/
build.xml
524 lines (456 loc) · 19.5 KB
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build.xml
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<!-- Build SnAP. It is also used by Hudson SnAP project. JUnit test is available for this build. -->
<project basedir="." default="build_all_SnAP" name="BUILD_SnAP">
<description>
Build SnAP.
Also used by Hudson SnAP project.
JUnit test is available for this build.
$Id: build_SNAPP.xml $
</description>
<!-- set global properties for this build -->
<property name="SNAPPdir" location="../SNAPP/" />
<property name="src" location="${SNAPPdir}/src" />
<property name="build" location="${SNAPPdir}/build" />
<property name="lib" location="${SNAPPdir}/lib" />
<property name="dist" location="${SNAPPdir}/dist" />
<property name="beast2path" location="../beast2" />
<property name="beast2build" location="${beast2path}/build" />
<property name="libBeast2" location="${beast2path}/lib" />
<property name="srcBeast2" location="${beast2path}/src" />
<property name="beast2classpath" location="${beast2path}/build" />
<property name="beastappclasspath" location="../BeastFX/build" />
<property name="BEASTLabsclasspath" location="../BEASTLabs/build" />
<property name="main_class_SnAP" value="snap.app.mcmc.SNAPPMCMC" />
<property name="main_class_TSA" value="snap.app.analysis.TreeSetAnalyser" />
<property name="report" value="${build}/junitreport"/>
<path id="classpath">
<fileset dir="${lib}" includes="**/*.jar"/>
<fileset dir="${libBeast2}" includes="antlr-runtime-4.7.jar"/>
<fileset dir="${libBeast2}" includes="jam.jar"/>
<pathelement path="${beast2classpath}"/>
<pathelement path="${beastappclasspath}"/>
<pathelement path="${BEASTLabsclasspath}"/>
</path>
<!-- start -->
<target name="init">
<echo message="${ant.project.name}: ${ant.file}" />
<available file="${SNAPPdir}/version.xml" property="versionAvailable"/>
<fail unless="versionAvailable">
** Required file version.xml does not exist. **
</fail>
<!-- Read package name and version from xml file -->
<xmlproperty file="${SNAPPdir}/version.xml" prefix="fromVersionFile" />
<property name="SNAPPversion" value="${fromVersionFile.package(version)}" />
</target>
<target name="clean">
<delete dir="${build}" />
</target>
<!-- clean previous build, and then compile Java source code, and Juint test -->
<target name="build_all_SnAP" depends="clean,compile-all,dist_all_SnAP"
description="Clean and Build all run-time stuff">
</target>
<!-- clean previous build, compile Java source code, and Junit test, and make the snap.jar -->
<target name="test" depends="clean,compile-all,junit,dist_all_SnAP"
description="Clean and Build all run-time stuff">
</target>
<!-- No JUnit Test, clean previous build, compile Java source code, and make the snap.jar -->
<target name="build_jar_all_SnAP_NoJUnitTest" depends="clean,compile-all,dist_all_SnAP"
description="Clean and Build all run-time stuff">
</target>
<!-- compile Java source code -->
<target name="compile-all" depends="init">
<mkdir dir="${build}" />
<!-- Compile the java code from ${src} into ${build} /bin -->
<javac srcdir="${src}" destdir="${build}" classpathref="classpath"
fork="true" includeantruntime='false'
memoryinitialsize="256m"
memorymaximumsize="256m">
<include name="snap/**/**" />
<!-- compile JUnit test classes -->
<include name="test/snap/**" />
<exclude name="snap/SNAPPHeatedMCMC.java"/>
<exclude name="snap/likelihood/SnAPForestLikelihood.java"/>
<exclude name="snap/app/analysis/SNAPPSkylineAnalyser.java"/>
