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build.xml
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build.xml
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<!--
~ Copyright (c) 2012, The Broad Institute
~
~ Permission is hereby granted, free of charge, to any person
~ obtaining a copy of this software and associated documentation
~ files (the "Software"), to deal in the Software without
~ restriction, including without limitation the rights to use,
~ copy, modify, merge, publish, distribute, sublicense, and/or sell
~ copies of the Software, and to permit persons to whom the
~ Software is furnished to do so, subject to the following
~ conditions:
~
~ The above copyright notice and this permission notice shall be
~ included in all copies or substantial portions of the Software.
~ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
~ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
~ OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
~ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
~ HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
~ WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
~ FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
~ OTHER DEALINGS IN THE SOFTWARE.
-->
<project name="Sting" default="dist" basedir="."
xmlns:artifact="antlib:org.apache.maven.artifact.ant"
xmlns:ivy="antlib:org.apache.ivy.ant">
<description>Compile and distribute the Sting toolkit</description>
<!-- ******************************************************************************** -->
<!-- Properties -->
<!-- ******************************************************************************** -->
<!-- The system classpath should take precedence over classpaths specified in this file -->
<property name="build.sysclasspath" value="first" />
<!-- Use this prefix to access environment variables -->
<property environment="env"/>
<!-- Build defaults: -->
<property name="default.build.target" value="all" /> <!-- can be "all", "public" (public only), or "protected" (public + protected) -->
<property name="compile.scala.by.default" value="true" /> <!-- compile Scala by default? "true" or "false" -->
<property name="use.contracts.by.default" value="false" /> <!-- should contracts be built by default? "true" or "false -->
<!-- Top-level directories -->
<property name="build.dir" value="build" />
<property name="dist.dir" value="dist" />
<property name="lib.dir" value="lib" />
<property name="public.dir" value="public" />
<property name="private.dir" value="private" />
<property name="protected.dir" value="protected" />
<property name="external.dir" value="external" />
<!-- Source directories -->
<property name="java.public.source.dir" value="${public.dir}/java/src" />
<property name="java.private.source.dir" value="${private.dir}/java/src" />
<property name="java.protected.source.dir" value="${protected.dir}/java/src" />
<property name="scala.public.source.dir" value="${public.dir}/scala/src" />
<property name="scala.private.source.dir" value="${private.dir}/scala/src" />
<property name="scala.protected.source.dir" value="${protected.dir}/scala/src" />
<property name="queue-extensions.source.dir" value="${build.dir}/queue-extensions/src" />
<property name="R.public.scripts.dir" value="${public.dir}/R/scripts" />
<property name="R.private.scripts.dir" value="${private.dir}/R/scripts" />
<property name="R.protected.scripts.dir" value="${protected.dir}/R/scripts" />
<property name="R.public.src.dir" value="${public.dir}/R/src" />
<!-- Build directories -->
<property name="java.classes" value="${build.dir}/java/classes" />
<property name="scala.classes" value="${build.dir}/scala/classes" />
<property name="R.library.dir" value="${public.dir}/R" /> <!-- TODO: Installing libraries back into the source directory: intentionally avoids ant clean?? -->
<property name="R.tar.dir" value="${build.dir}/R/src" />
<property name="R.package.path" value="org/broadinstitute/sting/utils/R" />
<property name="R.script.staging.dir" value="${build.dir}/R/stage" />
<!-- Packaging system properties -->
<property name="package.xml.dir" value="${public.dir}/packages" />
<property name="package.output.dir" value="${dist.dir}/packages" />
<property name="staging.dir" value="staging" />
<property name="default.executable" value="none" />
<!-- GATKDocs/Javadoc/Scaladoc directories -->
<property name="gatkdocs.dir" value="gatkdocs" />
<property name="javadoc.dir" value="javadoc" />
<property name="scaladoc.dir" value="scaladoc" />
<!-- Resource file used for help text and version information -->
<property name="resource.file" value="StingText.properties" />
<property name="resource.path" value="${java.classes}/StingText.properties" />
<!-- Directory containing cryptographic keys used by the GATK -->
<property name="key.dir" value="${public.dir}/keys" />
<!-- Contracts for Java -->
<!-- Disabled by default -->
<!-- To enable, run with -Duse.contracts=true -->
<property name="java.contracts.dir" value="${build.dir}/java/contracts" />
