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build.xml
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build.xml
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<?xml version="1.0" encoding="UTF-8"?>
<project name="PhyloNet" basedir="." default="main">
<property name="src.dir" value="src"/>
<property name="build.dir" value="build"/>
<property name="classes.dir" value="${build.dir}/classes"/>
<property name="jar.dir" value="${build.dir}/jar"/>
<property name="lib.dir" value="lib"/>
<property name="report.dir" value="${build.dir}/junitreport" />
<path id="classpath">
<fileset dir="${lib.dir}" includes="*.jar"/>
</path>
<property name="main-class" value="edu.rice.cs.bioinfo.programs.phylonet.Program"/>
<patternset id="excluded.source.files">
<exclude name="edu/rice/cs/bioinfo/programs/phmm/**"/>
<exclude name="edu/rice/cs/bioinfo/programs/phmm/ex/**"/>
<exclude name="edu/rice/cs/bioinfo/programs/phmm/ex/mouse/**"/>
<exclude name="edu/rice/cs/bioinfo/programs/phmm/ex/three/**"/>
<exclude name="edu/rice/cs/bioinfo/programs/phmm/ex/gtprob/**"/>
<exclude name="edu/rice/cs/bioinfo/programs/phmm/ex/mouse2/**"/>
<exclude name="edu/rice/cs/bioinfo/programs/phmm/ex/mouse2/fasttree/**"/>
<exclude name="edu/rice/cs/bioinfo/programs/phmm/ex/mouse3/**"/>
<exclude name="edu/rice/cs/bioinfo/programs/phmm/ex/mouse4/**"/>
<exclude name="edu/rice/cs/bioinfo/programs/phmm/ex/simple/**"/>
<exclude name="edu/rice/cs/bioinfo/programs/phmm/ex/control/**"/>
<exclude name="edu/rice/cs/bioinfo/programs/phmm/ex/simple2/**"/>
<exclude name="edu/rice/cs/bioinfo/programs/phmm/ex/control2/**"/>
<exclude name="edu/rice/cs/bioinfo/programs/phmm/ex/control3/**"/>
<exclude name="edu/rice/cs/bioinfo/programs/phmm/ex/simple-gene-only/**"/>
<exclude name="edu/rice/cs/bioinfo/programs/phmm/ex/mouse-full-informative-only/**"/>
<exclude name="edu/rice/cs/bioinfo/programs/phmm/ex/mmd-array-spretus-wgs-control/**"/>
<exclude name="edu/rice/cs/bioinfo/programs/phmm/ex/control3-unconstrained-parental-trees/**"/>
<exclude name="edu/rice/cs/bioinfo/programs/phmm/ex/mouse-full-informative-only-unconstrained/**"/>
<exclude name="edu/rice/cs/bioinfo/programs/phmm/src/**"/>
<exclude name="edu/rice/cs/bioinfo/programs/phmm/src/be/**"/>
<exclude name="edu/rice/cs/bioinfo/programs/phmm/src/be/ac/**"/>
<exclude name="edu/rice/cs/bioinfo/programs/phmm/src/be/ac/ulg/**"/>
<exclude name="edu/rice/cs/bioinfo/programs/phmm/src/be/ac/ulg/montefiore/**"/>
<exclude name="edu/rice/cs/bioinfo/programs/phmm/src/be/ac/ulg/montefiore/run/**"/>
<exclude name="edu/rice/cs/bioinfo/programs/phmm/src/be/ac/ulg/montefiore/run/jahmm/**"/>
<exclude name="edu/rice/cs/bioinfo/programs/phmm/src/be/ac/ulg/montefiore/run/jahmm/io/**"/>
<exclude name="edu/rice/cs/bioinfo/programs/phmm/src/be/ac/ulg/montefiore/run/jahmm/apps/**"/>
<exclude name="edu/rice/cs/bioinfo/programs/phmm/src/be/ac/ulg/montefiore/run/jahmm/apps/cli/**"/>
<exclude name="edu/rice/cs/bioinfo/programs/phmm/src/be/ac/ulg/montefiore/run/jahmm/draw/**"/>
<exclude name="edu/rice/cs/bioinfo/programs/phmm/src/be/ac/ulg/montefiore/run/jahmm/phmm/**"/>
<exclude name="edu/rice/cs/bioinfo/programs/phmm/src/be/ac/ulg/montefiore/run/jahmm/test/**"/>
