build.xml

<?xml version="1.0"?>
<project name="cegr-tools">

  	<property name="src.dir" location="src" />	
  	<property name="lib.dir" location="lib" />
  	<property name="build.dir" location="build" />
  	<property name="build.classes.dir" location="${build.dir}/classes" />
  	<property name="build.dist.dir" location="${build.dir}/dist" />
  	<property name="build.unjar.dir" location="${build.dir}/unjar" />
  
	<path id="compile.classpath">
    <pathelement location="${build.classes.dir}"/>
 		<fileset dir="${lib.dir}">
        	<include name="**/*.jar"/>
      	</fileset>
  	</path>	

	<!-- ======================================================================= -->
	<!-- Target: init                                                            -->
	<!-- Depends:                                                                -->
	<!-- Description: Perform any initialization required to run other targets   -->
	<!-- ======================================================================= -->
	<target name="init">
		<mkdir dir="${build.classes.dir}" />
	    <mkdir dir="${build.dist.dir}" />
	</target>

	<!-- ======================================================================= -->
	<!-- Target: clean                                                           -->
	<!-- Depends: init                                                           -->
	<!-- Description: clean up files produced in the build                       -->
	<!-- ======================================================================= -->
	<target name="clean" depends="init" description="remove build output" >
		<delete dir="${build.dist.dir}"  failonerror="false"/>
		<delete dir="${build.classes.dir}"  failonerror="false"/>
		<delete dir="${build.unjar.dir}"  failonerror="false"/>
	</target>
	
	<!-- ======================================================================= -->
	<!-- Target: compile                                                         -->
	<!-- Depends: init                                                           -->
	<!-- Description: Compile the source code                                    -->
	<!-- ======================================================================= -->
	<target name="compile" depends="init" description="Compile the code" >
		<javac srcdir="${src.dir}"
			destdir="${build.classes.dir}"	
			classpathref="compile.classpath"
			debug="true"
			debuglevel="lines,vars,source"
			deprecation="yes"
			compiler="modern"
			verbose="no">		  
			<include name="**/*.java"/>
		</javac>
	</target>
	
	<!-- ======================================================================= -->
	<!-- Target: buildfilecopy                                                   -->
	<!-- Depends: init                                                           -->
	<!-- Description: Copies all non-source files required by utils              -->
	<!--              from the src directory to the build directory              -->
	<!-- ======================================================================= -->
	<target name="buildfilecopy" depends="init" description="Copy non-src files to the build dir" >
		<copy todir="${build.classes.dir}">
			<fileset dir="${src.dir}">
				<include name="**/*.gif"/>
				<include name="**/*.html"/>
				<include name="**/*.jpg"/>
				<include name="**/*.xml"/>
				<include name="**/*.txt"/>
				<include name="**/*.dtd"/>
				<include name="**/*.bat"/>
				<include name="**/*.exe"/>
				<include name="**/*.ico"/>
				<include name="**/*.png"/>
				<include name="**/*.properties"/>
			</fileset>
		</copy>
	</target>

	<!-- ======================================================================= -->
	<!-- Target: build                                                           -->
	<!-- Depends: compile, buildfilecopy                                         -->
	<!-- Description: Compiles all the client source files and copies other      -->
	<!--              required files to the build directory to create a usable   -->
	<!--              version of the utils module                                -->
	<!-- ======================================================================= -->
	<target name="build" depends="compile, buildfilecopy"
		description="build and copy files" >
	</target>
	
	
	<!-- ======================================================================= -->
	<!-- Targets: unjar*                                                         -->
	<!-- Description: unjars various required libraries					         -->
	<!-- ======================================================================= -->
	<target name="unjarall" depends="unjarpicard, unjarjfreechart"
		description="unjars all external libraries">
	</target>
	<target name="unjarpicard"
		description="unjars picard libraries">
	    <mkdir dir="${build.unjar.dir}.tmp" />
	    <unjar dest="${build.unjar.dir}.tmp">
	      <fileset dir="${lib.dir}">
			<include name="picard/**/*.jar"/>
	      </fileset>
	    </unjar>
	    <move file="${build.unjar.dir}.tmp" tofile="${build.unjar.dir}/picard" />
 	</target>
	<target name="unjarjfreechart"
		description="unjars jfreechart libraries">
	    <mkdir dir="${build.unjar.dir}.tmp" />
	    <unjar dest="${build.unjar.dir}.tmp">
	      <fileset dir="${lib.dir}">
			<include name="jfreechart/**/*.jar"/>
	      </fileset>
	    </unjar>
	    <move file="${build.unjar.dir}.tmp" tofile="${build.unjar.dir}/jfreechart" />
 	</target>
	
