build.xml

<project name="maltools" default="hello" basedir=".">

<property file="${basedir}/project.properties"/>
<property file="${basedir}/build.properties"/>


<!-- Unmodifable properties (unless you know what you are doing) -->

<property name="source.dir" value="${basedir}/src" />
<property name="source.cpp.dir" value="${source.dir}/cpp" />
<property name="source.java.dir" value="${source.dir}/java" />
<property name="source.perl.dir" value="${source.dir}/perl" />
<property name="resources.dir" value="${basedir}/resources" />
<property name="installer.dir" value="${basedir}/installer" />
<property name="conf.dir" value="${basedir}/conf" />
<property name="debug" value="off" />

<!-- tools && macros -->

<property name="tools.dir" value="${basedir}/tools" />
<property name="svn-get.exec" value="${tools.dir}/svn-get" />
<property name="git-get.exec" value="${tools.dir}/git-get" />
<property name="svn.exec" value="svn" />

<macrodef name="git-get">
  <attribute name="url" default=""/>
  <attribute name="dir" default=""/>
  <attribute name="branch" default="DEFAULT"/>
  <attribute name="commit" default="DEFAULT"/>
  <attribute name="patch" default="NONE"/>
  <sequential>
    <exec executable="${git-get.exec}" failonerror="true">
      <arg line="-c @{commit}" />
      <arg line="-b @{branch}" />
      <arg line="-p @{patch}" />
      <arg line="-pm .patch_applied" />
      <arg line="-bm .built" />
      <arg value="@{url}" />
      <arg value="@{dir}" />
    </exec>   
  </sequential>
</macrodef>

<macrodef name="svn-info">
  <attribute name="output" default="/dev/stdout"/>
  <attribute name="url" default="${basedir}"/>
  <sequential>
    <exec executable="${svn.exec}" failonerror="true" output="@{output}">
      <arg value="info" />
      <arg value="@{url}" />
    </exec>
  </sequential>
</macrodef>

<macrodef name="svn-get">
  <attribute name="url" default=""/>
  <attribute name="dir" default=""/>
  <attribute name="revision" default="HEAD"   />
  <sequential>
    <exec executable="${svn-get.exec}" failonerror="true">
      <arg line="-r @{revision}" />
      <arg value="@{url}"/>
      <arg value="@{dir}"/>
    </exec>
  </sequential>
</macrodef>

<macrodef name="make">
 <attribute name="dir" default="${basedir}"/>
 <attribute name="target" default="all" />
 <element name="options" optional="true" />
 <sequential>
   <exec dir="@{dir}" executable="${make.exec}" failonerror="true">
     <options/> 
     <arg line="@{target}" />
   </exec>
 </sequential>
</macrodef>

<macrodef name="cpan">
  <element name="packages" optional="false"/>
  <sequential>
    <exec executable="${cpan.exec}" failonerror="true">
      <packages/>
    </exec>
  </sequential>
</macrodef>

<!-- main targets -->

<target name="hello">
  <echo>
    Welcome to ${project.name} ${project.version}.

    Through this ANT build you should able to perform some set-up task
    to get the system work locally. 

    Peferably you should use the install 'install' target to customize and install the live system  

    ${user.name}@${basedir}$ ant install
  </echo>
</target>


<target name="eclipse.setup">
  <get src="http://mirror.lividpenguin.com/pub/apache//commons/math/source/commons-math-2.2-src.zip" dest="${3rdparty.dir}/commons-math-2.2-src.zip" />
</target>

<target name="install.config" unless="install.config">
   <input message="Select base command and configuration name"
          addproperty="install.name"
          defaultvalue="${install.name.default}" />

   <condition property="install.name.fail">
     <not>
       <available file="${conf.dir}/${install.name}.json" />
     </not>
   </condition>
   <fail if="install.name.fail">There is no configuration file available as ${conf.dir}/${install.name}.json for '${install.name}'</fail>
   <input message="Installation root directory?" 
          addproperty="install.dir" 
          defaultvalue="${install.dir.default}" />
   <property name="install.config" value="${install.config.default}" />
   <propertyfile file="${install.config}">
     <entry key="install.dir" value="${install.dir}" />
     <entry key="install.name" value="${install.name}" />
   </propertyfile>
</target>