<exclude name="edu/rice/cs/bioinfo/programs/phmm/src/be/ac/ulg/montefiore/run/jahmm/learn/**"/>
<exclude name="edu/rice/cs/bioinfo/programs/phmm/src/be/ac/ulg/montefiore/run/jahmm/toolbox/**"/>
<exclude name="edu/rice/cs/bioinfo/programs/phmm/src/be/ac/ulg/montefiore/run/distributions/**"/>
<exclude name="edu/rice/cs/bioinfo/programs/phmm/src/util/**"/>
<exclude name="edu/rice/cs/bioinfo/programs/phmm/src/reader/**"/>
<exclude name="edu/rice/cs/bioinfo/programs/phmm/src/runHmm/**"/>
<exclude name="edu/rice/cs/bioinfo/programs/phmm/src/META-INF/**"/>
<exclude name="edu/rice/cs/bioinfo/programs/phmm/src/optimize/**"/>
<exclude name="edu/rice/cs/bioinfo/programs/phmm/src/phylogeny/**"/>
<exclude name="edu/rice/cs/bioinfo/programs/phmm/src/containers/**"/>
<exclude name="edu/rice/cs/bioinfo/programs/phmm/src/substitutionModel/**"/>
<exclude name="edu/rice/cs/bioinfo/programs/phmm/misc/**"/>
<exclude name="edu/rice/cs/bioinfo/programs/phmm/templates/**"/>
<exclude name="edu/rice/cs/bioinfo/programs/phmm/templates/liu-et-al-2014-empirical/**"/>
<exclude name="edu/rice/cs/bioinfo/programs/phmm/templates/liu-et-al-2014-simulated/**"/>
<exclude name="edu/rice/cs/bioinfo/programs/rn2ms/**"/>
<exclude name="edu/rice/cs/bioinfo/programs/ms2dot/**"/>
<exclude name="edu/rice/cs/bioinfo/programs/rn2dot/**"/>
<exclude name="edu/rice/cs/bioinfo/programs/soranus/**"/>
<exclude name="edu/rice/cs/bioinfo/programs/soranus/views/**"/>
<exclude name="edu/rice/cs/bioinfo/programs/soranus/views/swing/**"/>
<exclude name="edu/rice/cs/bioinfo/programs/soranus/models/**"/>
<exclude name="edu/rice/cs/bioinfo/programs/soranus/models/data/**"/>
<exclude name="edu/rice/cs/bioinfo/programs/soranus/models/analysis/**"/>
<exclude name="edu/rice/cs/bioinfo/programs/soranus/models/factories/**"/>
<exclude name="edu/rice/cs/bioinfo/programs/soranus/models/fileRecogniser/**"/>
<exclude name="edu/rice/cs/bioinfo/programs/soranus/META-INF/**"/>
<exclude name="edu/rice/cs/bioinfo/programs/soranus/viewModels/**"/>
<exclude name="edu/rice/cs/bioinfo/programs/soranus/controllers/**"/>
<exclude name="edu/rice/cs/bioinfo/programs/morphylonet/**"/>
<exclude name="edu/rice/cs/bioinfo/programs/isolatepipeline/**"/>
<exclude name="edu/rice/cs/bioinfo/programs/mdcnetworksearch/**"/>
<exclude name="edu/rice/cs/bioinfo/programs/networksearchgen/**"/>
<exclude name="edu/rice/cs/bioinfo/programs/vaal2sequencings/**"/>
<exclude name="edu/rice/cs/bioinfo/programs/addreticulationedges/**"/>
<exclude name="edu/rice/cs/bioinfo/programs/addreticulationedges/META-INF/**"/>
<exclude name="edu/rice/cs/bioinfo/programs/InferTransMapSnitkin12/**"/>
<exclude name="edu/rice/cs/bioinfo/programs/richnewick2hybridsimnewick/**"/>
<exclude name="edu/rice/cs/bioinfo/programs/richnewick2hybridsimnewick/META-INF/**"/>
</patternset>
<target name="clean">
<delete dir="${build.dir}"/>
</target>
<target name="compile">
<mkdir dir="${classes.dir}"/>
<!-- add the argument bootclasspath="/path/to/java8/jre/lib/rt.jar" setting the path as appropriate for your system -->
<javac srcdir="${src.dir}" destdir="${classes.dir}" classpathref="classpath" includeantruntime="false" source="1.8" target="1.8" debug="true">
