build_tasks.xml

<project name="IGV" default="build" basedir=".">
    
    <!-- Properties--> 
    <property name="jar.name"      value="siphy.jar" />
    
    <!-- Source and lib directories -->
    <property name="src.dir"       value="${basedir}/src/" />
    <property name="lib.dir"       value="${basedir}/lib/" />
    
    <!-- Distribution directory.  Binary distribution is placed here -->
    <property name="dist.dir"      value="${basedir}/dist/" />
	<!--<property name="dist.dir"      value="/Volumes/seq_mgarber/" />-->
	<property name="build.dir"	value="${basedir}/build/"/>
    <property name="jar.path"      value="${dist.dir}${jar.name}" />
    <property name="dist.lib.dir"     value="${dist.dir}lib/" />
    
    <!-- build specific properties. These are normally set by Hudson during the build process -->
    <property name="version"       value="v1.0" />
	<property name="tilling.version" value="0.7.2" />
	
	<!-- All jar files in lib file -->
	<path id="master-classpath">
      <fileset dir="${lib.dir}">
        <include name="*.jar"/>
      </fileset>
    </path>

     
    <target name="init" >
 
        
        <mkdir dir="${build.dir}"/>
        <mkdir dir="${dist.dir}"/>

        <!-- Copy resource files to the tmp directory 
        <copy todir="${tmp.dir}" overwrite="true" >
            <fileset dir="${src.dir}">
                <exclude name="**/*.form"/>
                <exclude name="**/*.java"/>
                <exclude name="**/*.svn"/>
                <exclude name="**/manifest.mf"/>
            </fileset>
        </copy>-->

        <!-- Unzip jars to the tmp directory 
        <unzip dest="${tmp.dir}">
            <patternset>
                <include name="**/*"/>
                <exclude name="META-INF/**"/>
            </patternset>
            <fileset dir="${lib.dir}">
                <include name="**/*.jar"/>
            </fileset>
        </unzip>-->

    

        <tstamp>
            <format property="timestamp" pattern="MM/dd/yyyy hh:mm aa" />
        </tstamp>
        
        <echo message="Resource ${resource.dir}"/>
        <echo message="Version ${version}"/>
    </target>
    
    
    <target name="compile" depends="init">
        <javac srcdir="${src.dir}"  debug="on" destdir="${build.dir}">

            <classpath refid="master-classpath"/>
                <!--<pathelement path="${build.dir}"/>
            </classpath>-->
        </javac>
    </target>
	
	<target name="unpack" depends="init">
	    <!-- Unzip jars to the tmp directory -->
        <unzip dest="${build.dir}">
            <patternset>
                <include name="**/*"/>
                <exclude name="META-INF/**"/>
            </patternset>
            <fileset dir="${lib.dir}">
                <include name="**/*.jar"/>
            </fileset>
        </unzip>
	</target>
	
	<target name="copy.props" depends="init">
		<copy todir="${build.dir}" file ="${src.dir}log4j.properties"/>
	</target>
    
    
    <!-- build the siphy jar-->
    <target name="build" depends="compile, unpack, copy.props">  
        <jar destfile="${jar.path}" basedir="${build.dir}" compress="true">
           <!-- <classfileset dir="${build.dir}">
                <root classname="${main-class}"/>
            </classfileset>-->
            <manifest>
                <attribute name="Built-By" value="${user.name}" />
                <attribute name="Main-Class" value="broad.core.siphy.TreeScaler"/>
            </manifest>
			<!--<fileset dir="${lib.dir}">
        		<include name="*.jar"/>
      		</fileset>-->
        </jar>
    </target>
	
    <!-- build the window scanner jar-->
    <target name="wscanner" depends="compile, unpack, copy.props">  
        <jar destfile="${dist.dir}wscanner.jar" basedir="${build.dir}" compress="true">
           <!-- <classfileset dir="${build.dir}">
                <root classname="${main-class}"/>
            </classfileset>-->
            <manifest>
                <attribute name="Built-By" value="${user.name}" />
                <attribute name="Main-Class" value="broad.core.siphy.programs.WindowScanner"/>
            </manifest>
			<!--<fileset dir="${lib.dir}">
        		<include name="*.jar"/>
      		</fileset>-->
        </jar>
    </target>
	
    <!-- build the UMI dupmarker jar-->
    <target name="umidups" depends="compile, unpack,  copy.props">  
        <jar destfile="${dist.dir}markdups.jar" basedir="${build.dir}" compress="true">
           <!-- <classfileset dir="${build.dir}">
                <root classname="${main-class}"/>
            </classfileset>-->
            <manifest>
                <attribute name="Built-By" value="${user.name}" />
                <attribute name="Main-Class" value="nextgen.core.programs.MarkDuplicatesFromNameUMI"/>
            </manifest>
			<fileset dir="${lib.dir}">
        		<include name="*.jar"/>
      		</fileset>
        </jar>
    </target>

