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>com.example.project</groupId>
	<artifactId>example-project</artifactId>
	<version>0.1-SNAPSHOT</version>
	<packaging>jar</packaging>
	<name>Example Project</name>

	<!-- Inherit artifact from SonaType OSS pom.xml Following this article: 
		http://java.dzone.com/articles/deploy-maven-central -->
	<parent>
		<groupId>org.sonatype.oss</groupId>
		<artifactId>oss-parent</artifactId>
		<version>9</version>
	</parent>

	<properties>
		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
		<log4j.version>2.1</log4j.version>
	</properties>

	<dependencies>
		<!-- Jannovar core -->
		<dependency>
			<groupId>de.charite.compbio</groupId>
			<artifactId>jannovar-cli</artifactId>
			<version>0.14</version>
		</dependency>

		<!-- Jannovar bridge to HTSJDK -->
		<dependency>
			<groupId>de.charite.compbio</groupId>
			<artifactId>jannovar-htsjdk</artifactId>
			<version>0.14</version>
		</dependency>

		<!-- JUnit for testing -->
		<dependency>
			<groupId>junit</groupId>
			<artifactId>junit</artifactId>
			<version>4.11</version>
			<scope>test</scope>
		</dependency>
	</dependencies>

	<build>
		<plugins>
			<!-- JUnit testing -->
			<plugin>
				<groupId>org.apache.maven.plugins</groupId>
				<artifactId>maven-surefire-plugin</artifactId>
				<version>2.17</version>
				<configuration>
					<skipTests>false</skipTests>
					<forkCount>3</forkCount>
					<reuseForks>true</reuseForks>
					<argLine>${argLine} -Xms512m -Xmx1024m</argLine>
					<systemPropertyVariables>
						<user.language>en</user.language>
						<user.region>GB</user.region>
					</systemPropertyVariables>
				</configuration>
			</plugin>

			<!-- Javadoc generation. -->
			<plugin>
				<groupId>org.apache.maven.plugins</groupId>
				<artifactId>maven-javadoc-plugin</artifactId>
				<version>2.9</version>
				<!-- Uncomment this to get the Javadoc to show all members <configuration> 
					<show>private</show> </configuration> -->
			</plugin>

			<!-- Jacoco Coverage Reports -->
			<plugin>
				<groupId>org.jacoco</groupId>
				<artifactId>jacoco-maven-plugin</artifactId>
				<version>0.7.2.201409121644</version>
				<executions>
					<!-- Prepares the property pointing to the JaCoCo runtime agent which 
						is passed as VM argument when Maven the Surefire plugin is executed. -->
					<execution>
						<id>pre-unit-test</id>
						<goals>
							<goal>prepare-agent</goal>
						</goals>
					</execution>
					<!-- Ensures that the code coverage report for unit tests is created 
						after unit tests have been run. -->
					<execution>
						<id>post-unit-test</id>
						<phase>test</phase>
						<goals>
							<goal>report</goal>
						</goals>
					</execution>
				</executions>
			</plugin>

			<!-- Compilation -->
			<plugin>
				<groupId>org.apache.maven.plugins</groupId>
				<artifactId>maven-compiler-plugin</artifactId>
				<version>3.0</version>
				<configuration>
					<compilerArgument>-Xlint:all</compilerArgument>
					<showWarnings>true</showWarnings>
					<showDeprecation>true</showDeprecation>
					<source>${javaVersion}</source>
					<target>${javaVersion}</target>
				</configuration>
			</plugin>

			<!-- Make an executable jar and specify the main class and classpath -->
			<plugin>
				<groupId>org.apache.maven.plugins</groupId>
				<artifactId>maven-jar-plugin</artifactId>
				<version>2.5</version>
				<configuration>
					<archive>
						<manifest>
							<addClasspath>true</addClasspath>
							<classpathPrefix>lib/</classpathPrefix>
							<!-- set useUniqueVersions=false in order that the classpath has the 
								SNAPSHOT instead of the build number prefixed to the dependency -->
							<useUniqueVersions>false</useUniqueVersions>
							<mainClass>com.example.project.cli.Cli</mainClass>
						</manifest>
					</archive>
					<compilerArgument>-Xlint:all</compilerArgument>
					<showWarnings>true</showWarnings>
					<showDeprecation>true</showDeprecation>
				</configuration>
			</plugin>

			<!-- More JAR building -->
			<plugin>
				<groupId>org.apache.maven.plugins</groupId>
				<artifactId>maven-shade-plugin</artifactId>
				<version>2.2</version>
				<executions>
					<execution>
						<phase>package</phase>
						<goals>
							<goal>shade</goal>
						</goals>
						<configuration>
							<transformers>
								<transformer
									implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
									<mainClass>com.example.project.cli.Cli</mainClass>
								</transformer>
							</transformers>
						</configuration>
					</execution>
				</executions>
			</plugin>

		</plugins>
	</build>

</project>