build.xml

<project xmlns:ivy="antlib:org.apache.ivy.ant" name="genome-de-novo" default="first-build" basedir=".">
    <property name="VERSION" value="1.6.1"/>
    <tstamp>
        <format property="TODAY" pattern="dd-MMM-yyyy" locale="en"/>
    </tstamp>
    <tstamp>
        <format property="TODAY_TS" pattern="dd-MMM-yyyy HH:mm" locale="en"/>
    </tstamp>

    <property name="lib.dir" value="lib"/>
    <property name="ant.build.javac.source" value="1.7"/>
    <property name="ant.build.javac.target" value="1.7"/>

    <condition property="dist.version.suffix" value="-b${build.number}" else="">
        <isset property="build.number"/>
    </condition>


    <!-- Determine build version -->
    <exec executable="git" outputproperty="revision">
        <arg value="rev-parse"/>
        <arg value="--short"/>
        <arg value="HEAD"/>
    </exec>
    <exec executable="git" outputproperty="changes">
        <arg value="status"/>
        <arg value="-s"/>
        <arg value="-uno"/>
    </exec>

    <condition property="dist.version" 
            value="${VERSION} (revision ${revision}, ${TODAY})"
            else ="${VERSION} (revision ${revision}+ changes, ${TODAY_TS})" >
        <equals arg1="${changes}" arg2=""/>
    </condition>

    <echo message="${dist.version}" file="VERSION"/>
    <echo message="Version: ${dist.version}"/>


    <property name="dist.base.name" value="dist/itmo-assembler${dist.version.suffix}"/>

    <property name="dist.jar.name" value="${dist.base.name}.jar"/>
    <property name="dist.sh.name" value="${dist.base.name}.sh"/>
    <property name="dist.bat.name" value="${dist.base.name}.bat"/>
    <property name="dist.src.name" value="${dist.base.name}-src.jar"/>

    <path id="class.path">
        <fileset dir="lib/dev">
            <include name="**/*.jar" />
        </fileset>
    </path>
    <target name="first-build" depends="ivy.bootstrap,resolve,compile"/>


    <target name="compile">
        <mkdir dir="bin"/>
        <mkdir dir="bin/java"/>
        <javac srcdir="src/java" destdir="bin/java" debug="on">
            <classpath refid="class.path"/>
            <compilerarg value="-Xlint"/>
            <compilerarg line="-encoding utf-8"/>
        </javac>
        <exec executable="sh" failonerror="true">
            <arg value="./find_tools.sh"/>
        </exec>
    </target>

    <target name="clean">
        <delete failonerror="false" includeemptydirs="true">
            <fileset dir="bin/java"/>
            <fileset dir="bin/hadoop"/>
            <fileset dir="bin/dependencies"/>
            <fileset dir="bin/java-test"/>
        </delete>
    </target>

    <target name="resolve" description="--> retrieve dependencies with ivy">
        <taskdef resource="org/apache/ivy/ant/antlib.xml" uri="antlib:org.apache.ivy.ant" classpath="${ivy.home}/${ivy.jar.name}"/>
        <ivy:retrieve sync="true" pattern="${lib.dir}/[conf]/[artifact]-[revision](-[classifier]).[ext]" symlink="true"/>
    </target>

    <target name="clean-libs" description="--> clean libs">
        <echo message="Deleting lib dir" />
        <delete dir="${lib.dir}" />  
    </target>

    <target name="report">
        <mkdir dir="report" />
        <ivy:resolve type="${ivy.resolve.types}"/>
        <ivy:report todir="report" />
    </target>

  <property name="ivy.jar.version" value="2.5.0"/>
  <property name="ivy.jar.name" value="ivy-${ivy.jar.version}.jar"/>
  <property name="ivy.home" value="${user.home}/.ivy2"/>
  <available property="ivy.installed" file="${ivy.home}/${ivy.jar.name}"/>

 
  <target name="ivy.install" unless="ivy.installed">
    <mkdir dir="${ivy.home}"/>
    <get src="https://repo1.maven.org/maven2/org/apache/ivy/ivy/${ivy.jar.version}/${ivy.jar.name}" dest="${ivy.home}/${ivy.jar.name}"/>
  </target>
 

  <target name="ivy.bootstrap" depends="ivy.install" unless="ivy.bootstrapped">
    <taskdef resource="org/apache/ivy/ant/antlib.xml" uri="antlib:org.apache.ivy.ant" classpath="${ivy.home}/${ivy.jar.name}"/>
    <property name="ivy.bootstrapped" value="true"/> <!-- Avoid re-bootstrapping because it causes classloader issues. -->
  </target>

  
  <target name="compile-tests" depends="compile">
      <mkdir dir="bin"/>
      <mkdir dir="bin/java-test"/>
      <javac srcdir="test/java" destdir="bin/java-test" debug="on">
          <classpath>
              <path refid="class.path"/>
              <pathelement path="bin/java"/>
          </classpath>
          <compilerarg value="-Xlint"/>
      </javac>
  </target>

  <target name="test" depends="compile-tests">
      <mkdir dir="test-report" />
      <junit printsummary="yes" haltonfailure="no">
          <classpath>
              <pathelement path="bin/java-test/"/>
              <pathelement path="bin/java/"/>
              <path refid="class.path"/>
          </classpath>
          <formatter type="xml"/>
          <batchtest fork="yes" todir="./test-report">
              <fileset dir="./test/java">
                  <include name="**/*Test.java"/>
              </fileset>
          </batchtest>
      </junit>
  </target>

  <target name="package-prepare" depends="clean,resolve,compile">
      <mkdir dir="bin/dependencies"/>
      <unjar dest="bin/dependencies">
          <fileset dir="lib/standalone" includes="**/*.jar"/>
      </unjar>
      <delete dir="bin/dependencies/it/unimi/dsi/fastutil/chars"/>
      <delete dir="bin/dependencies/it/unimi/dsi/fastutil/doubles"/>
      <delete dir="bin/dependencies/it/unimi/dsi/fastutil/floats"/>
      <delete dir="bin/dependencies/it/unimi/dsi/fastutil/shorts"/>
  </target>

  <target name="hadoop" depends="package">
  </target>

  <target name="package-build">
      <mkdir dir="dist"/>

      <jar destfile="${dist.jar.name}" duplicate="preserve">
          <fileset dir="bin/java"/>
          <fileset file="log4j.properties"/>
          <fileset dir="bin/dependencies"/>
          <fileset dir="stuff" includes="images/*"/>
          <fileset file="COPYING"/>
          <fileset file="VERSION"/>
          <fileset file="TOOLS"/>
          <fileset file="config.properties"/> <!-- for hadoop -->
          <manifest>
              <attribute name="Main-Class"
                  value="ru.ifmo.genetics.Runner"/>
          </manifest>
      </jar>

      <concat destfile="${dist.sh.name}" binary="true">
          <filelist files="src/stub.sh,${dist.jar.name}"/>
      </concat> 
      <chmod file="${dist.sh.name}" perm="a+x"/>

      <concat destfile="${dist.bat.name}" binary="true">
          <filelist files="src/stub.bat,${dist.jar.name}"/>
      </concat>

      <jar destfile="${dist.src.name}">
          <fileset dir="src/java" includes="**/*.java"/>
          <fileset file="log4j.properties"/>
          <fileset file="COPYING"/>
          <fileset file="VERSION"/>
          <fileset file="TOOLS"/>
          <fileset file="config.properties"/> <!-- for hadoop -->
      </jar>
  </target>


  <target name="package" depends="package-prepare,package-build">
  </target>

</project>