<target name="init">
 <mkdir dir="${build.dir}" />
 <mkdir dir="${3rdparty.dir}" />
</target>

<target name="ivy.init" depends="init">
  <get src="${ivy.url}" dest="${ivy.jar}" usetimestamp="true" />
  <path id="ivy.classpath">
    <pathelement location="${ivy.jar}" />
  </path>
  <taskdef resource="org/apache/ivy/ant/antlib.xml" uri="antlib:org.apache.ivy.ant" classpathref="ivy.classpath"/>
  <taskdef name="ivy-retrieve" classname="org.apache.ivy.ant.IvyRetrieve"/>
  <taskdef name="ivy-cachepath" classname="org.apache.ivy.ant.IvyCachePath"/>
</target>

<target name="test.init" depends="ivy.init">
  <ivy-retrieve conf="test"/>
  <ivy-cachepath pathid="ivy.cachepath.test" conf="test" type="jar" />
  <taskdef name="junit" classname="org.apache.tools.ant.taskdefs.optional.junit.JUnitTask" classpathref="ivy.cachepath.test" />
</target>

<target name="samtools.init" depends="init">
  <svn-get url="${samtools.url}" dir="${samtools.dir}" revision="${samtools.rev}" />
  <make dir="${samtools.dir}/samtools" target="all" /> 
  <make dir="${samtools.dir}/samtools/bcftools" target="all" />
</target>

<target name="bwa.init" depends="init">
  <svn-get url="${bwa.url}" dir="${bwa.dir}" revision="${bwa.rev}" />
  <make dir="${bwa.dir}" target="all" />
</target>

<target name="picard.init" depends="init">
  <svn-get url="${picard.url}" dir="${picard.dir}" revision="${picard.rev}" />
  <exec executable="ant" failifexecutionfails="true" dir="${picard.dir}">
    <arg line="-lib lib/ant"/>
    <arg value="package-commands"/>
  </exec>
</target>


<target name="vcftools.init" depends="init">
  <svn-get url="${vcftools.url}" dir="${vcftools.dir}" revision="${vcftools.rev}" />
</target>


<target name="samtrak.init" depends="init">
  <svn-get url="${samtrak.url}" dir="${samtrak.dir}" revision="${samtrak.rev}" />
</target>


<target name="build" depends="cpp.build,java.build" />

<!-- cpp targets -->

<target name="cpp.init" depends="init, samtools.init">
</target>

<target name="cpp.build" depends="cpp.init, bwa.init">
 <mkdir dir="${build.cpp.dir}" />
 <mkdir dir="${build.cpp.dir}/obj" />
 <mkdir dir="${build.cpp.dir}/bin" />
 <make dir="${source.cpp.dir}" target="all" >
   <options>
     <env key="OBJDIR" value="${build.cpp.dir}/obj" />
     <env key="BINDIR" value="${build.cpp.dir}/bin" />
     <env key="SRCDIR" value="${source.cpp.dir}" />
     <env key="SAMTOOLS_DIR" value="${samtools.dir}" />
     <env key="CPP" value="g++" />
   </options>
 </make>
</target>

<!-- java targets -->

<path id="gatk.classpath">
  <fileset dir="${gatk.dir}/dist/">
    <include name="**/*.jar"/>
    <exclude name="**/malariagen.jar"/>
  </fileset>
</path>

<target name="gatk.get" depends="init">
  <git-get url="${gatk.url}" dir="${gatk.dir}" commit="${gatk.commit}" branch="${gatk.branch}" patch="${gatk.patch}" />
  <condition property="gatk.patched">
   <or> 
     <available file="${gatk.dir}/.patch_applied" property="${gatk.patched}" />
     <equals arg1="${gatk.patch}" arg2="NONE" />
   </or>
  </condition>
  <fail message="Gatk was not patched (missing ${gatk.dir}/.patch_applied)" unless="gatk.patched"/>
  <available file="${gatk.dir}/.built" property="${gatk.built}" />
</target>

