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>de.charite.compbio</groupId>
	<artifactId>Jannovar</artifactId>
	<version>0.12</version>
	<packaging>pom</packaging>
	<name>Jannovar</name>

	<modules>
		<module>jannovar-core</module>
		<module>jannovar-htsjdk</module>
		<module>jannovar-cli</module>
		<module>jannovar-filter</module>
	</modules>

	<licenses>
		<license>
			<name>BSD-style</name>
			<url>http://www.opensource.org/licenses/bsd-license.php</url>
			<distribution>repo</distribution>
		</license>
	</licenses>

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

	<dependencies>
		<!--Logging framework -->
		<dependency>
			<groupId>org.slf4j</groupId>
			<artifactId>slf4j-api</artifactId>
			<version>1.7.7</version>
		</dependency>
		<!-- Logging -->
		<dependency>
			<groupId>org.apache.logging.log4j</groupId>
			<artifactId>log4j-api</artifactId>
			<version>${log4j.version}</version>
		</dependency>
		<dependency>
			<groupId>org.apache.logging.log4j</groupId>
			<artifactId>log4j-core</artifactId>
			<version>${log4j.version}</version>
		</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>
				</configuration>
			</plugin>
		</plugins>
	</build>

	<!-- Sphinx Manual -->
	<reporting>
		<plugins>
			<plugin>
				<groupId>org.apache.maven.plugins</groupId>
				<artifactId>maven-project-info-reports-plugin</artifactId>
				<version>2.4</version>
				<reportSets>
					<reportSet>
						<reports></reports>
					</reportSet>
				</reportSets>
			</plugin>
			<plugin>
				<groupId>org.tomdz.maven</groupId>
				<artifactId>sphinx-maven-plugin</artifactId>
				<version>1.0.2</version>
				<configuration>
					<sourceDirectory>${basedir}/manual</sourceDirectory>
				</configuration>
			</plugin>
		</plugins>
	</reporting>

</project>