<property name="contracts.version" value="1.0-r139" />
<property name="cofoja.jar" value="${lib.dir}/cofoja-${contracts.version}.jar"/>
<property name="contract.dump.dir" value="dump" />
<!-- do we want to halt on failure of a unit test? default to yes (Bamboo uses 'no') -->
<property name="halt" value="yes" />
<!-- should our unit test output go to a file or the screen? false means it goes to the screen (default) true to file -->
<property name="usefile" value="false" />
<!-- To run tests with debugging, use -Dtest.debug=true -Dtest.debug.port=XXXX on the command line -->
<property name="test.debug.port" value="5005" /> <!-- override on the command line if desired -->
<property name="test.default.maxmemory" value="4g"/>
<!-- clover parameters -->
<property name="clover.jar" location="private/resources/clover/lib/clover.jar"/>
<property name="clover.instrument.level" value="method"/>
<taskdef resource="cloverlib.xml" classpath="${clover.jar}"/>
<!-- ******************************************************************************** -->
<!-- Filesets and paths -->
<!-- ******************************************************************************** -->
<!-- All the complexity of selecting among public/private/protected should be up here, not down in the targets -->
<patternset id="java.source.directories.pattern">
<include name="${java.public.source.dir}" />
<include name="${java.private.source.dir}" if="include.private" />
<include name="${java.protected.source.dir}" if="include.protected" />
</patternset>
<patternset id="java.source.files.pattern">
<include name="${java.public.source.dir}/**/*.java" />
<include name="${java.private.source.dir}/**/*.java" if="include.private" />
<include name="${java.protected.source.dir}/**/*.java" if="include.protected" />
</patternset>
<patternset id="scala.source.directories.pattern">
<include name="${scala.public.source.dir}" />
<include name="${scala.private.source.dir}" if="include.private" />
<include name="${scala.protected.source.dir}" if="include.protected" />
</patternset>
<patternset id="scala.source.files.pattern">
<include name="${scala.public.source.dir}/**/*.scala" />
<include name="${scala.private.source.dir}/**/*.scala" if="include.private" />
<include name="${scala.protected.source.dir}/**/*.scala" if="include.protected" />
</patternset>
<patternset id="R.script.source.directories.pattern">
<include name="${R.public.scripts.dir}" />
<include name="${R.private.scripts.dir}" if="include.private" />
<include name="${R.protected.scripts.dir}" if="include.protected" />
</patternset>
<patternset id="R.script.source.files.pattern">
<include name="${R.public.scripts.dir}/**/*.R" />
<include name="${R.private.scripts.dir}/**/*.R" if="include.private" />
<include name="${R.protected.scripts.dir}/**.*.R" if="include.protected" />
</patternset>
<path id="java.source.path">
<dirset dir="${basedir}">
<patternset refid="java.source.directories.pattern" />
</dirset>
</path>
<path id="scala.source.path">
<dirset dir="${basedir}">
<patternset refid="scala.source.directories.pattern" />
</dirset>
</path>
<path id="R.script.source.path">
<dirset dir="${basedir}">
<patternset refid="R.script.source.directories.pattern" />
</dirset>
</path>
<fileset id="java.source.files" dir="${basedir}">
<patternset refid="java.source.files.pattern" />
</fileset>
<fileset id="scala.source.files" dir="${basedir}">
<patternset refid="scala.source.files.pattern" />
</fileset>
<fileset id="R.script.source.files" dir="${basedir}">
<patternset refid="R.script.source.files.pattern" />
</fileset>
<fileset id="java.class.files" dir="${java.classes}" erroronmissingdir="false">
<include name="**/*.class"/>
</fileset>
<patternset id="dependency.mask" includes="*.jar" />
<path id="external.dependencies">
<fileset dir="${lib.dir}" erroronmissingdir="false">
<patternset refid="dependency.mask" />
</fileset>
</path>
<path id="scala.dependencies">
<path refid="external.dependencies" />
<pathelement location="${java.classes}" />
<!-- Need the resources as we will be running a command line program which needs the help text. -->
<pathelement location="${resource.path}" />
<!-- Add any previously compiled scala classes to the path. -->
<pathelement location="${scala.classes}" />
</path>
<path id="build.results">
<!-- Ensure that GenomeAnalysisTK.jar comes first in the path, as it contains overrides for certain classes in our dependencies -->
<pathelement location="${dist.dir}/GenomeAnalysisTK.jar" />
<!-- After GenomeAnalysisTK.jar we include all of the other jars in the dist directory -->
<fileset dir="${dist.dir}" erroronmissingdir="false">
<patternset refid="dependency.mask" />
<exclude name="GenomeAnalysisTK.jar" />
</fileset>
</path>
<fileset id="external.source.files" dir="${external.dir}" erroronmissingdir="false">
<include name="**/*.java" />
</fileset>
<path id="external.build.dir">
<path path="${java.classes}" />
</path>
<path id="external.dist.dir">
<path path="${dist.dir}" />
</path>
<!-- GATK dependencies consist of 3rd party plugins plus compiled GATK classes -->
