>
            </plugin>
        </plugins>
    </build>


</project>