build.xml

<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<!-- WARNING: Eclipse auto-generated file.
              Any modifications will be overwritten.
              To include a user specific buildfile here, simply create one in the same
              directory with the processing instruction <?eclipse.ant.import?>
              as the first entry and export the buildfile again. -->
<project basedir="." default="build" name="Argo-based-Dynamic-Workflow-Generator">
	<property environment="env"/>
	<property name="debuglevel" value="source,lines,vars"/>
	<property name="target" value="1.8"/>
	<property name="source" value="1.8"/>
	<property name="version" value="1.0"/>
	<property name="build.number" value="1.0"/>
	<property name="bwamem" value="argobwamemtemplate"/>
	<property name="templatespec" value="argoinvokedworkflowheadertemplate"/>
	<property name="workflowspec" value="argoinvokerworkflowheadertemplate"/>
	<property name="markduplicates" value="argomarkduplicatestemplate"/>
	<property name="querynamesort" value="argoquerynamesorttemplate"/>
	<property name="config" value="configurationfile"/>
	<path id="JUnit 5.libraryclasspath">
		<pathelement location="../../../../snap/eclipse/40/plugins/org.junit.jupiter.api_5.4.0.v20190212-2109.jar"/>
		<pathelement location="../../../../snap/eclipse/40/plugins/org.junit.jupiter.engine_5.4.0.v20190212-2109.jar"/>
		<pathelement location="../../../../snap/eclipse/40/plugins/org.junit.jupiter.migrationsupport_5.4.0.v20190212-2109.jar"/>
		<pathelement location="../../../../snap/eclipse/40/plugins/org.junit.jupiter.params_5.4.0.v20190212-2109.jar"/>
		<pathelement location="../../../../snap/eclipse/40/plugins/org.junit.platform.commons_1.4.0.v20190212-2109.jar"/>
		<pathelement location="../../../../snap/eclipse/40/plugins/org.junit.platform.engine_1.4.0.v20190212-2109.jar"/>
		<pathelement location="../../../../snap/eclipse/40/plugins/org.junit.platform.launcher_1.4.0.v20190212-2109.jar"/>
		<pathelement location="../../../../snap/eclipse/40/plugins/org.junit.platform.runner_1.4.0.v20190212-2109.jar"/>
		<pathelement location="../../../../snap/eclipse/40/plugins/org.junit.platform.suite.api_1.4.0.v20190212-2109.jar"/>
		<pathelement location="../../../../snap/eclipse/40/plugins/org.junit.vintage.engine_5.4.0.v20190212-2109.jar"/>
		<pathelement location="../../../../snap/eclipse/40/plugins/org.opentest4j_1.1.1.v20190212-2109.jar"/>
		<pathelement location="../../../../snap/eclipse/40/plugins/org.apiguardian_1.0.0.v20190212-2109.jar"/>
		<pathelement location="../../../../snap/eclipse/40/plugins/org.junit_4.12.0.v201504281640/junit.jar"/>
		<pathelement location="../../../../snap/eclipse/40/plugins/org.hamcrest.core_1.3.0.v20180420-1519.jar"/>
	</path>
	<path id="Argo-based-Dynamic-Workflow-Generator.classpath">
		<pathelement location="bin"/>
		<pathelement location="lib/commons-io-2.6/commons-io-2.6.jar"/>
		<path refid="JUnit 5.libraryclasspath"/>
		<pathelement location="argobwamemtemplate"/>
		<pathelement location="argoinvokedworkflowheadertemplate"/>
		<pathelement location="argoinvokerworkflowheadertemplate"/>
		<pathelement location="argomarkduplicatestemplate"/>
		<pathelement location="argoquerynamesorttemplate"/>
		<pathelement location="configurationfile"/>
	</path>
	<target name="init">
		<mkdir dir="bin"/>
		<copy includeemptydirs="false" todir="bin">
			<fileset dir="src">
				<exclude name="**/*.java"/>
			</fileset>
		</copy>
	</target>
	<target name="clean">
		<delete dir="bin"/>
	</target>
	<target depends="clean" name="cleanall"/>
	<target depends="build-subprojects,build-project" name="build"/>
	<target name="build-subprojects"/>
	<target depends="init" name="build-project">
		<echo message="${ant.project.name}: ${ant.file}"/>
		<javac debug="true" debuglevel="${debuglevel}" destdir="bin" includeantruntime="false" source="${source}" target="${target}">
			<src path="src"/>
			<classpath refid="Argo-based-Dynamic-Workflow-Generator.classpath"/>
		</javac>
	</target>
    <target name="jar">
        <mkdir dir="jar"/>
        <jar destfile="jar/ArgoDynamicWorkflowGenerator.jar" basedir="bin">
            <manifest>
                <attribute name="Main-Class" value="argoconfigurationfilereader.ArgoConfigurationFileBwaMem"/>
            </manifest>
        <!--	<zipgroupfileset dir="${bwamem}" includes="**/*.yaml"/> 
        	<zipgroupfileset dir="${config}" includes="**/*.config"/> 
        	<zipgroupfileset dir="${templatespec}" includes="**/*.yaml"/>
        	<zipgroupfileset dir="${workflowspec}" includes="**/*.yaml"/>
        	<zipgroupfileset dir="${markduplicates}" includes="**/*.yaml"/>
        	<zipgroupfileset dir="${querynamesort}" includes="**/*.yaml"/> -->
        </jar>
    </target>
	<target description="Build all projects which reference this project. Useful to propagate changes." name="build-refprojects"/>
	<target description="copy Eclipse compiler jars to ant lib directory" name="init-eclipse-compiler">
		<copy todir="${ant.library.dir}">
			<fileset dir="${ECLIPSE_HOME}/plugins" includes="org.eclipse.jdt.core_*.jar"/>
		</copy>
		<unzip dest="${ant.library.dir}">
			<patternset includes="jdtCompilerAdapter.jar"/>
			<fileset dir="${ECLIPSE_HOME}/plugins" includes="org.eclipse.jdt.core_*.jar"/>
		</unzip>
	</target>
	<target description="compile project with Eclipse compiler" name="build-eclipse-compiler">
		<property name="build.compiler" value="org.eclipse.jdt.core.JDTCompilerAdapter"/>
		<antcall target="build"/>
	</target>
	<target name="ArgoConfigurationFileBwaMem">
		<java classname="argoconfigurationfilereader.ArgoConfigurationFileBwaMem" failonerror="true" fork="yes">
			<classpath refid="Argo-based-Dynamic-Workflow-Generator.classpath"/>
		</java>
	</target>
	<target name="ArgoConfigurationFileBase">
		<java classname="argoconfigurationfilereader.ArgoConfigurationFileBase" failonerror="true" fork="yes">
			<classpath refid="Argo-based-Dynamic-Workflow-Generator.classpath"/>
		</java>
	</target>
</project>