<?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">
    <parent>
        <groupId>nl.systemsgenetics</groupId>
        <artifactId>systemsgenetics</artifactId>
        <version>1.0.0</version>
    </parent>
    <artifactId>eqtl-mapping-pipeline</artifactId>
    <version>1.2.5</version>
    <packaging>jar</packaging>
    <modelVersion>4.0.0</modelVersion>
    <dependencies>
        <dependency>
            <groupId>nl.systemsgenetics</groupId>
            <artifactId>genetica-libraries</artifactId>
            <version>1.0.2</version>
        </dependency>
        <dependency>
            <groupId>log4j</groupId>
            <artifactId>log4j</artifactId>
            <version>1.2.17</version>
        </dependency>
        <dependency>
            <groupId>nl.systemsgenetics</groupId>
            <artifactId>Genotype-IO</artifactId>
            <version>1.0.0</version>
        </dependency>
        <dependency>
            <groupId>net.sf.trove4j</groupId>
            <artifactId>trove4j</artifactId>
            <version>3.0.3</version>
        </dependency>
        <dependency>
            <groupId>commons-cli</groupId>
            <artifactId>commons-cli</artifactId>
            <version>1.2</version>
        </dependency>
        <dependency>
            <groupId>commons-beanutils</groupId>
            <artifactId>commons-beanutils</artifactId>
            <version>1.8.3</version>
        </dependency>
        <dependency>
            <groupId>commons-codec</groupId>
            <artifactId>commons-codec</artifactId>
            <version>1.5</version>
        </dependency>
        <dependency>
            <groupId>commons-digester</groupId>
            <artifactId>commons-digester</artifactId>
            <version>2.0</version>
        </dependency>
        <dependency>
            <groupId>net.sourceforge.parallelcolt</groupId>
            <artifactId>parallelcolt</artifactId>
            <version>0.10.0</version>
        </dependency>
        <dependency>
            <groupId>${project.groupId}</groupId>
            <artifactId>imputation-tool</artifactId>
            <version>1.0.2</version>
        </dependency>
        <dependency>
            <groupId>net.rforge</groupId>
            <artifactId>Rserve</artifactId>
            <version>0.6-8.1</version>
        </dependency>
        <dependency>
            <groupId>org.testng</groupId>
            <artifactId>testng</artifactId>
            <version>6.5.2</version>
            <scope>test</scope>
        </dependency>
        <dependency>
            <groupId>net.sf.opencsv</groupId>
            <artifactId>opencsv</artifactId>
            <version>2.3</version>
        </dependency>
    </dependencies>
    <build>
        <resources>
            <resource>
                <directory>src/main/resources</directory>
                <filtering>true</filtering>
                <includes>
                    <include>**/version.properties</include>
                </includes>
            </resource>
        </resources>
        <finalName>eqtl-mapping-pipeline-${project.version}</finalName>
        <plugins>
            <!-- The configuration of maven-assembly-plugin -->
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-assembly-plugin</artifactId>
                <version>2.4</version>
                <!-- The configuration of the plugin -->
                <configuration>
                    <!-- Specifies the configuration file of the assembly plugin -->
                    <descriptors>
                        <descriptor>src/main/assembly/assembly.xml</descriptor>
                    </descriptors>
                </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>
            <!-- The configuration of maven-jar-plugin -->
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-jar-plugin</artifactId>
                <version>2.3.1</version>
                <!-- The configuration of the plugin -->
                <configuration>
                    <!-- Configuration of the archiver -->
                    <archive>
                        <!-- Manifest specific configuration -->
                        <manifest>
                            <!-- Classpath is added to the manifest of the created jar file. -->
                            <addClasspath>true</addClasspath>
                            <!--
                             Configures the classpath prefix. This configuration option is
                             used to specify that all needed libraries are found under lib/
                             directory.
                            -->
                            <classpathPrefix>lib/</classpathPrefix>
                            <!-- Specifies the main class of the application -->
                            <mainClass>eqtlmappingpipeline.Main</mainClass>
                        </manifest>
                    </archive>
                </configuration>
            </plugin>
        </plugins>
    </build>	
</project>