</javac>
<copy todir="${build}">
<fileset dir="${src}" includes="**/*.properties"/>
<fileset dir="${src}" includes="**/*.png"/>
</copy>
<echo message="Successfully compiled." />
</target>
<!-- make the snap.jar and beauti.jar -->
<target name="dist_all_SnAP" depends="compile-all" description="create SnAP jar">
<!-- Create the distribution directory -->
<mkdir dir="${dist}" />
<!-- Put everything in ${build} into the snap.jar file -->
<jar jarfile="${dist}/snap.jar">
<manifest>
<attribute name="Built-By" value="${user.name}" />
<attribute name="Main-Class" value="${main_class_SnAP}" />
</manifest>
<zipgroupfileset dir="${lib}" includes="mtj.jar" />
<!--zipgroupfileset dir="${lib}" includes="beast.jar" /-->
<fileset dir="${beast2build}">
<include name="**/*.class"/>
</fileset>
<zipgroupfileset dir="${libBeast2}" includes="jam.jar"/>
<zipgroupfileset dir="${libBeast2}" includes="antlr-runtime-4.7.jar"/>
<fileset dir="${build}">
<include name="snap/**/*.class" />
<include name="snap/**/*.png" />
<include name="**/*.properties" />
</fileset>
</jar>
<!-- Put everything + beastii in ${build} into the snapii.jar file -->
<!--
<jar jarfile="${dist}/snapii.jar">
<manifest>
<attribute name="Built-By" value="${user.name}" />
<attribute name="Main-Class" value="${main_class_SnAP}" />
</manifest>
<zipgroupfileset dir="${lib}" includes="mtj.jar" />
<zipgroupfileset dir="${lib}" includes="beast.jar" />
<fileset dir="${build}">
<include name="snap/**/*.class" />
<include name="snap/**/*.png" />
<include name="beast/**/*.class" />
<include name="**/*.properties" />
</fileset>
<fileset dir="../beastii/build/">
<include name="beast/**/*.class" />
</fileset>
</jar>
-->
<jar jarfile="${dist}/snap.addon.jar">
<manifest>
<attribute name="Built-By" value="${user.name}" />
<attribute name="Main-Class" value="${main_class_SnAP}" />
</manifest>
<fileset dir="${build}">
<include name="snap/**/*.class" />
<include name="snap/**/*.png" />
<include name="**/*.properties" />
</fileset>
</jar>
<jar jarfile="${dist}/snap.src.jar">
<fileset dir="${src}">
<include name="snap/**/*.java" />
<include name="**/*.properties" />
<include name="snap/**/*.png" />
<include name="snap/**/*.xsl" />
</fileset>
</jar>
</target>
<!-- run snap.jar -->
<target name="run_SnAP">
<java jar="${dist}/snap.jar" fork="true" />
</target>
<!-- JUnit test -->
<target name="junit">
<mkdir dir="${report}" />
<junit printsummary="yes">
<classpath>
<path refid="classpath" />
<path location="${build}" />
</classpath>
<formatter type="xml" />
<batchtest fork="yes" todir="${report}">
<fileset dir="${src}">
<include name="test/**/*Test.java"/>
</fileset>
</batchtest>
</junit>
<echo message="JUnit test finished." />
</target>
<target name="junitreport">
<junitreport todir="${report}">
<fileset dir="${report}" includes="*.xml"/>
<report format="frames" todir="${report}"/>
</junitreport>
<echo message="JUnit test report finished." />
</target>
<target name="doc">
<exec executable="pdflatex" dir="${basedir}/doc">
<arg value="SNAPP.tex" />
</exec>
<exec executable="pdflatex" dir="${basedir}/doc">
<arg value="SNAPP.tex" />
</exec>
<copy file="doc/SNAPP.pdf" tofile="release/common/doc/SNAPP.pdf" />
</target>
<!-- Release -->
<property name="release_dir" value="release" />
<property name="copyright" value="SNAPP development team 2011-2022" />
<property name="SNAPP_name" value="SNAPP" />
<property name="BEAUti_name" value="BEAUti" />
<property name="TSA_name" value="TreeSetAnalyser" />
