build.xml

<?xml version="1.0"?>
<project name="pathlinker" default="jar" basedir=".">

  <property name="pathvisio.dir" value="E:\Program Files (x86)\pathvisio\common-bundles"/>
    <property name="jar.name" value="PathLinker.jar"/>
  <property name="lib.dir"     value="."/>    
        <path id="project.class.path">
        <fileset dir="${pathvisio.dir}/modules">
            <include name="org.pathvisio.core.jar"/>
            <include name="org.pathvisio.gui.jar"/>
            <include name="org.pathvisio.desktop.jar"/>
        </fileset>
        <fileset dir="${pathvisio.dir}/lib">
            <include name="org.eclipse.osgi.jar"/>
            <include name="felix.jar"/>
            <include name="org.bridgedb.jar"/>
            <include name="org.bridgedb.gui.jar"/>
            <include name="org.bridgedb.rdb.jar"/>
            <include name="org.bridgedb.rdb.construct.jar"/>
            <include name="org.bridgedb.bio.jar"/> 
            <include name="derby"/> 
            <include name="org.apache.xerces_2.9.0.v201101211617"/>
            <include name="org.wikipathways.client.bundle-3.2.0"/>
        	<include name="org.pathvisio.jgoodies.forms.jar"/>
        </fileset>
        <fileset dir="${lib.dir}" includes="**/*.jar"/>
     </path>
    <target name="prepare">
            <mkdir dir="build"/>            
            <unjar dest="build">
                    <patternset>
                          <include name="**/*.jar"/>             
                    </patternset>
                    <fileset dir="${lib.dir}">
                          <include name="**/*.jar"/>             
                    </fileset>
            </unjar>
            <mkdir dir="${bundle.dest}"/>
            <fail message="Can't find ${pathvisio.dir}/modules/org.pathvisio.core.jar, please specify the path to pathvisio with -Dpathvisio.dir=....">
                <condition>
                    <not><available file="${pathvisio.dir}/modules/org.pathvisio.core.jar"/></not>
                </condition>
            </fail>
        </target>

        <target name="clean">
            <delete dir="build"/>
            <delete file="${jar.name}"/>
        </target>

        <target name="compile" depends="prepare">
            <echo>Compiling: ${jar.name}</echo>
            <javac srcdir="src"
                   includes="**"
                   destdir="build"
                   debug="${debug.mode}">
           <classpath refid="project.class.path"/>
            </javac>
        </target>
    <target name="jar" depends="compile"> 
            <echo>Creating JAR: ${jar.name}</echo>
            <jar jarfile="${jar.name}" manifest="META-INF/MANIFEST.MF" >
                <fileset dir="build">
                    <include name="**/*"/>                  
                    </fileset>
                    <zipgroupfileset dir="${lib.dir}" includes="**/*.jar" />                    
         </jar>
        </target>

        <target name="install" depends="jar"> 
            <copy toDir="${bundle.dest}" flatten="true">
                <fileset dir=".">
                    <include name="${jar.name}"/>
                </fileset>
            </copy>
            <delete file="${jar.name}"/>
        </target>

        <target name="dist-clean" depends="clean">
            <delete dir="${bundle.dest}"/>
        </target>

        <target name="all" depends="install" description="Clean, compile, jar, install" />
    
</project>