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>VariantGraph</groupId>
    <artifactId>VariantGraph</artifactId>
    <version>1.0-SNAPSHOT</version>
    <properties>
        <maven.compiler.source>1.6</maven.compiler.source>
        <maven.compiler.target>1.6</maven.compiler.target>
    </properties>

    <build>
        <plugins>
            <plugin>
                <artifactId>maven-assembly-plugin</artifactId>
                <configuration>
                    <archive>
                        <manifest>
                            <mainClass>Main.MainCLI</mainClass>
                        </manifest>
                    </archive>
                    <descriptorRefs>
                        <descriptorRef>jar-with-dependencies</descriptorRef>
                    </descriptorRefs>
                </configuration>
                <executions>
                    <execution>
                        <id>make-assembly</id> <!-- this is used for inheritance merges -->
                        <phase>package</phase> <!-- bind to the packaging phase -->
                        <goals>
                            <goal>single</goal>
                        </goals>
                    </execution>
                </executions>
            </plugin>
        </plugins>
    </build>

    <dependencies>
        <dependency>
            <groupId>org.apache.jena</groupId>
            <artifactId>apache-jena-libs</artifactId>
            <type>pom</type>
            <version>2.13.0</version>
        </dependency>

        <dependency>
            <groupId>com.github.samtools</groupId>
            <artifactId>htsjdk</artifactId>
            <version>1.134</version>
        </dependency>


        <dependency>
            <groupId>junit</groupId>
            <artifactId>junit</artifactId>
            <version>4.10</version>
            <type>jar</type>
            <scope>compile</scope>
        </dependency>
        <dependency>
            <groupId>commons-cli</groupId>
            <artifactId>commons-cli</artifactId>
            <version>1.2</version>
        </dependency>
        <dependency>
            <groupId>org.apache.aries.application</groupId>
            <artifactId>application-modeller-standalone</artifactId>
            <version>1.0.1-SNAPSHOT</version>
            <scope>test</scope>
        </dependency>
        <dependency>
            <groupId>com.thewebsemantic</groupId>
            <artifactId>jenabean</artifactId>
            <version>1.0.6</version>
        </dependency>
        <dependency>
            <groupId>com.google.guava</groupId>
            <artifactId>guava</artifactId>
            <version>18.0</version>
        </dependency>
    </dependencies>

    <repositories>
        <repository>
            <id>apache-repo-snapshots</id>
            <url>http://repository.apache.org/content/repositories/snapshots/</url>
            <releases>
                <enabled>false</enabled>
            </releases>
            <snapshots>
                <enabled>true</enabled>
            </snapshots>
        </repository>

        <repository>
            <id>apache-repo-releases</id>
            <url>http://repository.apache.org/content/repositories/releases/</url>
            <releases>
                <enabled>true</enabled>
            </releases>
        </repository>

        <repository>
            <id>Jenabean</id>
            <url>http://jenabean.googlecode.com/svn/repo</url>
        </repository>
    </repositories>


</project>