<property name="common_dir" value="${release_dir}/common" />
<property name="Mac_dir" value="${release_dir}/Mac" />
<property name="Linux_dir" value="${release_dir}/Linux" />
<property name="Windows_dir" value="${release_dir}/Windows" />
<property name="tools_dir" value="${common_dir}/tools" />
<property name="Mac_package_dir" value="${Mac_dir}/${SNAPP_name}" />
<property name="Linux_package_dir" value="${Linux_dir}/${SNAPP_name}" />
<property name="Add_on_dir" value="${release_dir}/add-on" />
<property name="Windows_package_dir" value="${Windows_dir}/${SNAPP_name}" />
<!-- Need to either install Launch4j under {BEAST workspace}/${release}
or install it in the default directory and change the location of launch4j.dir -->
<target name="windows"
depends="build_jar_all_SnAP_NoJUnitTest,doc"
description="release Windows version of SNAPP, BEAUTI, DensiTree, TreeSetAnalyser">
<delete dir="${Windows_package_dir}" />
<!-- Create the release directory -->
<mkdir dir="${Windows_package_dir}" />
<property name="launch4j.dir" location="${Windows_dir}/launch4j" />
<taskdef name="launch4j"
classname="net.sf.launch4j.ant.Launch4jTask"
classpath="${launch4j.dir}/launch4j.jar :${launch4j.dir}/lib/xstream.jar" />
<copy todir="${Windows_package_dir}/doc">
<fileset dir="${common_dir}/doc" />
</copy>
<copy todir="${Windows_package_dir}/examples/">
<fileset dir="examples/">
<include name="*.xml" />
<include name="nexus/**" />
<exclude name="benchmark/**" />
</fileset>
</copy>
<copy file="${dist}/snap.jar" todir="${Windows_package_dir}/lib" />
<copy file="${dist}/snap.src.jar" todir="${Windows_package_dir}/lib" />
<copy file="${common_dir}/VERSION HISTORY.txt" todir="${Windows_package_dir}" />
<copy file="${common_dir}/README.txt" todir="${Windows_package_dir}" />
<!-- BEAUTi v?.?.?.exe -->
<launch4j configFile="${Windows_dir}/BEAUti_launch4j.xml"
jar="${dist}/snap.jar"
outfile="${Windows_package_dir}/${BEAUti_name}.exe"
fileVersion="${version_number}.0"
txtFileVersion="${version}"
productVersion="${version_number}.0"
txtProductVersion="${version}" />
<!-- SNAPP v?.?.?.exe -->
<launch4j configFile="${Windows_dir}/SNAPP_launch4j.xml"
jar="${dist}/snap.jar"
outfile="${Windows_package_dir}/${SNAPP_name}.exe"
fileVersion="${version_number}.0"
txtFileVersion="${version}"
productVersion="${version_number}.0"
txtProductVersion="${version}" />
<launch4j configFile="${Windows_dir}/TSA_launch4j.xml"
jar="${dist}/snap.jar"
outfile="${Windows_package_dir}/${TSA_name}.exe"
fileVersion="${version_number}.0"
txtFileVersion="${version}"
productVersion="${version_number}.0"
txtProductVersion="${version}" />
<launch4j configFile="${tools_dir}/DensiTree_launch4j.xml"
jar="${tools_dir}/DensiTree.jar"
outfile="${Windows_package_dir}/DensiTree.exe"
fileVersion="2.1.7.0"
txtFileVersion="2.1.7.0"
productVersion="2.1.7.0"
txtProductVersion="2.1.7.0" />
<copy todir="${Windows_package_dir}/fxtemplates/">
<fileset dir="fxtemplates/" />
</copy>
<zip destfile="${Windows_dir}/${SNAPP_name} v${version}.zip">
<zipfileset dir="${Windows_package_dir}" prefix="${SNAPP_name}" />
</zip>
<echo message="Windows version release is finished." />
</target>
<target name="linux"
depends="build_jar_all_SnAP_NoJUnitTest,doc"
description="release Linux/Unix version of SNAPP, BEAUTI, TreeSetAnalyser, DensiTree">
<delete dir="${Linux_package_dir}" />
<!-- Create the release directory -->
<mkdir dir="${Linux_package_dir}" />
<copy todir="${Linux_package_dir}/bin">
<fileset dir="${Linux_dir}/bin" />
</copy>