    <!-- build the fastq trimmer dupmarker jar-->
    <target name="fqtrimmer" depends="compile, unpack,  copy.props">  
        <jar destfile="${dist.dir}fqtrimmer.jar" basedir="${build.dir}" compress="true">
           <!-- <classfileset dir="${build.dir}">
                <root classname="${main-class}"/>
            </classfileset>-->
            <manifest>
                <attribute name="Built-By" value="${user.name}" />
                <attribute name="Main-Class" value="broad.pda.samtools.TrimFastqReads"/>
            </manifest>
			<fileset dir="${lib.dir}">
        		<include name="*.jar"/>
      		</fileset>
        </jar>
    </target>
	
	   <!-- build the ESAT jar-->
	    <target name="esat" depends="compile, unpack,  copy.props">  
	        <jar destfile="${dist.dir}esat.jar" basedir="${build.dir}" compress="true">
	           <!-- <classfileset dir="${build.dir}">
	                <root classname="${main-class}"/>
	            </classfileset>-->
	            <manifest>
	                <attribute name="Built-By" value="${user.name}" />
	                <attribute name="Main-Class" value="nextgen.core.esat.ESAT"/>
	            </manifest>
				<fileset dir="${lib.dir}">
	        		<include name="*.jar"/>
	      		</fileset>
	        </jar>
	    </target>
	
    <!-- build the fastq trimmer dupmarker jar-->
    <target name="fqsplitter" depends="compile, unpack">  
        <jar destfile="${dist.dir}fqsplitter.jar" basedir="${build.dir}" compress="true">
           <!-- <classfileset dir="${build.dir}">
                <root classname="${main-class}"/>
            </classfileset>-->
            <manifest>
                <attribute name="Built-By" value="${user.name}" />
                <attribute name="Main-Class" value="broad.pda.seq.fastq.FastqSplitterByBarcode"/>
            </manifest>
			<fileset dir="${lib.dir}">
        		<include name="*.jar"/>
      		</fileset>
        </jar>
    </target>

	  <!-- build the multiple alignment jar -->
	    <target name="ma" depends="compile, unpack">
	        <jar destfile="${dist.dir}ma.jar" basedir="${build.dir}" compress="true">
	           <!-- <classfileset dir="${build.dir}">
	                <root classname="${main-class}"/>
	            </classfileset>-->
	            <manifest>
	                <attribute name="Built-By" value="${user.name}" />
	                <attribute name="Main-Class" value="broad.core.multiplealignment.AlignmentExtractor"/>
	            </manifest>
				<fileset dir="${lib.dir}">
	        		<include name="*.jar"/>
	      		</fileset>
	        </jar>
	    </target>
	
    <target name="endseq" depends="compile, unpack">
        <jar destfile="${dist.dir}endseq.jar" basedir="${build.dir}" compress="true">
           <!-- <classfileset dir="${build.dir}">
                <root classname="${main-class}"/>
            </classfileset>-->
            <manifest>
                <attribute name="Built-By" value="${user.name}" />
                <attribute name="Main-Class" value="nextgen.core.scripture.AddEndRNASeqToScripture"/>
	            </manifest>
				<fileset dir="${lib.dir}">
	        		<include name="*.jar"/>
	      		</fileset>
	        </jar>
	    </target>
	
     <!-- build the tilling array analysis jar -->
    <target name="build_tilling_arrays" depends="compile, unpack">
        <jar destfile="${dist.dir}tilling.${tilling.version}.jar" basedir="${build.dir}" compress="true">
           <!-- <classfileset dir="${build.dir}">
                <root classname="${main-class}"/>
            </classfileset>-->
            <manifest>
                <attribute name="Built-By" value="${user.name}" />
                <attribute name="Main-Class" value="broad.pda.arrays.tilling.TillingArrayUtils"/>
            </manifest>
			<fileset dir="${lib.dir}">
        		<include name="*.jar"/>
      		</fileset>
        </jar>
    </target>
	