<target name="gatk.build" depends="gatk.get" unless="${gatk.built}">
  <ant dir="${gatk.dir}" target="core" inheritAll="false" />
  <touch file="${gatk.dir}/.built"/>
</target>

<target name="gatk.init" depends="gatk.build" />


<target name="java.init" depends="gatk.init,ivy.init">
  <mkdir dir="${build.java.dir}" />
  <mkdir dir="${build.java.dir}/classes" />
  <mkdir dir="${build.java.dir}/jars" />
  <ivy-retrieve conf="devel"/>
  <uptodate property="malariagen.jar.utd" targetfile="${build.java.dir}/jars/malariagen.jar">
    <srcfiles dir="${source.java.dir}/main" includes="**/*.java"/>
    <srcfiles dir="${gatk.dir}/dist" includes="**/*.jar"/>
  </uptodate>
</target>



<target name="malariagen.jar" depends="java.init" unless="malariagen.jar.utd">
  <javac srcdir="${source.java.dir}/main" debug="${debug}" destdir="${build.java.dir}/classes" classpathref="gatk.classpath" includeantruntime="false" />
  <jar basedir="${build.java.dir}/classes" destfile="${build.java.dir}/jars/malariagen.jar" />
</target>

<target name="java.lib" depends="malariagen.jar">
  <copy todir="${build.java.dir}/lib" preservelastmodified="true">
    <fileset dir="${gatk.dir}/lib" includes="**/*.jar" />
    <fileset dir="${build.java.dir}/jars" includes="malariagen.jar" />
  </copy>
  <uptodate property="Queue.jar.utd" targetfile="${build.java.dir}/dist/Queue.jar">
    <srcfiles dir="${build.java.dir}/lib" includes="**/*.jar"/>
  </uptodate>
</target>

<target name="java.build" depends="java.lib" unless="Queue.jar.utd" >
  <mkdir dir="${build.java.dir}/dist" />
  <ant dir="${gatk.dir}" target="core" inheritAll="false">
    <property name="lib.dir" value="${build.java.dir}/lib" />
    <property name="dist.dir" value="${build.java.dir}/dist" />
  </ant>
</target>

<target name="java.test.build" depends="java.lib, test.init">
  <mkdir dir="${build.java.dir}/test-classes" />
  <javac srcdir="${source.java.dir}/main" destdir="${build.java.dir}/test-classes" includeantruntime="false" debug="true">
    <classpath refid="gatk.classpath" />
    <classpath refid="ivy.cachepath.test" />
    <classpath>
      <pathelement location="${build.java.dir}/classes" />
    </classpath>
  </javac> 
</target>


<target name="java.test" depends="java.test.build, test.init">
  <mkdir dir="${build.java.dir}/test-reports" />
  <junit>
    <classpath refid="gatk.classpath" />
    <classpath refid="ivy.cachepath.test" />
    <classpath>
       <pathelement location="${build.java.dir}/test-classes" />
       <pathelement location="${build.java.dir}/classes" />
    </classpath>
    <batchtest haltonerror="true" todir="${build.java.dir}/test-report" >
       <fileset	dir="${source.java.dir}/test"> 
         <include name="**/*Test.java" />
         <exclude name="**/BaseTest.java" />
         <exclude name="**/WalkerTest.java" />
       </fileset>
    </batchtest>
  </junit> 
</target>

<target name="install-devel">
  <antcall target="dist.layout">
    <param name="dist.layout.dir" value="${dist.dir}/layout-devel" />
    <param name="install.config" value="${resources.dir}/devel.config" />
    <param file="${resources.dir}/devel.config" />
  </antcall>
</target>

<target name="svn-info">
  <svn-info output="myass"/>
</target>

<target name="dist.layout" depends="build,samtrak.init,vcftools.init,picard.init">
  <mkdir dir="${dist.layout.dir}/bin" />
  <mkdir dir="${dist.layout.dir}/lib/java" />
  <mkdir dir="${dist.layout.dir}/lib/perl" />
  <mkdir dir="${dist.layout.dir}/resources" />

