1338 lines
61 KiB
XML
1338 lines
61 KiB
XML
<!--
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~ Copyright (c) 2012, The Broad Institute
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~
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~ Permission is hereby granted, free of charge, to any person
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~ obtaining a copy of this software and associated documentation
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~ files (the "Software"), to deal in the Software without
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~ restriction, including without limitation the rights to use,
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~ copy, modify, merge, publish, distribute, sublicense, and/or sell
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~ copies of the Software, and to permit persons to whom the
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~ Software is furnished to do so, subject to the following
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~ conditions:
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~
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~ The above copyright notice and this permission notice shall be
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~ included in all copies or substantial portions of the Software.
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~ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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~ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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~ OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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~ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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~ HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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~ WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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~ FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
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~ OTHER DEALINGS IN THE SOFTWARE.
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-->
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<project name="Sting" default="dist" basedir="." xmlns:ivy="antlib:org.apache.ivy.ant">
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<description>Compile and distribute the Sting toolkit</description>
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<!-- ******************************************************************************** -->
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<!-- Properties -->
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<!-- ******************************************************************************** -->
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<!-- The system classpath should take precedence over classpaths specified in this file -->
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<property name="build.sysclasspath" value="first" />
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<!-- Use this prefix to access environment variables -->
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<property environment="env"/>
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<!-- Build defaults: -->
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<property name="default.build.target" value="all" /> <!-- can be "all", "public" (public only), or "protected" (public + protected) -->
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<property name="compile.scala.by.default" value="true" /> <!-- compile Scala by default? "true" or "false" -->
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<property name="use.contracts.by.default" value="false" /> <!-- should contracts be built by default? "true" or "false -->
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<!-- Top-level directories -->
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<property name="build.dir" value="build" />
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<property name="dist.dir" value="dist" />
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<property name="lib.dir" value="lib" />
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<property name="public.dir" value="public" />
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<property name="private.dir" value="private" />
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<property name="protected.dir" value="protected" />
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<property name="external.dir" value="external" />
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<!-- Source directories -->
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<property name="java.public.source.dir" value="${public.dir}/java/src" />
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<property name="java.private.source.dir" value="${private.dir}/java/src" />
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<property name="java.protected.source.dir" value="${protected.dir}/java/src" />
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<property name="scala.public.source.dir" value="${public.dir}/scala/src" />
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<property name="scala.private.source.dir" value="${private.dir}/scala/src" />
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<property name="scala.protected.source.dir" value="${protected.dir}/scala/src" />
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<property name="queue-extensions.source.dir" value="${build.dir}/queue-extensions/src" />
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<property name="R.public.scripts.dir" value="${public.dir}/R/scripts" />
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<property name="R.private.scripts.dir" value="${private.dir}/R/scripts" />
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<property name="R.protected.scripts.dir" value="${protected.dir}/R/scripts" />
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<property name="R.public.src.dir" value="${public.dir}/R/src" />
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<!-- Build directories -->
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<property name="java.classes" value="${build.dir}/java/classes" />
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<property name="scala.classes" value="${build.dir}/scala/classes" />
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<property name="R.library.dir" value="${public.dir}/R" /> <!-- TODO: Installing libraries back into the source directory: intentionally avoids ant clean?? -->