	
    <!-- build add paired end edges jar -->
    <target name="build_paired" depends="compile, unpack">
        <jar destfile="${dist.dir}pairends.jar" basedir="${build.dir}" compress="true">
           <!-- <classfileset dir="${build.dir}">
                <root classname="${main-class}"/>
            </classfileset>-->
            <manifest>
                <attribute name="Built-By" value="${user.name}" />
                <attribute name="Main-Class" value="broad.pda.seq.segmentation.AddPairedEndEdges"/>
            </manifest>
			<fileset dir="${lib.dir}">
        		<include name="*.jar"/>
      		</fileset>
        </jar>
    </target>	
	<!-- build the seq  analysis jar -->
    <target name="scripture" depends="compile, unpack,copy.props">
        <jar destfile="${dist.dir}scripture.jar" basedir="${build.dir}" compress="true">
           <!-- <classfileset dir="${build.dir}">
                <root classname="${main-class}"/>
            </classfileset>-->
            <manifest>
                <attribute name="Built-By" value="${user.name}" />
                <attribute name="Main-Class" value="nextgen.core.scripture.BuildScriptureCoordinateSpace"/>
            </manifest>
			<fileset dir="${lib.dir}">
        		<include name="*.jar"/>
      		</fileset>
        </jar>
    </target>
	
    <target name="crispr" depends="compile, unpack,copy.props">
        <jar destfile="${dist.dir}crispr.jar" basedir="${build.dir}" compress="true">
           <!-- <classfileset dir="${build.dir}">
                <root classname="${main-class}"/>
            </classfileset>-->
            <manifest>
                <attribute name="Built-By" value="${user.name}" />
                <attribute name="Main-Class" value="nextgen.editing.CRISPRDesigner"/>
            </manifest>
			<fileset dir="${lib.dir}">
        		<include name="*.jar"/>
      		</fileset>
        </jar>
    </target>
	
	
	<!-- build the seq  analysis jar -->
    <target name="dge" depends="compile, unpack,copy.props">
        <jar destfile="${dist.dir}dge.jar" basedir="${build.dir}" compress="true">
           <!-- <classfileset dir="${build.dir}">
                <root classname="${main-class}"/>
            </classfileset>-->
            <manifest>
                <attribute name="Built-By" value="${user.name}" />
                <attribute name="Main-Class" value="broad.pda.geneexpression.dge.DGE"/>
            </manifest>
			<fileset dir="${lib.dir}">
        		<include name="*.jar"/>
      		</fileset>
        </jar>
    </target>
	
	<target name="pipeline" depends="compile,unpack,copy.props">
        <jar destfile="${dist.dir}pipeline.jar" basedir="${build.dir}" compress="true">
           <!-- <classfileset dir="${build.dir}">
                <root classname="${main-class}"/>
            </classfileset>-->
            <manifest>
                <attribute name="Built-By" value="${user.name}" />
                <attribute name="Main-Class" value="broad.core.util.PipelineAutomator"/>
            </manifest>
     		<fileset dir="${lib.dir}">
             	<include name="*.jar"/>
           	</fileset>
        </jar>
	</target>
	
	
    <target name="alnutils" depends="compile, unpack,copy.props">
        <jar destfile="${dist.dir}alnutils.jar" basedir="${build.dir}" compress="true">
           <!-- <classfileset dir="${build.dir}">
                <root classname="${main-class}"/>
            </classfileset>-->
            <manifest>
                <attribute name="Built-By" value="${user.name}" />
                <attribute name="Main-Class" value="broad.pda.seq.alignment.AlignmentUtils"/>
            </manifest>
			<fileset dir="${lib.dir}">
        		<include name="*.jar"/>
      		</fileset>
        </jar>
    </target>
	
    <target name="scripturelite" depends="compile">
        <jar destfile="${dist.dir}scripturelite.jar" basedir="${build.dir}" compress="true">
           <!-- <classfileset dir="${build.dir}">
                <root classname="${main-class}"/>
            </classfileset>-->
            <manifest>
                <attribute name="Built-By" value="${user.name}" />
                <attribute name="Main-Class" value="broad.pda.seq.segmentation.ContinuousDataAlignmentModel"/>
            </manifest>
        </jar>
    </target>
	
	<!-- build the seq  analysis jar -->
    <target name="qpcr" depends="compile, unpack">
        <jar destfile="${dist.dir}qpcr.jar" basedir="${build.dir}" compress="true">
           <!-- <classfileset dir="${build.dir}">
                <root classname="${main-class}"/>
            </classfileset>-->
            <manifest>
                <attribute name="Built-By" value="${user.name}" />
                <attribute name="Main-Class" value="broad.pda.rnaseq.expression.DigitalExpressionPrimerDesigner"/>
            </manifest>
			<fileset dir="${lib.dir}">
        		<include name="*.jar"/>
      		</fileset>
        </jar>
    </target>
	
