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>Je</groupId>
	<artifactId>Je</artifactId>
	<version>2.0.RC</version>
	<name>Je</name>
	<description>Je provides command line utilities to deal with barcoded FASTQ files with or without Unique Molecular Index (UMI)</description>

	<licenses>
		<license>
			<name>MIT</name>
			<url><![CDATA[https://opensource.org/licenses/MIT]]></url>
		</license>
	</licenses>

	<properties>
		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
		<log.level>INFO</log.level>
	</properties>

	<!-- Building is a little tricky due to the custom picard. Each time you 
		modify picard (meaning you have a git clone of both picard and htsjdk), you 
		need to build picard with ant i.e. 'ant build' This creates jars in the dist 
		picard/folder and the 2 important ones are : (1) picard.jar (2) htsjdk_lib_dir/htsjdk-1.140.jar 
		You then need to add these in your local mvn repo so that they are found 
		by maven, this is performed by the src/shell/install-picard-deps-in-mvn-repos_from-git.sh 
		(you need to adapt path in there first !) The script also takes care of replacing 
		the jars in Je/lib to make sure we always distribute with the right custom 
		picard jars You can now build Je ! 
		
		TODO : Good news, my changes have been merged in picard so you should be able to switch to normal picard at next picard release
	-->



	<build>

		<resources>
			<resource>
				<directory>${basedir}/src/main/java</directory>
				<includes>
					<include>**/*.java</include>
				</includes>
			</resource>
			<!-- Resource def needed to overwrite properties dynamically in eg log4j.xml -->

			<resource>
				<directory>${basedir}/src/main/resources</directory>
				<includes>
					<include>log4j.xml</include>
					<include>*.properties</include>
				</includes>
				<filtering>true</filtering>
			</resource>
			
			<resource>
				<directory>${basedir}/src/test/resources</directory>
				<excludes>
					<exclude>log4j.xml</exclude>
					<exclude>**/*.txt</exclude>
				</excludes>
			</resource>

		</resources>

		<plugins>

			<!-- Define a plugin that embeds all dependences (jars) in the final jar -->
			<plugin>
				<groupId>org.apache.maven.plugins</groupId>
				<artifactId>maven-assembly-plugin</artifactId>
				<configuration>
					<archive>
						<manifest>
							<mainClass>org.embl.gbcs.je.Je</mainClass>
						</manifest>
					</archive>
					<descriptorRefs>
						<descriptorRef>jar-with-dependencies</descriptorRef>
					</descriptorRefs>
				</configuration>
				<!-- 			
				Bind to packaging phase: the package phase will now produce 2 jars: 
					- the 'usual' one 
					- one with all dependencies bundled 
				-->
				<executions>
					<execution>
						<phase>package</phase>
						<goals>
							<goal>single</goal>
						</goals>
					</execution>
				</executions>
			</plugin>
		</plugins> 
	</build>


	<profiles>
		<profile>
			<!-- Profile to get a test jar for testing against the embase dev db -->
			<id>test</id>
			<build>
				<plugins>
					<plugin>
						<groupId>org.codehaus.mojo</groupId>
						<artifactId>properties-maven-plugin</artifactId>
						<version>1.0.0</version>
						<executions>
							<execution>
								<phase>initialize</phase>
								<goals>
									<goal>read-project-properties</goal>
								</goals>
								<configuration>
									<files>
										<file>config/test.properties</file>
									</files>
								</configuration>
							</execution>
						</executions>
					</plugin>
					<plugin>
						<groupId>org.apache.maven.plugins</groupId>
						<artifactId>maven-assembly-plugin</artifactId>
						<configuration>
							<finalName>je_bundle-TEST</finalName>
							<appendAssemblyId>false</appendAssemblyId>
							<archive>
								<manifestEntries>
									<Implementation-Version>${project.version}</Implementation-Version>
								</manifestEntries>
							</archive>
						</configuration>
					</plugin>
				</plugins>
			</build>

		</profile>
		<profile>
			<!-- Profile to get the production jar for EMBL -->
			<id>embl</id>
			<build>
				<plugins>
					<plugin>
						<groupId>org.codehaus.mojo</groupId>
						<artifactId>properties-maven-plugin</artifactId>
						<version>1.0.0</version>
						<executions>
							<execution>
								<phase>initialize</phase>
								<goals>
									<goal>read-project-properties</goal>
								</goals>
								<configuration>
									<files>
										<file>config/embl.properties</file>
									</files>
								</configuration>
							</execution>
						</executions>
					</plugin>
					<plugin>
						<groupId>org.apache.maven.plugins</groupId>
						<artifactId>maven-assembly-plugin</artifactId>
						<configuration>
							<finalName>je_embl_${project.version}_bundle</finalName>
							<appendAssemblyId>false</appendAssemblyId>
							<archive>
								<manifestEntries>
									<Implementation-Version>${project.version}</Implementation-Version>
								</manifestEntries>
							</archive>
						</configuration>
					</plugin>
				</plugins>
			</build>
		</profile>

		<profile>
			<!-- Profile to get the production jar for public use -->
			<id>public</id>
			<build>
				<plugins>
					<plugin>
						<groupId>org.codehaus.mojo</groupId>
						<artifactId>properties-maven-plugin</artifactId>
						<version>1.0.0</version>
						<executions>
							<execution>
								<phase>initialize</phase>
								<goals>
									<goal>read-project-properties</goal>
								</goals>
								<configuration>
									<files>
										<file>config/public.properties</file>
									</files>
								</configuration>
							</execution>
						</executions>
					</plugin>
					<plugin>
						<groupId>org.apache.maven.plugins</groupId>
						<artifactId>maven-assembly-plugin</artifactId>
						<configuration>
							<finalName>je_${project.version}_bundle</finalName>
							<appendAssemblyId>false</appendAssemblyId>
							<archive>
								<manifestEntries>
									<Implementation-Version>${project.version}</Implementation-Version>
								</manifestEntries>
							</archive>
						</configuration>
					</plugin>
				</plugins>
			</build>

		</profile>
	</profiles>


	<dependencies>

		<dependency>
			<groupId>org.embl.gbcs.embase</groupId>
			<artifactId>jembase_api</artifactId>
			<version>1.0</version>
		</dependency>

		<dependency>
			<groupId>org.embl.cg.utilitytools</groupId>
			<artifactId>ut_utils</artifactId>
			<version>1.0.1</version>
		</dependency>
	
		<dependency>
			<groupId>org.slf4j</groupId>
			<artifactId>slf4j-api</artifactId>
			<version>1.7.7</version>
		</dependency>
		<dependency>
			<groupId>org.slf4j</groupId>
			<artifactId>slf4j-log4j12</artifactId>
			<version>1.7.7</version>
		</dependency>

		<dependency>
			<groupId>mysql</groupId>
			<artifactId>mysql-connector-java</artifactId>
			<version>5.1.25</version>
		</dependency>
		

		<dependency>
			<groupId>org.apache.commons</groupId>
			<artifactId>commons-lang3</artifactId>
			<version>3.3.2</version>
		</dependency>

		<dependency>
			<groupId>junit</groupId>
			<artifactId>junit</artifactId>
			<version>4.11</version>
			<scope>test</scope>
		</dependency>
		<dependency>
			<groupId>org.broadinstitute</groupId>
			<artifactId>picard</artifactId>
			<version>2.9.4</version>
		</dependency>
	</dependencies>


</project>