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<property name="R.tar.dir" value="${build.dir}/R/src" />
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<property name="R.package.path" value="org/broadinstitute/sting/utils/R" />
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<property name="R.script.staging.dir" value="${build.dir}/R/stage" />
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<!-- Packaging system properties -->
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<property name="package.xml.dir" value="${public.dir}/packages" />
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<property name="package.output.dir" value="${dist.dir}/packages" />
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<property name="staging.dir" value="staging" />
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<property name="default.executable" value="none" />
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<!-- Javadoc/Scaladoc directories -->
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<property name="javadoc.dir" value="javadoc" />
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<property name="scaladoc.dir" value="scaladoc" />
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<!-- Resource file used for help text and version information -->
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<property name="resource.file" value="StingText.properties" />
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<property name="resource.path" value="${java.classes}/StingText.properties" />
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<!-- Directory containing cryptographic keys used by the GATK -->
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<property name="key.dir" value="${public.dir}/keys" />
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<!-- Contracts for Java -->
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<!-- By default, enabled only for test targets -->
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<!-- To disable for test targets, run with -Duse.contracts=false -->
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<!-- To enable for non-test targets, run with -Duse.contracts=true -->
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<property name="java.contracts.dir" value="${build.dir}/java/contracts" />
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<property name="contracts.version" value="1.0-20110609" />
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<property name="cofoja.jar" value="${lib.dir}/cofoja-${contracts.version}.jar"/>
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<property name="contract.dump.dir" value="dump" />
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<property name="gatkdocs.dir" value="gatkdocs" />
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<!-- do we want to halt on failure of a unit test? default to yes (Bamboo uses 'no') -->
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<property name="halt" value="yes" />
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<!-- should our unit test output go to a file or the screen? false means it goes to the screen (default) true to file -->
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<property name="usefile" value="false" />
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<!-- To run tests with debugging, use -Dtest.debug=true -Dtest.debug.port=XXXX on the command line -->
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<property name="test.debug.port" value="5005" /> <!-- override on the command line if desired -->
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<!-- ******************************************************************************** -->
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<!-- Filesets and paths -->
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<!-- ******************************************************************************** -->
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<!-- All the complexity of selecting among public/private/protected should be up here, not down in the targets -->
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<patternset id="java.source.directories.pattern">
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<include name="${java.public.source.dir}" />
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<include name="${java.private.source.dir}" if="include.private" />
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<include name="${java.protected.source.dir}" if="include.protected" />
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</patternset>
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<patternset id="java.source.files.pattern">
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<include name="${java.public.source.dir}/**/*.java" />
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<include name="${java.private.source.dir}/**/*.java" if="include.private" />
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<include name="${java.protected.source.dir}/**/*.java" if="include.protected" />
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</patternset>
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<patternset id="scala.source.directories.pattern">
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<include name="${scala.public.source.dir}" />
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<include name="${scala.private.source.dir}" if="include.private" />
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<include name="${scala.protected.source.dir}" if="include.protected" />
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</patternset>
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<patternset id="scala.source.files.pattern">
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<include name="${scala.public.source.dir}/**/*.scala" />
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<include name="${scala.private.source.dir}/**/*.scala" if="include.private" />
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<include name="${scala.protected.source.dir}/**/*.scala" if="include.protected" />
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</patternset>
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<patternset id="R.script.source.directories.pattern">
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<include name="${R.public.scripts.dir}" />
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<include name="${R.private.scripts.dir}" if="include.private" />
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<include name="${R.protected.scripts.dir}" if="include.protected" />
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</patternset>