		<!-- build the seq  analysis jar -->
    <target name="build_blat_tools" depends="compile, unpack">
        <jar destfile="${dist.dir}blat.jar" basedir="${build.dir}" compress="true">
           <!-- <classfileset dir="${build.dir}">
                <root classname="${main-class}"/>
            </classfileset>-->
            <manifest>
                <attribute name="Built-By" value="${user.name}" />
                <attribute name="Main-Class" value="broad.pda.blat.PSLXToSAM"/>
            </manifest>
			<fileset dir="${lib.dir}">
        		<include name="*.jar"/>
      		</fileset>
        </jar>
    </target>
	
    <target name="alncounter" depends="compile, unpack">
        <jar destfile="${dist.dir}alncounter.jar" basedir="${build.dir}" compress="true">
           <!-- <classfileset dir="${build.dir}">
                <root classname="${main-class}"/>
            </classfileset>-->
            <manifest>
                <attribute name="Built-By" value="${user.name}" />
                <attribute name="Main-Class" value="broad.pda.seq.alignment.SlideAndCount"/>
            </manifest>
			<fileset dir="${lib.dir}">
        		<include name="*.jar"/>
      		</fileset>
        </jar>
    </target>
	
	<!-- build the gene tools jar -->
    <target name="genetools" depends="compile, unpack">
        <jar destfile="${dist.dir}genetools.jar" basedir="${build.dir}" compress="true">
           <!-- <classfileset dir="${build.dir}">
                <root classname="${main-class}"/>
            </classfileset>-->
            <manifest>
                <attribute name="Built-By" value="${user.name}" />
                <attribute name="Main-Class" value="broad.pda.gene.GeneTools"/>
            </manifest>
			<fileset dir="${lib.dir}">
        		<include name="*.jar"/>
      		</fileset>
        </jar>
    </target>
	
	<!-- build the gene tools jar -->
    <target name="genetoolslite" depends="compile">
        <jar destfile="${dist.dir}genetoolslite.jar" basedir="${build.dir}" compress="true">
           <!-- <classfileset dir="${build.dir}">
                <root classname="${main-class}"/>
            </classfileset>-->
            <manifest>
                <attribute name="Built-By" value="${user.name}" />
                <attribute name="Main-Class" value="broad.pda.gene.GeneTools"/>
            </manifest>
        </jar>
    </target>
	
	<!-- build the annotation tools jar -->
    <target name="annotation" depends="compile, unpack">
        <jar destfile="${dist.dir}annotation.jar" basedir="${build.dir}" compress="true">
           <!-- <classfileset dir="${build.dir}">
                <root classname="${main-class}"/>
            </classfileset>-->
            <manifest>
                <attribute name="Built-By" value="${user.name}" />
                <attribute name="Main-Class" value="broad.core.annotation.AnnotationUtils"/>
            </manifest>
			<fileset dir="${lib.dir}">
        		<include name="*.jar"/>
      		</fileset>
        </jar>
    </target>
	
	<!-- build the annotation tools jar -->
    <target name="rnaseq" depends="compile, unpack">
        <jar destfile="${dist.dir}rnaseqpipe.jar" basedir="${build.dir}" compress="true">
           <!-- <classfileset dir="${build.dir}">
                <root classname="${main-class}"/>
            </classfileset>-->
            <manifest>
                <attribute name="Built-By" value="${user.name}" />
                <attribute name="Main-Class" value="broad.pda.seq.alignment.RNASeqAlignmentPipeline"/>
            </manifest>
			<fileset dir="${lib.dir}">
        		<include name="*.jar"/>
      		</fileset>
        </jar>
    </target>
	
		<!-- build the seq  analysis jar -->
    <target name="nanostring" depends="compile, unpack">
        <jar destfile="${dist.dir}nanostring.jar" basedir="${build.dir}" compress="true">
           <!-- <classfileset dir="${build.dir}">
                <root classname="${main-class}"/>
            </classfileset>-->
            <manifest>
                <attribute name="Built-By" value="${user.name}" />
                <attribute name="Main-Class" value="broad.pda.nanostring.NanostringUtils"/>
            </manifest>
			<fileset dir="${lib.dir}">
        		<include name="*.jar"/>
      		</fileset>
        </jar>
    </target>
	
	<target name="bamextractor" depends="compile, unpack">
        <jar destfile="${dist.dir}bamextractor.jar" basedir="${build.dir}" compress="true">
            <manifest>
                <attribute name="Built-By" value="${user.name}" />
                <attribute name="Main-Class" value="broad.pda.seq.alignment.sam.ExtractRegion"/>
            </manifest>
    		<fileset dir="${lib.dir}">
            	<include name="*.jar"/>
          	</fileset>
        </jar>
	</target>
 
  
    <!-- Clean all generated artifacts -->    
    <target name="clean">
        <delete dir="${build.dir}" />
        <delete dir="${dist.dir}" />
    </target>
    
    <target name="all" depends="clean, build"/>
    
</project>