<path id="external.gatk.classpath">
<path path="${java.classes}"/>
<path refid="external.dependencies" />
</path>
<!-- the path for resources that need to go into the GATK jar;
any additional resources should go into this set. -->
<path id="gatk.resources">
<fileset dir="${java.public.source.dir}">
<include name="**/resources/*" />
<include name="**/templates/*" />
</fileset>
<fileset dir="${java.private.source.dir}" erroronmissingdir="false">
<include name="**/resources/*" if="include.private" />
<include name="**/templates/*" if="include.private" />
</fileset>
<fileset dir="${java.protected.source.dir}" erroronmissingdir="false">
<include name="**/resources/*" if="include.protected" />
<include name="**/templates/*" if="include.protected" />
</fileset>
</path>
<!-- ******************************************************************************** -->
<!-- Ivy Retrieve -->
<!-- ******************************************************************************** -->
<target name="init.resolve" unless="init.resolve.done">
<!-- ivy properties -->
<property name="ivy.install.version" value="2.2.0"/>
<property name="ivy.home" value="${user.home}/.ant"/>
<property name="ivy.jar.dir" value="${ivy.home}/${lib.dir}"/>
<property name="ivy.jar.file" value="ivy-${ivy.install.version}.jar"/>
<property name="ivy.settings.dir" value="settings"/>
<property file="${ivy.settings.dir}/ivysettings.properties"/>
<property name="maven-ant-tasks.install.version" value="2.1.3"/>
<property name="maven-ant-tasks.jar.file" value="maven-ant-tasks-${maven-ant-tasks.install.version}.jar"/>
<mkdir dir="${lib.dir}"/>
<mkdir dir="${ivy.jar.dir}"/>
<!-- Comment out the following lines to build the GATK without a network connection, assuming you have all of the libraries cached already -->
<get src="http://repo1.maven.org/maven2/org/apache/ivy/ivy/${ivy.install.version}/${ivy.jar.file}"
dest="${ivy.jar.dir}/${ivy.jar.file}"
usetimestamp="true"/>
<taskdef resource="org/apache/ivy/ant/antlib.xml"
uri="antlib:org.apache.ivy.ant"
classpath="${ivy.jar.dir}/${ivy.jar.file}"/>
<get src="http://repo1.maven.org/maven2/org/apache/maven/maven-ant-tasks/${maven-ant-tasks.install.version}/${maven-ant-tasks.jar.file}"
dest="${ivy.jar.dir}/${maven-ant-tasks.jar.file}"
usetimestamp="true"/>
<taskdef resource="org/apache/maven/artifact/ant/antlib.xml"
uri="antlib:antlib:org.apache.maven.artifact.ant"
classpath="${ivy.jar.dir}/${maven-ant-tasks.jar.file}"/>
<!-- End network lines -->
<ivy:settings file="${ivy.settings.dir}/ivysettings.xml"/>
<property name="init.resolve.done" value="true"/>
</target>
<target name="resolve" depends="init.resolve,init" description="locate and download library dependencies">
<property name="ivy.conf" value="default"/>
<ivy:retrieve file="ivy.xml" conf="${ivy.conf}" />
<!-- Remove old versions of ivy jars AFTER the ivy:retrieve has been class loaded. -->
<delete file="${ivy.jar.dir}/ivy-2.0.0.jar"/>
<delete file="${ivy.jar.dir}/ivy-2.2.0-rc1.jar"/>
</target>
<!-- ******************************************************************************** -->
<!-- Initialization -->
<!-- ******************************************************************************** -->
<!-- Targets for generating the build version -->
<target name="git.describe">
<exec executable="git" outputproperty="git.describe.output" resultproperty="git.describe.exit.value" failonerror="false">
<arg line="describe --long" />
</exec>
<condition property="git.describe.succeeded">
<equals arg1="${git.describe.exit.value}" arg2="0" />
</condition>
</target>
<target name="tagged.build.version" depends="git.describe" if="git.describe.succeeded">
<property name="build.version" value="${git.describe.output}" />
</target>
<target name="git.rev-parse" depends="git.describe" unless="git.describe.succeeded">
<exec executable="git" outputproperty="git.rev-parse.output" resultproperty="git.rev-parse.exit.value" failonerror="false">
<arg line="rev-parse --short HEAD" />
</exec>
<condition property="git.rev-parse.succeeded">
<equals arg1="${git.rev-parse.exit.value}" arg2="0" />
</condition>
</target>
<target name="untagged.build.version" depends="git.rev-parse" if="git.rev-parse.succeeded">
<property name="build.version" value="${git.rev-parse.output}" />
</target>
<target name="generate.build.version" depends="tagged.build.version, untagged.build.version">
<!-- Set build.version to exported if no other value has been set -->
<property name="build.version" value="exported" />
</target>
<!-- INIT OVERRIDES: call these targets BEFORE init to override build defaults -->
<target name="init.build.publiconly">
<property name="build.target" value="public" />
</target>
<target name="init.build.publicprotectedonly">
<property name="build.target" value="protected" />
</target>
<target name="init.build.all">
<property name="build.target" value="all" />
</target>
<target name="init.javaonly">
<property name="compile.scala" value="false" />
</target>
<target name="init.javaandscala">
<property name="compile.scala" value="true" />