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<patternset id="R.script.source.files.pattern">
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<include name="${R.public.scripts.dir}/**/*.R" />
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<include name="${R.private.scripts.dir}/**/*.R" if="include.private" />
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<include name="${R.protected.scripts.dir}/**.*.R" if="include.protected" />
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</patternset>
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<path id="java.source.path">
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<dirset dir="${basedir}">
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<patternset refid="java.source.directories.pattern" />
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</dirset>
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</path>
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<path id="scala.source.path">
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<dirset dir="${basedir}">
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<patternset refid="scala.source.directories.pattern" />
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</dirset>
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</path>
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<path id="R.script.source.path">
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<dirset dir="${basedir}">
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<patternset refid="R.script.source.directories.pattern" />
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</dirset>
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</path>
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<fileset id="java.source.files" dir="${basedir}">
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<patternset refid="java.source.files.pattern" />
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</fileset>
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<fileset id="scala.source.files" dir="${basedir}">
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<patternset refid="scala.source.files.pattern" />
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</fileset>
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<fileset id="R.script.source.files" dir="${basedir}">
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<patternset refid="R.script.source.files.pattern" />
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</fileset>
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<fileset id="java.class.files" dir="${java.classes}" erroronmissingdir="false">
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<include name="**/*.class"/>
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</fileset>
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<patternset id="dependency.mask" includes="*.jar">
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<exclude name="testng*.jar" />
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<exclude name="bcel*.jar" />
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</patternset>
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<path id="external.dependencies">
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<fileset dir="${lib.dir}" erroronmissingdir="false">
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<patternset refid="dependency.mask" />
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</fileset>
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</path>
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<path id="scala.dependencies">
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<path refid="external.dependencies" />
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<pathelement location="${java.classes}" />
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<!-- Need the resources as we will be running a command line program which needs the help text. -->
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<pathelement location="${resource.path}" />
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<!-- Add any previously compiled scala classes to the path. -->
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<pathelement location="${scala.classes}" />
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</path>
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<fileset id="external.source.files" dir="${external.dir}" erroronmissingdir="false">
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<include name="**/*.java" />
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</fileset>
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<pathconvert property="external.build.dir">
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<path path="${java.classes}"/>
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</pathconvert>
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<pathconvert property="external.dist.dir">
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<path path="${dist.dir}" />
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</pathconvert>
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<!-- GATK dependencies consist of 3rd party plugins plus compiled GATK classes -->
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<pathconvert property="external.gatk.classpath">
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<path path="${java.classes}"/>
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<path refid="external.dependencies" />
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</pathconvert>
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<!-- the path for resources that need to go into the GATK jar;
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any additional resources should go into this set. -->
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<path id="gatk.resources">
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<fileset dir="${basedir}">
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<include name="${java.public.source.dir}/**/templates/*" />
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<include name="${java.private.source.dir}/**/templates/*" if="include.private" />
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<include name="${java.protected.source.dir}/**/templates/*" if="include.protected" />
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</fileset>
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</path>
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<path id="build.results">
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<fileset dir="${dist.dir}">
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<patternset refid="dependency.mask" />