<patternset refid="excluded.source.files"/>
</javac>
</target>
<target name="jar" depends="compile">
<mkdir dir="${jar.dir}"/>
<jar destfile="${jar.dir}/${ant.project.name}.jar" basedir="${classes.dir}">
<manifest>
<attribute name="Main-Class" value="${main-class}"/>
</manifest>
<zipfileset excludes="META-INF/*" src="${basedir}/lib/colt-1.2.0.jar"/>
<zipfileset excludes="META-INF/*" src="${basedir}/lib/jfreechart-1.0.13.jar"/>
<zipfileset excludes="META-INF/*" src="${basedir}/lib/reflections-0.9.12.jar"/>
<zipfileset excludes="META-INF/*" src="${basedir}/lib/jcommon-1.0.16.jar"/>
<zipfileset excludes="META-INF/*" src="${basedir}/lib/antlr-runtime-3.5.2.jar"/>
<zipfileset excludes="META-INF/*" src="${basedir}/lib/jung-algorithms-2.0.1.jar"/>
<zipfileset excludes="META-INF/*" src="${basedir}/lib/mockito-all-1.10.19.jar"/>
<zipfileset excludes="META-INF/*" src="${basedir}/lib/freehep-jminuit-1.0.2.jar"/>
<zipfileset excludes="META-INF/*" src="${basedir}/lib/collections-generic-4.01.jar"/>
<zipfileset excludes="META-INF/*" src="${basedir}/lib/concurrent-1.3.4.jar"/>
<zipfileset excludes="META-INF/*" src="${basedir}/lib/commons-math3-3.3.jar"/>
<zipfileset excludes="META-INF/*" src="${basedir}/lib/guava-18.0.jar"/>
<zipfileset excludes="META-INF/*" src="${basedir}/lib/gson-2.8.7.jar"/>
<zipfileset excludes="META-INF/*" src="${basedir}/lib/Jeigen-onefat.jar"/>
<zipfileset excludes="META-INF/*" src="${basedir}/lib/jna-4.1.0.jar"/>
<zipfileset excludes="META-INF/*" src="${basedir}/lib/guava-19.0.jar"/>
<zipfileset excludes="META-INF/*" src="${basedir}/lib/jama-1.0.3.jar"/>
<zipfileset excludes="META-INF/*" src="${basedir}/lib/jung-graph-impl-2.0.1.jar"/>
<zipfileset excludes="META-INF/*" src="${basedir}/lib/jblas-1.2.5.jar"/>
<zipfileset excludes="META-INF/*" src="${basedir}/lib/convolutionlib.jar"/>
<zipfileset excludes="META-INF/*" src="${basedir}/lib/hamcrest-core-1.3.jar"/>
<zipfileset excludes="META-INF/*" src="${basedir}/lib/jung-api-2.0.1.jar"/>
<zipfileset excludes="META-INF/*" src="${basedir}/lib/joda-time-2.10.10.jar"/>
<zipfileset excludes="META-INF/*" src="${basedir}/lib/junit-4.13.2.jar"/>
<zipfileset excludes="META-INF/*" src="${basedir}/lib/javassist-3.26.0-GA.jar"/>
<zipfileset excludes="META-INF/*" src="${basedir}/lib/commons-io-2.9.0.jar"/>
<zipfileset excludes="META-INF/*" src="${basedir}/lib/jahmm-0.6.1.jar"/>
</jar>
</target>
<target name="run" depends="jar">
<java fork="true" classname="${main-class}">
<classpath>
<path refid="classpath"/>
<path location="${jar.dir}/${ant.project.name}.jar"/>
</classpath>
</java>
</target>
<target name="clean-build" depends="clean,jar"/>
<target name="main" depends="clean,run"/>
<target name="junit" depends="jar">
<mkdir dir="${report.dir}" />
<junit printsummary="yes" failureproperty="junitfailed">
<!--showoutput='yes'-->
<classpath>
<path refid="classpath" />
<path location="${jar.dir}/${ant.project.name}.jar"/>
</classpath>
<formatter type="xml" />
<batchtest fork="yes" todir="${report.dir}">
<fileset dir="${src.dir}">
<include name="edu/rice/cs/bioinfo/programs/phylonet/**/?*Test.java" />
</fileset>
</batchtest>
</junit>
<echo message="JUnit test finished." />
</target>
</project>