</target>
<target name="init.usecontracts">
<property name="use.contracts" value="true" />
</target>
<!-- INIT -->
<target name="init" depends="generate.build.version">
<tstamp>
<format property="build.timestamp" pattern="yyyy/MM/dd HH:mm:ss"/>
</tstamp>
<!-- These properties should be overridden before init is called if the defaults are not desired -->
<property name="build.target" value="${default.build.target}" />
<property name="compile.scala" value="${compile.scala.by.default}" />
<property name="use.contracts" value="${use.contracts.by.default}" />
<property name="executable" value="${default.executable}" />
<!-- Determine what should be built -->
<condition property="include.scala">
<equals arg1="${compile.scala}" arg2="true" />
</condition>
<condition property="include.private">
<and>
<available file="${private.dir}" />
<equals arg1="${build.target}" arg2="all" />
</and>
</condition>
<condition property="include.protected">
<and>
<available file="${protected.dir}" />
<or>
<equals arg1="${build.target}" arg2="all" />
<equals arg1="${build.target}" arg2="protected" />
</or>
</and>
</condition>
<condition property="include.contracts">
<equals arg1="${use.contracts}" arg2="true" />
</condition>
<condition property="include.external">
<available file="${external.dir}"/>
</condition>
<!-- Construct display strings for the build properties print out -->
<condition property="include.scala.display.string" value="yes" else="no">
<isset property="include.scala" />
</condition>
<condition property="include.private.display.string" value="yes" else="no">
<isset property="include.private" />
</condition>
<condition property="include.protected.display.string" value="yes" else="no">
<isset property="include.protected" />
</condition>
<condition property="include.external.display.string" value="yes" else="no">
<isset property="include.external" />
</condition>
<condition property="include.contracts.display.string" value="yes" else="no">
<isset property="include.contracts" />
</condition>
<!-- Print out build properties -->
<echo message="BUILD PROPERTIES" />
<echo message="Include Scala? : ${include.scala.display.string}" />
<echo message="Include Private? : ${include.private.display.string}" />
<echo message="Include Protected? : ${include.protected.display.string}" />
<echo message="Include External? : ${include.external.display.string}" />
<echo message="Include Contracts? : ${include.contracts.display.string}" />
<echo message="Source revision : ${build.version}" />
<echo message="Build time : ${build.timestamp}" />
<!-- Create the build directory structure used by compile -->
<mkdir dir="${build.dir}"/>
<mkdir dir="${lib.dir}"/>
<mkdir dir="${java.classes}"/>
<mkdir dir="${java.contracts.dir}"/>
</target>
<!-- ******************************************************************************** -->
<!-- Java Compilation -->
<!-- ******************************************************************************** -->
<target name="gatk.compile.internal.source" depends="init,resolve">
<javac fork="true" memoryMaximumSize="512m" destdir="${java.classes}" debug="true" debuglevel="lines,vars,source" classpathref="external.dependencies" tempdir="${java.io.tmpdir}">
<src refid="java.source.path" />
<compilerarg value="-proc:none" />
</javac>
</target>
<target name="gatk.compile.external.source" depends="gatk.compile.internal.source" if="include.external">
<subant target="compile" genericantfile="build.xml">
<property name="build.dir" refid="external.build.dir" />
<property name="dist.dir" refid="external.dist.dir" />
<property name="gatk.classpath" refid="external.gatk.classpath" />
<fileset dir="${external.dir}" includes="*/build.xml" erroronmissingdir="false" />
</subant>
</target>
<target name="gatk.compile.source" depends="gatk.compile.internal.source,gatk.compile.external.source" description="Compile the GATK source" />
<target name="gatk.contracts" depends="gatk.compile.source" if="include.contracts">
<javac fork="true" memoryMaximumSize="512m" destdir="${java.contracts.dir}" debug="true" debuglevel="lines,vars,source" tempdir="${java.io.tmpdir}" >
<src refid="java.source.path" />
<classpath>
<path refid="external.dependencies" />
<pathelement path="${java.classes}" />
</classpath>
<compilerarg value="-Acom.google.java.contract.debug"/>
<compilerarg value="-Acom.google.java.contract.dump=${contract.dump.dir}"/>
<compilerarg value="-proc:only"/>
</javac>
</target>
<target name="gatk.compile" depends="init,resolve,gatk.compile.source,gatk.contracts" />
<!-- ******************************************************************************** -->
<!-- Scala Compilation -->
<!-- ******************************************************************************** -->
<target name="init.queue-extensions.generate" depends="gatk.compile">
<condition property="uptodate.queue-extensions.generate">
<or>
<not>
<isset property="include.scala"/>
</not>
<uptodate targetfile="${queue-extensions.source.dir}">
<srcfiles refid="java.class.files"/>