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</fileset>
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</path>
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<!-- ******************************************************************************** -->
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<!-- Ivy Retrieve -->
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<!-- ******************************************************************************** -->
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<target name="init.resolve" unless="init.resolve.done">
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<!-- ivy properties -->
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<property name="ivy.install.version" value="2.2.0"/>
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<property name="ivy.home" value="${user.home}/.ant"/>
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<property name="ivy.jar.dir" value="${ivy.home}/${lib.dir}"/>
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<property name="ivy.jar.file" value="ivy-${ivy.install.version}.jar"/>
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<property name="ivy.settings.dir" value="settings"/>
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<property file="${ivy.settings.dir}/ivysettings.properties"/>
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<mkdir dir="${lib.dir}"/>
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<mkdir dir="${ivy.jar.dir}"/>
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<!-- Comment out the following two lines to build the GATK without a network connection, assuming you have all of the libraries cached already -->
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<get src="http://repo1.maven.org/maven2/org/apache/ivy/ivy/${ivy.install.version}/${ivy.jar.file}"
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dest="${ivy.jar.dir}/${ivy.jar.file}"
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usetimestamp="true"/>
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<taskdef resource="org/apache/ivy/ant/antlib.xml"
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uri="antlib:org.apache.ivy.ant"
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classpath="${ivy.jar.dir}/${ivy.jar.file}"/>
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<ivy:settings file="${ivy.settings.dir}/ivysettings.xml"/>
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<property name="init.resolve.done" value="true"/>
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</target>
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<target name="resolve" depends="init.resolve,init" description="locate and download library dependencies">
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<property name="ivy.conf" value="default"/>
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<ivy:retrieve file="ivy.xml" conf="${ivy.conf}" />
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<!-- Remove old versions of ivy jars AFTER the ivy:retrieve has been class loaded. -->
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<delete file="${ivy.jar.dir}/ivy-2.0.0.jar"/>
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<delete file="${ivy.jar.dir}/ivy-2.2.0-rc1.jar"/>
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</target>
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<!-- ******************************************************************************** -->
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<!-- Initialization -->
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<!-- ******************************************************************************** -->
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<!-- Targets for generating the build version -->
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<target name="git.describe">
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<exec executable="git" outputproperty="git.describe.output" resultproperty="git.describe.exit.value" failonerror="false">
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<arg line="describe --long" />
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</exec>
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<condition property="git.describe.succeeded">
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<equals arg1="${git.describe.exit.value}" arg2="0" />
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</condition>
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</target>
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<target name="tagged.build.version" depends="git.describe" if="git.describe.succeeded">
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<property name="build.version" value="${git.describe.output}" />
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</target>
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<target name="git.rev-parse" depends="git.describe" unless="git.describe.succeeded">
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<exec executable="git" outputproperty="git.rev-parse.output" resultproperty="git.rev-parse.exit.value" failonerror="false">
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<arg line="rev-parse HEAD" />
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</exec>
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<condition property="git.rev-parse.succeeded">
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<equals arg1="${git.rev-parse.exit.value}" arg2="0" />
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</condition>
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</target>
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<target name="untagged.build.version" depends="git.rev-parse" if="git.rev-parse.succeeded">
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<property name="build.version" value="${git.rev-parse.output}" />
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</target>
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<target name="generate.build.version" depends="tagged.build.version, untagged.build.version">
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<!-- Set build.version to exported if no other value has been set -->
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<property name="build.version" value="exported" />
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</target>
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<!-- INIT OVERRIDES: call these targets BEFORE init to override build defaults -->
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<target name="init.publiconly">
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<property name="build.target" value="public" />