	<!-- ======================================================================= -->
	<!-- Target: makealljars                                                     -->
	<!-- Description: Makes all executable jar files                             -->
	<!-- ======================================================================= -->
	<target name="makealljars" depends="makebamtoscidxjar, makefourcolorplotjar, makepairedendcrossplotjar, 
					makepehistogramjar, maketagpileupjar, makefilterforpipseqjar"
					description="make all executable jars" >
	</target>

	<!-- ======================================================================= -->
	<!-- Targets: makefilterforpipseqjar                                         -->
	<!-- Description: make an executable jar for filterforPIPseq			     -->
	<!-- ======================================================================= -->
	<target name="makefilterforpipseqjar" depends="init, build, unjarpicard" 
		description="make an executable jar for filterforPIPseq" >
	    <javac srcdir="${src.dir}"
		   destdir="${build.classes.dir}"	
		   classpathref="compile.classpath"
		   debug="true"
		   debuglevel="lines,vars,source"
		   deprecation="yes"
		   compiler="modern"
		   verbose="no">		  
	      <include name="org/seqcode/cegrtools/filterforPIPseq/*.java"/>
	    </javac>
		<jar destfile="${build.dist.dir}/filterforPIPseq.jar" manifest="manifests/filterforPIPseq_manifest.txt">	    
	      <fileset dir="${src.dir}" includes="**/filterforPIPseq/*.java"/>
	      <fileset dir="${build.classes.dir}" includes="**/filterforPIPseq/*.class"/>
		  <fileset dir="${build.unjar.dir}/picard"/>
	    </jar>  
	    <chmod file="${build.dist.dir}/filterforPIPseq.jar" perm="755"/>
	</target>

	<!-- ======================================================================= -->
	<!-- Targets: makebamtoscidxjar                                              -->
	<!-- Description: make an executable jar for BAMtoscIDX					     -->
	<!-- ======================================================================= -->
	<target name="makebamtoscidxjar" depends="init, build, unjarpicard" 
		description="make an executable jar for BAMtoscIDX" >
	    <javac srcdir="${src.dir}"
		   destdir="${build.classes.dir}"	
		   classpathref="compile.classpath"
		   debug="true"
		   debuglevel="lines,vars,source"
		   deprecation="yes"
		   compiler="modern"
		   verbose="no">		  
	      <include name="org/seqcode/cegrtools/bamtoscidx/**/*.java"/>
	    </javac>
		<jar destfile="${build.dist.dir}/BAMtoscIDX.jar" manifest="manifests/bamtoscidx_manifest.txt">	    
	      <fileset dir="${src.dir}" includes="**/bamtoscidx/*.java"/>
	      <fileset dir="${build.classes.dir}" includes="**/bamtoscidx/*.class"/>
		  <fileset dir="${build.unjar.dir}/picard"/>
	    </jar>  
	    <chmod file="${build.dist.dir}/BAMtoscIDX.jar" perm="755"/>
	</target>
	
	<!-- ======================================================================= -->
	<!-- Targets: makefourcolorplotjar                                              -->
	<!-- Description: make an executable jar for FourColorPlot					     -->
	<!-- ======================================================================= -->
	<target name="makefourcolorplotjar" depends="init, build" 
		description="make an executable jar for FourColorPlot" >
	    <javac srcdir="${src.dir}"
		   destdir="${build.classes.dir}"	
		   classpathref="compile.classpath"
		   debug="true"
		   debuglevel="lines,vars,source"
		   deprecation="yes"
		   compiler="modern"
		   verbose="no">		  
	      <include name="org/seqcode/cegrtools/fourcolorplot/**/*.java"/>
	    </javac>
		<jar destfile="${build.dist.dir}/FourColorPlot.jar" manifest="manifests/fourcolorplot_manifest.txt">	    
	      <fileset dir="${src.dir}" includes="**/fourcolorplot/**/*.java"/>
	      <fileset dir="${build.classes.dir}" includes="**/fourcolorplot/**/*.class"/>
	    </jar>  
	    <chmod file="${build.dist.dir}/FourColorPlot.jar" perm="755"/>
	</target>