<srcfiles file="${queue-extensions.gatk.jar}"/>
</uptodate>
</or>
</condition>
</target>
<!-- NOTE: Extracting help first to avoid "Unable to load help text. Help output will be sparse." warning message. -->
<target name="queue-extensions.generate" depends="gatk.compile,extracthelp,init.queue-extensions.generate" unless="uptodate.queue-extensions.generate" description="generate GATK modules for Queue">
<mkdir dir="${queue-extensions.source.dir}"/>
<echo>Generating Queue GATK extensions...</echo>
<java fork="true" failonerror="true" classname="org.broadinstitute.sting.queue.extensions.gatk.GATKExtensionsGenerator" >
<arg value="-outDir" />
<arg path="${queue-extensions.source.dir}" />
<arg value="-l" />
<arg value="WARN" />
<classpath>
<file file="${queue-extensions.gatk.jar}"/>
<path refid="scala.dependencies"/>
</classpath>
</java>
<touch>
<file file="${queue-extensions.source.dir}"/>
</touch>
</target>
<target name="init.scala.compile" depends="resolve" description="Initializes the scala ant tasks from scala-compiler.jar">
<path id="scala.classpath">
<fileset dir="${lib.dir}">
<include name="scala-compiler-*.jar"/>
<include name="scala-library-*.jar"/>
</fileset>
</path>
<taskdef resource="scala/tools/ant/antlib.xml">
<classpath refid="scala.classpath"/>
</taskdef>
</target>
<!-- Scala depends on the java compile -->
<target name="scala.compile" depends="init,resolve,gatk.compile,queue-extensions.generate,init.scala.compile" if="include.scala">
<mkdir dir="${scala.classes}"/>
<echo>Building Scala...</echo>
<scalac fork="true" jvmargs="-Xmx512m" destdir="${scala.classes}" classpathref="scala.dependencies" deprecation="yes" unchecked="yes">
<src refid="scala.source.path" />
<src path="${queue-extensions.source.dir}" />
<include name="**/*.scala" />
</scalac>
</target>
<!-- ******************************************************************************** -->
<!-- Sting Resource File Generation -->
<!-- ******************************************************************************** -->
<target name="init.extracthelp" depends="gatk.compile">
<loadfile property="properties.version" srcfile="${basedir}/${resource.path}" failonerror="false" quiet="true">
<filterchain>
<linecontains>
<contains value="org.broadinstitute.sting.gatk.CommandLineGATK.version"/>
</linecontains>
<tokenfilter>
<replaceregex pattern="^.*\.(.*?)$" replace="\1"/>
</tokenfilter>
<striplinebreaks/>
</filterchain>
</loadfile>
<!-- This fileset will contain only source files modified since the resource file was last generated,
or all source files if the resource file doesn't exist -->
<fileset dir="${basedir}" id="modified.source.files">
<patternset refid="java.source.files.pattern" />
<include name="${external.dir}/**/*.java"/>
<depend targetdir="${basedir}">
<mapper type="merge" to="${resource.path}"/>
</depend>
</fileset>
<!-- Set the sources.modified property only if our fileset of modified source files is non-empty -->
<pathconvert refid="modified.source.files" property="sources.modified" setonempty="false"/>
<!-- Due to a limitation in the doclet API, we always need to pass package-info files to javadoc -->
<fileset dir="${basedir}" id="package.info.files">
<include name="${java.public.source.dir}/**/package-info.java"/>
<include name="${java.private.source.dir}/**/package-info.java" if="include.private" />
<include name="${java.protected.source.dir}/**/package-info.java" if="include.protected" />
<include name="${external.dir}/**/package-info.java"/>
</fileset>
<condition property="uptodate.extracthelp">
<or>
<isset property="disable.help"/>
<and>
<not>
<isset property="sources.modified"/>
</not>
<equals arg1="${properties.version}" arg2="${build.version}"/>
</and>
</or>
</condition>
</target>
<target name="extracthelp" depends="init.extracthelp" unless="uptodate.extracthelp"
description="Extract help key/value pair file from the JavaDoc tags.">
<path id="doclet.classpath">
<path refid="external.dependencies" />
<pathelement location="${java.classes}" />
<pathelement location="${clover.jar}" />
</path>
<javadoc doclet="org.broadinstitute.sting.utils.help.ResourceBundleExtractorDoclet"
docletpathref="doclet.classpath"
classpathref="external.dependencies"
classpath="${java.classes}"
maxmemory="2g"
additionalparam="-build-timestamp "${build.timestamp}" -absolute-version ${build.version} -out ${basedir}/${resource.path} -quiet">
<sourcefiles>
<union>
<fileset refid="modified.source.files"/>
<fileset refid="package.info.files"/>
</union>
</sourcefiles>
</javadoc>
</target>
<!-- ******************************************************************************** -->
<!-- Build Jars -->
<!-- ******************************************************************************** -->
<target name="sting.compile" depends="gatk.compile, scala.compile" />
<target name="init.jar" depends="sting.compile,extracthelp">
<mkdir dir="${dist.dir}"/>
<copy todir="${dist.dir}">
<fileset dir="${lib.dir}" includes="*.jar"/>
</copy>
</target>
<target name="R.public.tar">
<mkdir dir="${R.tar.dir}/${R.package.path}" />