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</target>
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<target name="init.publicprotectedonly">
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<property name="build.target" value="protected" />
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</target>
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<target name="init.javaonly">
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<property name="compile.scala" value="false" />
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</target>
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<target name="init.javaandscala">
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<property name="compile.scala" value="true" />
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</target>
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<target name="init.usecontracts">
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<property name="use.contracts" value="true" />
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</target>
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<!-- INIT -->
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<target name="init" depends="generate.build.version">
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<tstamp>
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<format property="build.timestamp" pattern="yyyy/MM/dd HH:mm:ss"/>
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</tstamp>
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<!-- These properties should be overridden before init is called if the defaults are not desired -->
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<property name="build.target" value="${default.build.target}" />
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<property name="compile.scala" value="${compile.scala.by.default}" />
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<property name="use.contracts" value="${use.contracts.by.default}" />
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<property name="executable" value="${default.executable}" />
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<!-- Determine what should be built -->
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<condition property="include.scala">
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<equals arg1="${compile.scala}" arg2="true" />
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</condition>
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<condition property="include.private">
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<and>
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<available file="${private.dir}" />
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<equals arg1="${build.target}" arg2="all" />
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</and>
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</condition>
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<condition property="include.protected">
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<and>
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<available file="${protected.dir}" />
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<or>
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<equals arg1="${build.target}" arg2="all" />
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<equals arg1="${build.target}" arg2="protected" />
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</or>
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</and>
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</condition>
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<condition property="include.contracts">
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<equals arg1="${use.contracts}" arg2="true" />
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</condition>
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<condition property="include.external">
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<available file="${external.dir}"/>
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</condition>
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<!-- Construct display strings for the build properties print out -->
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<condition property="include.scala.display.string" value="yes" else="no">
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<isset property="include.scala" />
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</condition>
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<condition property="include.private.display.string" value="yes" else="no">
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<isset property="include.private" />
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</condition>
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<condition property="include.protected.display.string" value="yes" else="no">
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<isset property="include.protected" />
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</condition>
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<condition property="include.external.display.string" value="yes" else="no">
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<isset property="include.external" />
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</condition>
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<condition property="include.contracts.display.string" value="yes" else="no">
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<isset property="include.contracts" />
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</condition>
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<!-- Print out build properties -->
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<echo message="BUILD PROPERTIES" />
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<echo message="Include Scala? : ${include.scala.display.string}" />
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<echo message="Include Private? : ${include.private.display.string}" />
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<echo message="Include Protected? : ${include.protected.display.string}" />
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<echo message="Include External? : ${include.external.display.string}" />
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<echo message="Include Contracts? : ${include.contracts.display.string}" />
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<echo message="Source revision : ${build.version}" />
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<echo message="Build time : ${build.timestamp}" />
