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build.xml
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build.xml
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<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<project basedir="." default="build" name="Medusa">
<property name="target" value="1.8"/>
<property name="source" value="1.8"/>
<path id="libs">
<pathelement location="lib/biojava3-core-3.0.8.jar"/>
<pathelement location="lib/commons-cli-1.2.jar"/>
<pathelement location="lib/gson-2.2.4.jar"/>
</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-project,makeJar,archive" name="build"/>
<target depends="init" name="build-project">
<echo message="${ant.project.name}: ${ant.file}"/>
<javac srcdir="src" destdir="bin" source="${source}" target="${target}" includeantruntime="false">
<src path="src"/>
<classpath refid="libs"/>
</javac>
</target>
<target depends="build-project" name="makeJar">
<jar destfile="medusa.jar" filesetmanifest="mergewithoutmain">
<manifest>
<attribute name="Main-Class" value="Scaffolder"/>
<attribute name="Class-Path" value="."/>
</manifest>
<fileset dir="bin"/>
<zipfileset excludes="META-INF/*.SF" src="lib/biojava3-core-3.0.8.jar"/>
<zipfileset excludes="META-INF/*.SF" src="lib/commons-cli-1.2.jar"/>
<zipfileset excludes="META-INF/*.SF" src="lib/gson-2.2.4.jar"/>
</jar>
</target>
<target depends="makeJar" name="archive">
<tar destfile="medusa.tar.gz" compression="gzip">
<tarfileset dir="${basedir}" prefix="medusa">
<include name="medusa.jar" />
<include name="LICENSE" />
<include name="README.md" />
</tarfileset>
<tarfileset filemode="755" dir="${basedir}/medusa_scripts" prefix="medusa/medusa_scripts">
<include name="*" />
</tarfileset>
<tarfileset filemode="755" dir="${basedir}/medusa_testing" prefix="medusa/medusa_testing">
<include name="*" />
</tarfileset>
<tarfileset filemode="755" dir="${basedir}/test" prefix="medusa/test">
<include name="*" />
</tarfileset>
<tarfileset filemode="755" dir="${basedir}/test/reference_genomes" prefix="medusa/test/reference_genomes">
<include name="*" />
</tarfileset>
</tar>
</target>
</project>