<tar compression="gzip" basedir="${R.public.src.dir}/${R.package.path}" includes="gsalib/**" destfile="${R.tar.dir}/${R.package.path}/gsalib.tar.gz" />
</target>
<target name="R.script.stage">
<mkdir dir="${R.script.staging.dir}" />
<copy todir="${R.script.staging.dir}" overwrite="true">
<fileset refid="R.script.source.files" />
<!-- remove the initial path components (eg., public/R/scripts) when doing the copy -->
<!-- ant 1.8.2 has a cutdirsmapper, but ant versions < 1.8.2 are too common to use it -->
<mapper type="regexp" from="^(${R.public.scripts.dir}|${R.private.scripts.dir}|${R.protected.scripts.dir})/(.*)" to="\2" />
</copy>
</target>
<target name="sting-utils.jar" depends="gatk.compile, init.jar, R.public.tar, R.script.stage">
<jar jarfile="${dist.dir}/StingUtils.jar">
<fileset dir="${java.classes}" includes="**/sting/utils/**/*.class"/>
<fileset dir="${java.classes}" includes="**/sting/commandline/**/*.class"/>
<fileset dir="${java.classes}" includes="**/sting/pipeline/**/*.class"/>
<fileset dir="${java.classes}" includes="**/sting/tools/**/*.class"/>
<fileset dir="${java.classes}" includes="**/sting/jna/**/*.class"/>
<fileset dir="${java.classes}" includes="net/sf/picard/**/*.class"/>
<fileset dir="${java.classes}" includes="net/sf/samtools/**/*.class"/>
<fileset dir="${R.tar.dir}">
<include name="**/${R.package.path}/**/*.tar.gz"/>
</fileset>
<fileset dir="${R.script.staging.dir}">
<include name="**/sting/utils/**/*.R"/>
</fileset>
<manifest>
<attribute name="Premain-Class" value="org.broadinstitute.sting.utils.instrumentation.Sizeof" />
</manifest>
</jar>
</target>
<target name="na12878kb.jar" depends="gatk.compile,init.jar">
<jar jarfile="${dist.dir}/na12878kb.jar">
<fileset dir="${java.classes}">
<include name="org/broadinstitute/sting/utils/GenomeLocParser*.class"/>
<include name="org/broadinstitute/sting/utils/GenomeLoc.class"/>
<include name="org/broadinstitute/sting/utils/HasGenomeLocation.class"/>
<include name="org/broadinstitute/sting/utils/BaseUtils*.class"/>
<include name="org/broadinstitute/sting/utils/Utils.class"/>
<include name="org/broadinstitute/sting/utils/MRUCaching*.class"/>
<include name="org/broadinstitute/sting/utils/exceptions/**/*.class"/>
<include name="org/broadinstitute/sting/gatk/walkers/na12878kb/core/**/*.class"/>
<include name="net/sf/picard/reference/FastaSequenceFile.class"/>
</fileset>
<fileset dir="${java.private.source.dir}">
<include name="org/broadinstitute/sting/gatk/walkers/na12878kb/core/resources/**/*"/>
</fileset>
</jar>
</target>
<target name="gatk.jar" depends="gatk.compile, init.jar, R.script.stage" description="generate the GATK distribution">
<jar jarfile="${dist.dir}/GenomeAnalysisTK.jar">
<path refid="gatk.resources"/>
<fileset dir="${java.contracts.dir}" />
<fileset dir="${java.classes}">
<include name="${resource.file}" />
<include name="**/sting/gatk/**/*.class" />
<include name="**/sting/alignment/**/*.class"/>
</fileset>
<fileset dir="${R.script.staging.dir}">
<include name="**/sting/gatk/**/*.R"/>
<include name="**/sting/alignment/**/*.R"/>
</fileset>
<fileset dir="${key.dir}">
<include name="**/*.key"/>
</fileset>
<manifest>
<attribute name="Main-Class" value="org.broadinstitute.sting.gatk.CommandLineGATK" />
</manifest>
</jar>
<jar jarfile="${dist.dir}/Aligner.jar">
<fileset dir="${java.classes}" includes="**/sting/alignment/**/*.class" />
</jar>
<subant target="dist" genericantfile="build.xml">
<property name="build.dir" refid="external.build.dir" />
<property name="dist.dir" refid="external.dist.dir" />
<property name="gatk.classpath" refid="external.gatk.classpath" />
<fileset dir="${external.dir}" includes="*/build.xml" erroronmissingdir="false" />
</subant>
</target>
<target name="scala.jar" depends="scala.compile, init.jar" if="include.scala">
<jar jarfile="${dist.dir}/GATKScala.jar">
<fileset dir="${scala.classes}">
<include name="org/broadinstitute/sting/scala/**/*.class"/>
</fileset>
</jar>
</target>
<target name="queue.jar" depends="scala.compile, init.jar, R.script.stage" if="include.scala">
<jar jarfile="${dist.dir}/Queue.jar">
<fileset dir="${scala.classes}">
<include name="org/broadinstitute/sting/queue/**/*.class"/>
</fileset>
<fileset dir="${java.classes}">
<include name="org/broadinstitute/sting/queue/**/*.class" />
</fileset>
<fileset dir="${R.script.staging.dir}">
<include name="org/broadinstitute/sting/queue/**/*.R"/>
</fileset>
<manifest>
<attribute name="Main-Class" value="org.broadinstitute.sting.queue.QCommandLine" />
</manifest>
</jar>
</target>
<target name="sting.jar" depends="sting-utils.jar, gatk.jar, queue.jar" />
<target name="init.manifests" depends="sting.jar">
<pathconvert property="jar.classpath" pathsep=" ">
<flattenmapper/>
<fileset dir="${dist.dir}" includes="*.jar"/>
<filelist files="GATKScala.jar"/>
</pathconvert>
</target>
<target name="sting-utils.manifests" depends="sting-utils.jar, init.manifests">
<jar jarfile="${dist.dir}/StingUtils.jar" update="true">
<manifest>
<attribute name="Class-Path" value="${jar.classpath}"/>
</manifest>