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<!-- Create the build directory structure used by compile -->
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<mkdir dir="${build.dir}"/>
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<mkdir dir="${lib.dir}"/>
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<mkdir dir="${java.classes}"/>
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<mkdir dir="${java.contracts.dir}"/>
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</target>
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<!-- ******************************************************************************** -->
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<!-- Java Compilation -->
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<!-- ******************************************************************************** -->
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<target name="gatk.compile.internal.source" depends="init,resolve">
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<javac fork="true" memoryMaximumSize="512m" destdir="${java.classes}" debug="true" debuglevel="lines,vars,source" classpathref="external.dependencies" tempdir="${java.io.tmpdir}">
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<src refid="java.source.path" />
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<compilerarg value="-proc:none" />
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</javac>
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</target>
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<target name="gatk.compile.external.source" depends="gatk.compile.internal.source" if="include.external">
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<subant target="compile" genericantfile="build.xml">
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<property name="build.dir" value="${external.build.dir}" />
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<property name="dist.dir" value="${external.dist.dir}" />
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<property name="gatk.classpath" value="${external.gatk.classpath}" />
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<fileset dir="${external.dir}" includes="*/build.xml" erroronmissingdir="false" />
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</subant>
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</target>
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<target name="gatk.compile.source" depends="gatk.compile.internal.source,gatk.compile.external.source" description="Compile the GATK source" />
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<target name="gatk.contracts" depends="gatk.compile.source" if="include.contracts">
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<javac fork="true" memoryMaximumSize="512m" destdir="${java.contracts.dir}" debug="true" debuglevel="lines,vars,source" tempdir="${java.io.tmpdir}" >
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<src refid="java.source.path" />
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<classpath>
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|
<path refid="external.dependencies" />
|
|
<pathelement path="${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}" />
|
|
</path>
|
|
|
|
<javadoc doclet="org.broadinstitute.sting.utils.help.ResourceBundleExtractorDoclet"
|
|
docletpathref="doclet.classpath"
|
|
classpathref="external.dependencies"
|
|
classpath="${java.classes}"
|
|
additionalparam="-build-timestamp "${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}">
|
|
<include name="**/utils/**/*.class"/>
|
|
<exclude name="**/utils/codecs/vcf/**/*.class"/>
|
|
<exclude name="**/utils/variantcontext/**/*.class"/>
|
|
</fileset>
|
|
<fileset dir="${java.classes}" includes="**/commandline/**/*.class"/>
|
|
<fileset dir="${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="${R.script.staging.dir}">
|
|
<include name="**/utils/**/*.R"/>
|
|
</fileset>
|
|
<manifest>
|
|
<attribute name="Premain-Class" value="org.broadinstitute.sting.utils.instrumentation.Sizeof" />
|
|
</manifest>
|
|
</jar>
|
|
</target>
|
|
|
|
<target name="vcf.jar" depends="gatk.compile,init.jar">
|
|
<jar jarfile="${dist.dir}/vcf.jar">
|
|
<fileset dir="${java.classes}">
|
|
<include name="org/broadinstitute/sting/utils/codecs/vcf/**/*.class"/>
|
|
<include name="org/broadinstitute/sting/utils/codecs/bcf2/**/*.class"/>
|
|
<include name="org/broadinstitute/sting/utils/variantcontext/**/*.class"/>
|
|
<include name="org/broadinstitute/sting/utils/exceptions/**"/>
|
|
<include name="org/broadinstitute/sting/utils/help/DocumentedGATKFeature.class"/>
|
|
</fileset>
|
|
</jar>
|
|
</target>
|
|
|
|
<target name="gatk.jar" depends="gatk.compile, init.jar, R.script.stage" description="generate the GATK distribution">
|
|
<jar jarfile="${dist.dir}/GenomeAnalysisTK.jar">
|
|
<path refid="gatk.resources"/>
|
|
<fileset dir="${java.contracts.dir}" />
|
|
<fileset dir="${java.classes}">
|
|
<include name="${resource.file}" />
|
|
<include name="**/gatk/**/*.class" />
|
|
<include name="**/alignment/**/*.class"/>
|
|
</fileset>
|
|
<fileset dir="${R.script.staging.dir}">
|
|
<include name="**/gatk/**/*.R"/>
|
|
<include name="**/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="${java.classes}" includes="**/alignment/**/*.class" />
|
|
</jar>
|
|
|
|
<subant target="dist" genericantfile="build.xml">
|
|
<property name="build.dir" value="${external.build.dir}" />
|
|
<property name="dist.dir" value="${external.dist.dir}" />
|
|
<property name="gatk.classpath" value="${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="${R.script.staging.dir}">
|
|
<include name="org/broadinstitute/sting/queue/**/*.R"/>
|
|
</fileset>
|
|
<manifest>
|
|
<attribute name="Main-Class" value="org.broadinstitute.sting.queue.QCommandLine" />
|
|
</manifest>
|
|
</jar>
|
|
</target>
|
|
|
|
<target name="sting.jar" depends="sting-utils.jar, vcf.jar, gatk.jar, queue.jar" />
|
|
|
|
<target name="init.manifests" depends="sting.jar">
|
|
<pathconvert property="jar.classpath" pathsep=" ">
|
|
<flattenmapper/>
|
|
<fileset dir="${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}"
|
|
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.buildgatkfull" depends="init.publicprotectedonly, init.javaonly">
|
|
<property name="executable" value="GenomeAnalysisTK" />
|
|
</target>
|
|
|
|
<target name="init.buildgatklite" depends="init.publiconly, init.javaonly">
|
|
<property name="executable" value="GenomeAnalysisTKLite" />
|
|
</target>
|
|
|
|
<target name="init.buildqueuefull" depends="init.publicprotectedonly, init.javaandscala">
|
|
<property name="executable" value="Queue" />
|
|
</target>
|
|
|
|
<target name="init.buildqueuelite" depends="init.publiconly, init.javaandscala">
|
|