<chmod dir="${Linux_package_dir}/bin" perm="755" includes="**/**" />
<copy todir="${Linux_package_dir}/doc">
<fileset dir="${common_dir}/doc" />
</copy>
<copy todir="${Linux_package_dir}/examples/">
<fileset dir="examples/">
<include name="*.xml" />
<include name="nexus/**" />
<exclude name="benchmark/**" />
</fileset>
</copy>
<copy file="${common_dir}/icons/snapp.png" todir="${Linux_package_dir}/images" />
<copy file="${common_dir}/icons/beauti.png" todir="${Linux_package_dir}/images" />
<copy file="${dist}/snap.jar" todir="${Linux_package_dir}/lib" />
<copy file="${dist}/snap.src.jar" todir="${Linux_package_dir}/lib" />
<copy file="${tools_dir}/DensiTree.jar" todir="${Linux_package_dir}/lib" />
<copy file="${tools_dir}/DensiTree.png" todir="${Linux_package_dir}/images" />
<copy todir="${Linux_package_dir}/fxtemplates/">
<fileset dir="fxtemplates/" />
</copy>
<copy file="${common_dir}/VERSION HISTORY.txt" todir="${Linux_package_dir}" />
<copy file="${common_dir}/README.txt" todir="${Linux_package_dir}" />
<!-- Only works under Unix or NonStop Kernel (Tandem) -->
<!-- <chmod dir="${Linux_package_dir}/bin" perm="755" includes="**/**"/-->
<!-- [ANT Bug 550] the tar task change the mode of the executables files, have to tar manaully -->
<echo message="Have to tar manaully, because [ANT Bug 550] the tar task change the mode of the executables files." />
<echo message="Linux/Unix version release is finished." />
</target>
<property name="jarbundler_dir" value="/Applications/eclipse/plugins/org.apache.ant_1.8.2.v20110505-1300/lib" />
<target name="mac"
depends="build_jar_all_SnAP_NoJUnitTest"
description="release Mac version of SNAPP, BEAUTI, TreeSetAnalyser, DensiTree">
<delete dir="${Mac_package_dir}" />
<!-- Create the release directory -->
<mkdir dir="${Mac_package_dir}" />
<copy todir="${Mac_package_dir}/bin">
<fileset dir="${Linux_dir}/bin" />
</copy>
<chmod dir="${Mac_package_dir}/bin" perm="755" includes="**/**" />
<copy todir="${Mac_package_dir}/doc">
<fileset dir="${common_dir}/doc" />
</copy>
<copy todir="${Mac_package_dir}/examples/">
<fileset dir="examples/">
<include name="*.xml" />
<include name="nexus/**" />
<exclude name="benchmark/**" />
</fileset>
</copy>
<!-- <copy todir="${Mac_package_dir}/native">
<fileset dir="${common_dir}/native" />
</copy>
<copy file="${dist}/beauti.jar" todir="${Mac_package_dir}/lib" /> -->
<copy file="${dist}/snap.jar" todir="${Mac_package_dir}/lib" />
<copy file="${dist}/snap.src.jar" todir="${Mac_package_dir}/lib" />
<copy file="${common_dir}/VERSION HISTORY.txt" todir="${Mac_package_dir}" />
<copy file="${common_dir}/README.txt" todir="${Mac_package_dir}" />
<taskdef name="jarbundler"
classname="net.sourceforge.jarbundler.JarBundler"
classpath="${jarbundler_dir}/jarbundler-2.2.0.jar" />
<!-- create a jar bundle for the mac -->
<jarbundler dir="${Mac_package_dir}"
name="${SNAPP_name}"
mainclass="${main_class_SnAP}"
icon="${common_dir}/icons/snapp.icns"
jvmversion="1.6+"
vmoptions="-Xmx1024M"
arguments="-window -working -options"
version="${version}"
infostring="${SNAPP_name}, ${copyright}"
bundleid="${main_class_SnAP}">
<jarfileset dir="${Mac_package_dir}/lib">
<include name="**/snap.jar" />
<!-- <include name="**/beast-beagle.jar" /> -->
</jarfileset>
<!-- <jarfileset dir="${Mac_package_dir}/lib">
<include name="libNucleotideLikelihoodCore.jnilib" />
</jarfileset> -->
<javaproperty name="apple.laf.useScreenMenuBar" value="true" />
<javaproperty name="java.library.path" value="$JAVAROOT:/usr/local/lib" />