</jar>
</target>
<target name="gatk.manifests" depends="gatk.jar, init.manifests">
<jar jarfile="${dist.dir}/GenomeAnalysisTK.jar" update="true">
<manifest>
<attribute name="Class-Path" value="${jar.classpath}"/>
</manifest>
</jar>
</target>
<target name="queue.manifests" depends="queue.jar, init.manifests" if="include.scala">
<jar jarfile="${dist.dir}/Queue.jar" update="true" >
<manifest>
<attribute name="Class-Path" value="${jar.classpath}" />
</manifest>
</jar>
</target>
<target name="sting.manifests" depends="sting-utils.manifests, gatk.manifests, queue.manifests" />
<!-- ******************************************************************************** -->
<!-- Top-Level Build Targets -->
<!-- ******************************************************************************** -->
<target name="dist" depends="sting.manifests" />
<target name="gatk" depends="init.javaonly, sting.manifests" />
<target name="queue" depends="dist" /> <!-- Obsolete target. Now just an alias for dist -->
<target name="scala" depends="scala.jar" description="build the scala directory" />
<!-- ******************************************************************************** -->
<!-- GATKDocs -->
<!-- ******************************************************************************** -->
<target name="gatkdocs" depends="gatk.compile" description="Extract help key/value pair file from the JavaDoc tags.">
<path id="doclet.classpath">
<path refid="external.dependencies" />
<pathelement location="${java.classes}" />
</path>
<!-- Run with -Dgatkdocs.include.hidden=true to include documentation for hidden features -->
<condition property="gatkdocs.include.hidden.arg" value="-include-hidden" else="">
<isset property="gatkdocs.include.hidden" />
</condition>
<javadoc doclet="org.broadinstitute.sting.utils.help.GATKDoclet"
docletpathref="doclet.classpath"
classpathref="external.dependencies"
classpath="${java.classes}"
maxmemory="2g"
additionalparam="${gatkdocs.include.hidden.arg} -private -build-timestamp "${build.timestamp}" -absolute-version ${build.version} -quiet"> <!-- -test to only do DocumentationTest walker -->
<sourcefiles>
<fileset refid="java.source.files"/>
</sourcefiles>
</javadoc>
</target>
<!-- ******************************************************************************** -->
<!-- Javadoc -->
<!-- ******************************************************************************** -->
<target name="init.javadoc">
<mkdir dir="${javadoc.dir}" />
</target>
<target name="javadoc" depends="init.javadoc,resolve">
<javadoc destdir="${javadoc.dir}" classpathref="external.dependencies">
<fileset refid="java.source.files" />
<sourcepath path="${external.dir}" />
</javadoc>
</target>
<!-- ******************************************************************************** -->
<!-- Scaladoc -->
<!-- ******************************************************************************** -->
<target name="init.scaladoc">
<mkdir dir="${scaladoc.dir}" />
</target>
<!-- NOTE: the scaladoc target requires that the environment variable ANT_OPTS has been set to "-Xmx1G" -->
<target name="scaladoc" depends="resolve,queue-extensions.generate,init.scala.compile,scala.compile,init.scaladoc">
<scaladoc srcdir="${basedir}" destdir="${scaladoc.dir}" classpathref="scala.dependencies" deprecation="yes" unchecked="yes">
<patternset refid="scala.source.files.pattern" />
<include name="${queue-extensions.source.dir}/**/*.scala" />
</scaladoc>
</target>
<!-- ******************************************************************************** -->
<!-- Release-related tasks -->
<!-- ******************************************************************************** -->
<target name="init.executable.gatkfull" depends="init.build.publicprotectedonly, init.javaonly">
<property name="executable" value="GenomeAnalysisTK" />
</target>
<target name="init.executable.gatkall" depends="init.build.all, init.javaonly">
<property name="executable" value="GenomeAnalysisTK" />
</target>
<target name="init.executable.queuefull" depends="init.build.publicprotectedonly, init.javaandscala">
<property name="executable" value="Queue" />
</target>
<target name="init.executable.queueall" depends="init.build.all, init.javaandscala">
<property name="executable" value="Queue" />
</target>
<target name="require.executable">
<condition property="no.executable.defined">
<or>
<equals arg1="${executable}" arg2="none" />
<equals arg1="${executable}" arg2="$${executable}" />
</or>
</condition>
<fail message="No executable defined. Call a more specific packaging/release target, or define an executable manually" if="no.executable.defined" />
</target>
<!-- Unzip all classes from their current locations and assemble them in a staging directory -->
<target name="stage" description="stage files for distribution">
<mkdir dir="${staging.dir}"/>
<!--
HACK: Create the edu directory before EDU on case-insensitive mac filesystems.
The ivy dependency colt -> concurrent contains an EDU.oswego package which
BCEL doesn't even pull in but messes up edu.mit.broad.
