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>edu.cmu.cs.lane</groupId>
	<artifactId>genetic-pipeline</artifactId>
	<version>1.0</version>
	<dependencies>
	
		<dependency>
			<groupId>commons-io</groupId>
			<artifactId>commons-io</artifactId>
			<version>2.4</version>
		</dependency>
		<dependency>
			<groupId>commons-configuration</groupId>
			<artifactId>commons-configuration</artifactId>
			<version>1.6</version>
		</dependency>
		<dependency> 
			<groupId>mysql</groupId>
			<artifactId>mysql-connector-java</artifactId>
			<version>5.1.6</version>
		</dependency>
		<dependency>
			<groupId>log4j</groupId>
			<artifactId>log4j</artifactId>
			<version>1.2.17</version>
		</dependency>
		<dependency>
			<groupId>org.json</groupId>
			<artifactId>json</artifactId>
			<version>20090211</version>
		</dependency>
		<dependency>
			<groupId>org.mongodb</groupId>
			<artifactId>mongo-java-driver</artifactId>
			<version>2.10.1</version>
		</dependency>
		<dependency>
			<groupId>junit</groupId>
			<artifactId>junit</artifactId>
			<version>4.11</version>
		</dependency>
		<dependency>
			<groupId>org.apache.commons</groupId>
			<artifactId>commons-math</artifactId>
			<version>2.0</version>
		</dependency>
		<dependency>
			<groupId>org.apache.commons</groupId>
			<artifactId>commons-math3</artifactId>
			<version>3.0</version>
		</dependency>
		<dependency>
			<groupId>org.jblas</groupId>
			<artifactId>jblas</artifactId>
			<version>1.2.3</version>
		</dependency>
		<dependency>
        	<groupId>org.apache.commons</groupId>
        	<artifactId>commons-compress</artifactId>
        	<version>1.0</version>
      	</dependency>
 		
<!--		
        <dependency>
            <groupId>org.UJMP</groupId>
            <artifactId>UJMP</artifactId>
            <version>0.2.5</version>
            <scope>system</scope>
            <systemPath>${project.basedir}/lib/ujmp-complete-0.2.5.jar</systemPath>
        </dependency>
        <dependency>
            <groupId>org.UJMP</groupId>
            <artifactId>UJMP-sources</artifactId>
            <version>0.2.5</version>
            <scope>system</scope>
            <systemPath>${project.basedir}/lib/ujmp-complete-0.2.5-sources.jar</systemPath>
        </dependency>
-->        
     
	</dependencies>
	<build>
		<plugins>
			<plugin>
				<groupId>org.apache.maven.plugins</groupId>
				<artifactId>maven-compiler-plugin</artifactId>
		        <version>2.3.2</version>
				<configuration>
					<source>1.6</source>
					<target>1.6</target>
				</configuration>
			</plugin>
			<plugin>
				<groupId>org.codehaus.mojo</groupId>
				<artifactId>exec-maven-plugin</artifactId>
				<version>1.2.1</version>
				<executions>
					<execution>
						<goals>
							<goal>exec</goal>
						</goals>
					</execution>
				</executions>
				<configuration>
					<executable>make</executable>
					<workingDirectory>${basedir}/src/main/jni</workingDirectory>
					<arguments>
						<argument>OUT_DIR=${basedir}/src/main/resources</argument>
					</arguments>
    			</configuration>
			</plugin>
			<plugin>
				<artifactId>maven-assembly-plugin</artifactId>
				<configuration>
					<archive>
						<manifest>
							<mainClass>fully.qualified.MainClass</mainClass>
						</manifest>
					</archive>
					<descriptorRefs>
						<descriptorRef>jar-with-dependencies</descriptorRef>
					</descriptorRefs>
				</configuration>
			</plugin> 
		</plugins>
	</build>
</project>