<property name="executable" value="QueueLite" />
|
|
</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="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! -->
|
|
<target name="package.gatk.full" depends="init.buildgatkfull,package" />
|
|
|
|
<target name="package.gatk.lite" depends="init.buildgatklite,package" />
|
|
|
|
<target name="package.queue.full" depends="init.buildqueuefull,package" />
|
|
|
|
<target name="package.queue.lite" depends="init.buildqueuelite,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.gatk.lite" depends="package.gatk.lite,release" />
|
|
|
|
<target name="release.queue.full" depends="package.queue.full,release" />
|
|
|
|
<target name="release.queue.lite" depends="package.queue.lite,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>
|
|
|
|
|
|
<!-- ******************************************************************************** -->
|
|
<!-- Clean -->
|
|
<!-- ******************************************************************************** -->
|
|
|
|
<target name="clean.gatkdocs">
|
|
<delete dir="${gatkdocs.dir}"/>
|
|
</target>
|
|
|
|
<target name="clean.javadoc">
|
|
<delete dir="${javadoc.dir}" />
|
|
</target>
|
|
|
|
<target name="clean.scaladoc">
|
|
<delete dir="${scaladoc.dir}" />
|
|
</target>
|
|
|
|
<target name="clean.gsalib">
|
|
<!-- Currently not cleaning out the lib during 'ant clean' -->
|
|
<exec executable="R" failonerror="false">
|
|
<arg line="R CMD REMOVE gsalib" />
|
|
</exec>
|
|
</target>
|
|
|
|
<target name="clean" description="clean up" depends="clean.javadoc,clean.scaladoc,clean.gatkdocs">
|
|
<delete dir="${build.dir}"/>
|
|
<delete dir="${lib.dir}"/>
|
|
<delete dir="${contract.dump.dir}"/>
|
|
<delete dir="${staging.dir}"/>
|
|
<delete dir="${dist.dir}"/>
|
|
<delete dir="${pipelinetest.dir}"/>
|
|
</target>
|
|
|
|
|
|
<!-- ******************************************************************************** -->
|
|
<!-- gsalib -->
|
|
<!-- ******************************************************************************** -->
|
|
|
|
<!-- Build gsalib R module -->
|
|
<target name="gsalib">
|
|
<exec executable="R" failonerror="true">
|
|
<arg line="R CMD INSTALL --preclean ${R.public.src.dir}/${R.package.path}/gsalib" />
|
|
</exec>
|
|
</target>
|
|
|
|
|
|
<!-- ***************************************************************************** -->
|
|
<!-- *********** Tests and associated tasks ********* -->
|
|
<!-- ***************************************************************************** -->
|
|
|
|
<!-- Properties and Paths -->
|
|
|
|
<property name="java.test.classes" value="${build.dir}/java/testclasses"/>
|
|
<property name="java.public.test.sources" value="${public.dir}/java/test"/>
|
|
<property name="java.private.test.sources" value="${private.dir}/java/test"/>
|
|
<property name="java.protected.test.sources" value="${protected.dir}/java/test"/>
|
|
<property name="scala.test.classes" value="${build.dir}/scala/testclasses"/>
|
|
<property name="scala.public.test.sources" value="${public.dir}/scala/test"/>
|
|
<property name="scala.private.test.sources" value="${private.dir}/scala/test"/>
|
|
<property name="scala.protected.test.sources" value="${protected.dir}/scala/test"/>
|
|
<property name="pipelinetest.dir" value="pipelinetests" />
|
|
<property name="report" value="${build.dir}/report"/>
|
|
<property name="iwww.report.dir" value="${user.home}/private_html/report"/>
|
|
<property name="test.output" value="${dist.dir}/test"/>
|
|
<property name="testng.jar" value="${lib.dir}/testng-5.14.1.jar"/>
|
|
<property name="test.maxmemory" value="4g"/> <!-- provide a ceiling on the memory that unit/integration tests can consume. -->
|
|
|
|
<path id="java.test.source.path">
|
|
<dirset dir="${basedir}">
|
|
<include name="${java.public.test.sources}" />
|
|
<include name="${java.private.test.sources}" if="include.private" />
|
|
<include name="${java.protected.test.sources}" if="include.protected" />
|
|
</dirset>
|
|
</path>
|
|
|
|
<path id="scala.test.source.path">
|
|
<dirset dir="${basedir}">
|
|
<include name="${scala.public.test.sources}" />
|
|
<include name="${scala.private.test.sources}" if="include.private" />
|
|
<include name="${scala.protected.test.sources}" if="include.protected" />
|
|
</dirset>
|
|
</path>
|
|
|
|
<path id="testng.dependencies">
|
|
<fileset dir="${lib.dir}">
|
|
<include name="jcommander*.jar"/>
|
|
<include name="guice*.jar"/>
|
|
<include name="junit*.jar"/>
|
|
<include name="bsh*.jar"/>
|
|
<include name="snakeyaml*.jar"/>
|
|
<include name="reportng*.jar"/>
|
|
</fileset>
|
|
</path>
|
|
|
|
<path id="testng.default.classpath">
|
|
<pathelement location="${java.classes}" />
|
|
<pathelement location="${scala.classes}" />
|
|
<pathelement location="${java.contracts.dir}" />
|
|
<pathelement location="${java.test.classes}" />
|
|
<pathelement location="${scala.test.classes}" />
|
|
<pathelement location="${R.tar.dir}" />
|
|
<path refid="R.script.source.path" />
|
|
<pathelement location="${key.dir}" />
|
|
<path refid="external.dependencies" />
|
|
</path>
|
|
|
|
<!-- Test targets -->
|
|
|
|
<target name="test.init.compile">
|
|
<mkdir dir="${java.test.classes}"/>
|
|
<mkdir dir="${scala.test.classes}"/>
|
|
<antcall target="resolve">
|
|
<param name="ivy.conf" value="test"/>
|
|
</antcall>
|
|
</target>
|
|
|
|
<target name="test.java.internal.compile" depends="dist,test.init.compile">
|
|
<echo message="Sting: Compiling java test cases!"/>
|
|
<javac fork="true" memoryMaximumSize="512m" destdir="${java.test.classes}" debug="true" optimize="on" tempdir="${java.io.tmpdir}">
|
|
<src refid="java.test.source.path" />
|
|
<classpath>
|
|
<path refid="external.dependencies" />
|
|
<pathelement location="${java.classes}"/>
|
|
<pathelement location="${java.contracts.dir}"/>
|
|
<pathelement location="${testng.jar}"/>
|
|
</classpath>
|
|
<compilerarg value="-proc:none"/>
|
|
</javac>
|
|
</target>
|
|
|
|
<target name="test.java.external.compile" depends="dist,test.init.compile,test.java.internal.compile" if="include.external">
|
|
<echo message="Sting: Compiling external java test cases!"/>
|
|
<javac fork="true" memoryMaximumSize="512m" destdir="${java.test.classes}" debug="true" optimize="on" tempdir="${java.io.tmpdir}" srcdir="${external.dir}">
|
|
<include name="*/test/**/*.java"/>
|
|
<classpath>
|
|
<path refid="external.dependencies" />
|
|
<pathelement location="${java.test.classes}"/>
|
|
<pathelement location="${java.classes}"/>
|
|
<pathelement location="${java.contracts.dir}"/>
|
|
<pathelement location="${testng.jar}"/>
|
|
</classpath>
|
|
<compilerarg value="-proc:none"/>
|
|
</javac>
|
|
</target>
|
|
|
|
<target name="test.java.compile" depends="test.java.internal.compile, test.java.external.compile"/>
|
|
|
|