</jarbundler>
<jarbundler dir="${Mac_package_dir}"
name="${TSA_name}"
mainclass="${main_class_TSA}"
icon="${common_dir}/icons/tsa.icns"
jvmversion="1.6+"
vmoptions="-Xmx1024M"
arguments="-window -working -options"
version="${version}"
infostring="${TSA_name}, ${copyright}"
bundleid="${main_class_TSA}">
<jarfileset dir="${Mac_package_dir}/lib">
<include name="**/snap.jar" />
</jarfileset>
<javaproperty name="apple.laf.useScreenMenuBar" value="true" />
<javaproperty name="java.library.path" value="$JAVAROOT:/usr/local/lib" />
</jarbundler>
<jarbundler dir="${Mac_package_dir}"
name="${BEAUti_name}"
mainclass="beast.app.beauti.Beauti"
icon="${common_dir}/icons/beauti.icns"
jvmversion="1.6+"
vmoptions="-Xmx1024M -Xdock:name="BEAUti 2""
arguments="-template fxtemplates/SNAPP.xml"
version="${version}"
infostring="${BEAUti_name}, ${copyright}"
bundleid="beast.app.beauti.Beauti">
<jarfileset dir="${Mac_package_dir}/lib">
<include name="**/snap.jar" />
</jarfileset>
<javaproperty name="apple.laf.useScreenMenuBar" value="true" />
<javaproperty name="java.library.path" value="$JAVAROOT" />
</jarbundler>
<!-- ant copy will not redirect the source, so that have to re-bundler it -->
<jarbundler dir="${Mac_package_dir}"
name="DensiTree"
mainclass="viz.DensiTree"
icon="${tools_dir}/DensiTree.icns"
jvmversion="1.6+"
vmoptions="-Xmx1024M"
arguments=""
version="2.1.3"
infostring="DensiTree, http://compevol.auckland.ac.nz/software/DensiTree/"
bundleid="viz.DensiTree">
<jarfileset dir="${tools_dir}">
<include name="**/DensiTree.jar" />
</jarfileset>
<javaproperty name="apple.laf.useScreenMenuBar" value="true" />
<javaproperty name="java.library.path" value="$JAVAROOT/lib" />
</jarbundler>
<copy todir="${Mac_package_dir}/fxtemplates/">
<fileset dir="fxtemplates/" />
</copy>
<echo message="Building disk image." />
<!-- create disk image -->
<exec executable="/usr/bin/hdiutil">
<arg value="create" />
<arg value="-ov" />
<arg value="-srcfolder" />
<arg value="${Mac_package_dir}" />
<arg value="-volname" />
<arg value="${SNAPP_name}" />
<arg value="-imagekey" />
<arg value="zlib-level=6" />
<arg value="${Mac_dir}/${SNAPP_name} v${version}.dmg" />
</exec>
<echo message="Mac version release is finished." />
</target>
<!--
-->
<target name="addon"
depends="build_jar_all_SnAP_NoJUnitTest"
description="release BEAST 2 add-on version of SNAPP">
<delete dir="${Add_on_dir}" />
<!-- Create the release directory -->
<mkdir dir="${Add_on_dir}" />
<mkdir dir="${Add_on_dir}/lib" />
<mkdir dir="${Add_on_dir}/fxtemplates" />
<mkdir dir="${Add_on_dir}/examples" />
<mkdir dir="${Add_on_dir}/examples/nexus" />
<mkdir dir="${Add_on_dir}/doc" />
<copy todir="${Add_on_dir}">
<fileset file="version.xml"/>
</copy>
<copy todir="${Add_on_dir}/lib">
<fileset dir="${dist}" includes="snap.addon.jar" />
</copy>
<copy todir="${Add_on_dir}">
<fileset dir="${dist}" includes="snap.src.jar" />
</copy>
<copy todir="${Add_on_dir}/fxtemplates">
<fileset file="fxtemplates/SNAPP.xml" />
</copy>
<copy file="doc/SNAPP.pdf" tofile="${Add_on_dir}/doc/SNAPP.pdf" />
<copy todir="${Add_on_dir}/examples" >
<fileset dir="examples" includes="*.xml" />
<fileset dir="examples" includes="*.json" />
</copy>
<copy todir="${Add_on_dir}/examples/nexus" >
<fileset dir="examples/nexus" includes="*.nex" />
</copy>
<jar jarfile="${dist}/SNAPP.addon.v${SNAPPversion}.zip">
<fileset dir="${Add_on_dir}">
<include name="**/*" />
</fileset>
</jar>
<echo message="Add-on v${SNAPPversion} release is finished." />
</target>
</project>