-->
<mkdir dir="${staging.dir}/edu"/>
<unjar dest="${staging.dir}" overwrite="false">
<fileset dir="${dist.dir}">
<patternset refid="dependency.mask" />
</fileset>
</unjar>
<!-- HACK: The GATK jar itself contains overrides for some core classes. Make sure the GATK.jar is unrolled last. -->
<unjar dest="${staging.dir}" overwrite="true">
<fileset dir="${dist.dir}" includes="**/GenomeAnalysisTK.jar"/>
</unjar>
</target>
<!-- Build a package consisting of all supporting files. Don't call this target directly. Call one of the specific packaging targets below -->
<target name="package" depends="require.clean,dist,stage,require.executable" description="bundle up an executable for distribution">
<mkdir dir="${package.output.dir}" />
<xslt destdir="${package.output.dir}" style="${package.xml.dir}/CreatePackager.xsl" useImplicitFileset="false">
<flattenmapper/>
<fileset dir="${package.xml.dir}">
<include name="${executable}.xml" />
</fileset>
<fileset dir="${external.dir}" erroronmissingdir="false">
<include name="*/${executable}.xml" />
</fileset>
</xslt>
<ant antfile="${package.output.dir}/${executable}.xml" target="package" />
</target>
<!-- Package specific versions of the GATK/Queue. ALWAYS do an ant clean before invoking these! -->
<!-- GATK "full" == public + protected, ie., the standard binary release of the GATK -->
<target name="package.gatk.full" depends="init.executable.gatkfull,package" />
<!-- GATK "all" == public + protected + private. Should never be publicly released -->
<target name="package.gatk.all" depends="init.executable.gatkall,package" />
<target name="package.queue.full" depends="init.executable.queuefull,package" />
<target name="package.queue.all" depends="init.executable.queueall,package" />
<!-- Release a build. Don't call this target directly. Call one of the specific release targets below -->
<target name="release" depends="require.executable" description="release a build, putting each file in a location specified by the package">
<ant antfile="${package.output.dir}/${executable}.xml" target="release" />
</target>
<!-- Release specific versions of the GATK/Queue. ALWAYS do an ant clean before invoking these! -->
<target name="release.gatk.full" depends="package.gatk.full,release" />
<target name="release.queue.full" depends="package.queue.full,release" />
<!-- Build a subset of picard with only those classes we need by completely abusing the packaging system -->
<!-- TODO: Reuse as much as possible of the 'stage' and 'package' targets -->
<target name="build-picard-private" depends="resolve">
<!-- Build out a classpath -->
<pathconvert property="required.picard.jars" pathsep=":">
<fileset dir="${basedir}">
<include name="${staging.dir}" />
<include name="${lib.dir}/picard-*.*.*.jar" />
<include name="${lib.dir}/sam-*.jar" />
</fileset>
</pathconvert>
<echo message="required.picard.jars=${required.picard.jars}" />
<!-- Stage picard-private -->
<delete dir="${staging.dir}" />
<mkdir dir="${staging.dir}" />
<unjar src="${picard.dist.dir}/picard-private.jar" dest="${staging.dir}" overwrite="true" />
<!-- Use the packaging system to extract parts of picard-private we need -->
<mkdir dir="${package.output.dir}" />
<xslt in="${package.xml.dir}/PicardPrivate.xml" out="${package.output.dir}/BuildPicardPrivate.xml" style="${package.xml.dir}/CreatePackager.xsl" />
<ant antfile="${package.output.dir}/BuildPicardPrivate.xml">
<property name="additional.jars" value="${required.picard.jars}" />
</ant>
</target>
<!-- Maven install a package consisting of all supporting files. Don't call this target directly. Call one of the specific packaging targets below -->
<target name="mvninstall" depends="package" description="maven install a package into .m2/repository">
<property name="mvn.build.version" value="0.0.2" />
<!--
We should use the build version or better yet a git tag version, but tags are currently missing. Alternatively how do we then depend on the LATEST?
<property name="mvn.build.version" value="${build.version}" />
-->
<artifact:pom id="${executable}.pom" groupId="org.broadinstitute.sting" artifactId="${executable}" version="${mvn.build.version}" name="${executable}" />
<artifact:writepom pomRefId="${executable}.pom" file="${package.output.dir}/${executable}-${build.version}/${executable}.pom.xml"/>
<artifact:install file="${package.output.dir}/${executable}-${build.version}/${executable}.jar">
<artifact:pom file="${package.output.dir}/${executable}-${build.version}/${executable}.pom.xml" />
</artifact:install>
</target>
<!-- Maven install specific versions of the GATK/Queue. ALWAYS do an ant clean before invoking these! -->
<target name="mvninstall.gatk.full" depends="package.gatk.full,mvninstall" />
<target name="mvninstall.queue.all" depends="package.queue.all,mvninstall" />
<target name="mvninstall.queue.full" depends="package.queue.full,mvninstall" />
<!-- ******************************************************************************** -->
<!-- Clean -->
<!-- ******************************************************************************** -->
<target name="clean.gatkdocs">