  <copy todir="${dist.layout.dir}/bin">
    <fileset dir="${resources.dir}/scripts" />
    <filterset filtersfile="${install.config}" />
  </copy>

  <copy todir="${dist.layout.dir}/bin">
     <fileset dir="${build.cpp.dir}/bin" />
     <fileset dir="${source.perl.dir}/scripts" />
  </copy>
  <copy todir="${dist.layout.dir}/bin" flatten="true">
     <fileset dir="${samtools.dir}">
       <include name="**/samtools/samtools" />
       <include name="**/samtools/bcftools/bcftools" />
       <include name="**/samtools.pl" />
       <include name="**/vcfutils.pl" />
     </fileset>
     <fileset dir="${bwa.dir}" includes="**/bwa" />
  </copy>
  <!--svn-info output="${dist.layout.dir}/svn-info.txt" /-->

  <move file="${dist.layout.dir}/bin/base" tofile="${dist.layout.dir}/bin/${install.name}" />

  <copy todir="${dist.layout.dir}/lib/java">
     <fileset dir="${build.java.dir}/dist" />
  </copy>

  <copy todir="${dist.layout.dir}/lib/java/picard-commands">
     <fileset dir="${picard.dir}/dist" includes="**/*.jar" />
  </copy>

  <copy todir="${dist.layout.dir}/lib/perl">
     <fileset dir="${vcftools.dir}/perl" includes="**/*.pm" />
     <fileset dir="${samtrak.dir}/modules" />
     <fileset dir="${source.perl.dir}/modules" />
  </copy>

  <copy todir="${dist.layout.dir}/lib/perl" flatten="true">
     <fileset dir="${resources.dir}/pgv_pipeline/variation_filtering2">
       <include name="**/Variation.pm" />
       <include name="**/gff2json.pm" />
     </fileset>
  </copy>

  <copy todir="${dist.layout.dir}/resources">
     <fileset dir="${resources.dir}" >
       <exclude name="**/test/**" />
       <exclude name="**/scripts/**" />
       <exclude name="**/*.bam*" />
       <exclude name="**/*.vcf*" />
       <exclude name="**/*.fa*" />
     </fileset>
  </copy>
  
  <copy todir="${dist.layout.dir}/resources/gatk/R">
     <fileset dir="${gatk.dir}/public/R" />
  </copy>

  <copy todir="${dist.layout.dir}/conf">
     <fileset dir="${conf.dir}" />
     <filterset filtersfile="${install.config}" />
  </copy>
  <chmod perm="a+rx" type="file" dir="${dist.layout.dir}/bin" includes="**/*" />
  <chmod perm="a+rx" type="file" dir="${dist.layout.dir}/resources/pgv_pipeline/variation_filtering2" includes="**/*.pl" />
</target>

<target name="install" depends="install.config,dist.layout">
  <fail message="Cannot find install configuration ${install.config}">
    <condition>
      <not>
        <available file="${install.config}" type="file" />
      </not>
    </condition>
  </fail>
  <property file="${install.config}" />
  <fail message="Installation directory not specified in configuration" unless="install.dir" />
  <mkdir dir="${install.dir}" />
  <copy todir="${install.dir}"> 
    <fileset dir="${dist.layout.dir}" />
  </copy>
  <chmod perm="a+rx" type="file" dir="${install.dir}/bin" includes="**/*" />
  <chmod perm="a+rx" type="file" dir="${install.dir}/resources/pgv_pipeline/variation_filtering2" includes="**/*.pl" />
</target>
	
<target name="java.clean">
	<delete dir="${build.java.dir}" />
</target>
	
<target name="dist.clean">
    <delete dir="${dist.dir}" />
</target>
	
<target name="dist.layout.clean">
    <delete dir="${dist.layout.dir}" />
</target>
	
<target name="clean" depends="java.clean,dist.layout.clean">
</target>

</project>