<assembly
	xmlns="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.2"
	xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
	xsi:schemaLocation="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.2 http://maven.apache.org/xsd/assembly-1.1.2.xsd">
	<id>bundle</id>
	<formats>
		<format>tar.gz</format>
	</formats>

<!-- 	<moduleSets>
	
		<moduleSet>
		<useAllReactorProjects>true</useAllReactorProjects>	 
			<includes>
				<include>${groupId}:biojava3-core</include>
				<include>${groupId}:biojava3-alignment</include>
				<include>${groupId}:biojava3-structure</include>
				<include>${groupId}:biojava3-structure-gui</include>				
			</includes>
			<binaries>
				<outputDirectory>modules/${artifactId}</outputDirectory>
				<outputDirectory>./modules/</outputDirectory>
				<unpack>false</unpack>
				<includeDependencies>true</includeDependencies>
				   <dependencySets>
                    <dependencySet>
                        <unpack>false</unpack>
                        <scope>compile</scope>
                        
                    </dependencySet>
                </dependencySets>
			</binaries>
			  
		</moduleSet>
	</moduleSets> -->
	<fileSets>
		<fileSet>
			<directory>${project.basedir}/src/main/assembly/</directory>
			<outputDirectory>.</outputDirectory>
			<includes>
				<include>*.sh</include>
				<include>db.out</include>
				<include>example.lst</include>
				<include>LICENSE</include>
			</includes>
		</fileSet>
	</fileSets>
	<dependencySets>
		  <dependencySet>
            <outputDirectory>jars</outputDirectory>
            <includes>                               
				<include>${groupId}:biojava3-core</include>
				<include>${groupId}:biojava3-alignment</include>
				<include>${groupId}:biojava3-structure</include>
				<include>${groupId}:biojava3-structure-gui</include>				
				<include>net.sourceforge.jmol:jmol</include>
				<include>javaws:javaws</include>
            </includes>
        </dependencySet>
	</dependencySets>

</assembly>