	<!-- ======================================================================= -->
	<!-- Targets: makepairedendcrossplotjar                                      -->
	<!-- Description: make an executable jar for PairedendCrossPlot			     -->
	<!-- ======================================================================= -->
	<target name="makepairedendcrossplotjar" depends="init, build" 
		description="make an executable jar for PairedendCrossPlot" >
	    <javac srcdir="${src.dir}"
		   destdir="${build.classes.dir}"	
		   classpathref="compile.classpath"
		   debug="true"
		   debuglevel="lines,vars,source"
		   deprecation="yes"
		   compiler="modern"
		   verbose="no">		  
	      <include name="org/seqcode/cegrtools/pairedendcrossplot/*.java"/>
	    </javac>
		<jar destfile="${build.dist.dir}/PairedendCrossPlot.jar" manifest="manifests/pairedendcrossplot_manifest.txt">	    
	      <fileset dir="${src.dir}" includes="**/pairedendcrossplot/**/*.java"/>
	      <fileset dir="${build.classes.dir}" includes="**/pairedendcrossplot/**/*.class"/>
	    </jar>  
	    <chmod file="${build.dist.dir}/PairedendCrossPlot.jar" perm="755"/>
	</target>

	<!-- ======================================================================= -->
	<!-- Targets: makepehistogramjar                                             -->
	<!-- Description: make an executable jar for PEHistogram				     -->
	<!-- ======================================================================= -->
	<target name="makepehistogramjar" depends="init, build, unjarpicard, unjarjfreechart" 
		description="make an executable jar for PEHistogram" >
	    <javac srcdir="${src.dir}"
		   destdir="${build.classes.dir}"	
		   classpathref="compile.classpath"
		   debug="true"
		   debuglevel="lines,vars,source"
		   deprecation="yes"
		   compiler="modern"
		   verbose="no">		  
	      <include name="org/seqcode/cegrtools/pehistogram/**/*.java"/>
	    </javac>
		<jar destfile="${build.dist.dir}/PEHistogram.jar" manifest="manifests/pehistogram_manifest.txt">	    
	      <fileset dir="${src.dir}" includes="**/pehistogram/**/*.java"/>
	      <fileset dir="${build.classes.dir}" includes="**/pehistogram/**/*.class"/>
		  <fileset dir="${build.unjar.dir}/picard"/>
		  <fileset dir="${build.unjar.dir}/jfreechart"/>
	    </jar>  
	    <chmod file="${build.dist.dir}/PEHistogram.jar" perm="755"/>
	</target>
	
	<!-- ======================================================================= -->
	<!-- Targets: maketagpileupjar                                               -->
	<!-- Description: make an executable jar for TagPileup				     -->
	<!-- ======================================================================= -->
	<target name="maketagpileupjar" depends="init, build, unjarpicard" 
		description="make an executable jar for TagPileup" >
	    <javac srcdir="${src.dir}"
		   destdir="${build.classes.dir}"	
		   classpathref="compile.classpath"
		   debug="true"
		   debuglevel="lines,vars,source"
		   deprecation="yes"
		   compiler="modern"
		   verbose="no">		  
	      <include name="org/seqcode/cegrtools/tagpileup/**/*.java"/>
	    </javac>
		<jar destfile="${build.dist.dir}/TagPileup.jar" manifest="manifests/tagpileup_manifest.txt">	    
	      <fileset dir="${src.dir}" includes="**/tagpileup/**/*.java"/>
	      <fileset dir="${build.classes.dir}" includes="**/tagpileup/**/*.class"/>
		  <fileset dir="${build.unjar.dir}/picard"/>
	    </jar>  
	    <chmod file="${build.dist.dir}/TagPileup.jar" perm="755"/>
	</target>
	
	
</project>