<target name="test.scala.compile" depends="test.java.compile,scala.compile" if="include.scala">
|
|
<echo message="Scala: Compiling test cases!"/>
|
|
<scalac fork="true" jvmargs="-Xmx512m" destdir="${scala.test.classes}" deprecation="yes" unchecked="yes">
|
|
<src refid="scala.test.source.path" />
|
|
<classpath>
|
|
<path refid="scala.dependencies"/>
|
|
<pathelement location="${java.test.classes}"/>
|
|
<pathelement location="${testng.jar}"/>
|
|
</classpath>
|
|
</scalac>
|
|
</target>
|
|
|
|
<!-- NOTE: contracts enabled for all tests -->
|
|
<target name="test.compile" depends="init.usecontracts,dist,test.java.compile,test.scala.compile" />
|
|
|
|
|
|
<!-- Run test macro -->
|
|
<macrodef name="run-test">
|
|
<attribute name="testtype"/>
|
|
<attribute name="outputdir"/>
|
|
<attribute name="runfailed"/>
|
|
|
|
<sequential>
|
|
<condition property="run.failed.tests">
|
|
<equals arg1="@{runfailed}" arg2="true"/>
|
|
</condition>
|
|
|
|
<!-- Get the pipeline run type. Default to dry. -->
|
|
<condition property="pipeline.run" value="dry" else="${pipeline.run}">
|
|
<equals arg1="${pipeline.run}" arg2="$${pipeline.run}" />
|
|
</condition>
|
|
|
|
<condition property="cofoja.jvm.args" value="-javaagent:${cofoja.jar} -Dcom.google.java.contract.log.contract=false" else="">
|
|
<isset property="include.contracts" />
|
|
</condition>
|
|
|
|
<condition property="debug.jvm.args" value="-Xdebug -Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=${test.debug.port}" else="">
|
|
<isset property="test.debug" />
|
|
</condition>
|
|
|
|
<mkdir dir="@{outputdir}"/>
|
|
|
|
<echo message="" />
|
|
<echo message="Test Classpath ID: ${testng.classpath}" />
|
|
<property name="test.classpath.display.string" refid="${testng.classpath}" />
|
|
<echo message="Test Classpath: ${test.classpath.display.string}" />
|
|
<echo message="" />
|
|
<echo message="Sting: Running @{testtype} test cases!"/>
|
|
|
|
<taskdef resource="testngtasks" classpath="${testng.jar}"/>
|
|
<testng outputDir="@{outputdir}"
|
|
classpathref="${testng.classpath}"
|
|
haltOnFailure="false" failureProperty="test.failure"
|
|
verbose="2"
|
|
workingDir="${basedir}"
|
|
useDefaultListeners="false"
|
|
listeners="org.testng.reporters.FailedReporter,org.testng.reporters.JUnitXMLReporter,org.broadinstitute.sting.StingTextReporter,org.uncommons.reportng.HTMLReporter">
|
|
<jvmarg value="-Xmx${test.maxmemory}" />
|
|
<jvmarg value="-ea" />
|
|
<jvmarg value="-Djava.awt.headless=true" />
|
|
<jvmarg value="-Dpipeline.run=${pipeline.run}" />
|
|
<jvmarg value="-Djava.io.tmpdir=${java.io.tmpdir}" />
|
|
<jvmarg line="${cofoja.jvm.args}"/>
|
|
<jvmarg line="${debug.jvm.args}"/>
|
|
|
|
<!-- NOTE: To run tests with debugging, use -Dtest.debug=true -Dtest.debug.port=XXXX on the command line -->
|
|
|
|
<classfileset dir="${java.test.classes}" includes="**/@{testtype}.class"/>
|
|
<classfileset dir="${java.external.test.classes}" erroronmissingdir="false">
|
|
<include name="**/@{testtype}.class" if="include.external"/>
|
|
</classfileset>
|
|
<classfileset dir="${scala.test.classes}" erroronmissingdir="false">
|
|
<include name="**/@{testtype}*.class" if="include.scala"/>
|
|
</classfileset>
|
|
|
|
<xmlfileset dir="${basedir}">
|
|
<include name="@{testtype}" if="run.failed.tests"/>
|
|
</xmlfileset>
|
|
</testng>
|
|
|
|
<!-- generate a report for Bamboo or Hudson to read in -->
|
|
<junitreport todir="@{outputdir}">
|
|
<fileset dir="@{outputdir}">
|
|
<include name="*/*.xml"/>
|
|
</fileset>
|
|
<report format="noframes" todir="@{outputdir}"/>
|
|
</junitreport>
|
|
|
|
<!-- copy the report to our private_html directory for easy viewing in a broswer -->
|
|
<mkdir dir="${iwww.report.dir}/@{testtype}"/>
|
|
<copy todir="${iwww.report.dir}/@{testtype}" verbose="true">
|
|
<fileset dir="@{outputdir}"/>
|
|
</copy>
|
|
|
|
<fail message="test failed" if="test.failure" />
|
|
</sequential>
|
|
</macrodef>
|
|
|
|
|
|
<target name="test.init">
|
|
<property name="testng.classpath" value="testng.default.classpath" />
|
|
</target>
|
|
|
|
<target name="init.testgatkjar">
|
|
<path id="gatk.binary.release.tests.classpath">
|
|
<path refid="testng.dependencies" />
|
|
<path>
|
|
<fileset dir="${package.output.dir}">
|
|
<include name="**/${executable}.jar" />
|
|
</fileset>
|
|
</path>
|
|
<pathelement location="${java.contracts.dir}" />
|
|
<pathelement location="${java.test.classes}" />
|
|
<pathelement location="${scala.test.classes}" />
|
|
<pathelement location="${scala.classes}" />
|
|
<path>
|
|
<fileset dir="${lib.dir}">
|
|
<include name="scala*.jar"/>
|
|
<include name="jna*.jar"/>
|
|
</fileset>
|
|
</path>
|
|
</path>
|
|
<property name="testng.classpath" value="gatk.binary.release.tests.classpath" />
|
|
</target>
|
|
|
|
<target name="init.testqueuejar">
|
|
<path id="queue.binary.release.tests.classpath">
|
|
<path refid="testng.dependencies" />
|
|
<path>
|
|
<fileset dir="${package.output.dir}">
|
|
<include name="**/${executable}.jar" />
|
|
</fileset>
|
|
</path>
|
|
<pathelement location="${java.contracts.dir}" />
|
|
<pathelement location="${java.test.classes}" />
|
|
<pathelement location="${scala.test.classes}" />
|
|
</path>
|
|
<property name="testng.classpath" value="queue.binary.release.tests.classpath" />
|
|
</target>
|
|
|
|
|
|
<target name="committests" depends="unittest,integrationtest,pipelinetest" />
|
|
|
|
<!-- Order of the dependencies is significant in the *.release.tests targets -->
|
|
<target name="gatkfull.binary.release.tests" depends="init.usecontracts,package.gatk.full,init.testgatkjar,unittest,integrationtest" />
|
|
|
|
<target name="gatklite.binary.release.tests" depends="init.usecontracts,package.gatk.lite,init.testgatkjar,unittest,integrationtest" />
|
|
|
|
<target name="queuefull.binary.release.tests" depends="init.usecontracts,package.queue.full,init.testqueuejar,pipelinetest" />
|
|
|
|
<target name="queuelite.binary.release.tests" depends="init.usecontracts,package.queue.lite,init.testqueuejar,pipelinetest" />
|
|
|
|
|
|
<!-- Our four different test types: UnitTest, IntegrationTest, LargeScaleTest, PipelineTest -->
|
|
<target name="unittest" depends="test.compile,test.init" description="Run unit tests">
|
|
<condition property="ttype" value="*UnitTest" else="${single}">
|
|
<not><isset property="single"/></not>
|
|
</condition>
|
|
<run-test testtype="${ttype}" outputdir="${report}/${ttype}" runfailed="false"/>
|
|
</target>
|
|
|
|
<!-- Keep the alias "test" for "unittest" for backwards compatibility -->
|
|
<target name="test" depends="unittest" />
|
|
|
|
<target name="integrationtest" depends="test.compile,test.init" description="Run integration tests">
|
|
<condition property="itype" value="*IntegrationTest" else="${single}">
|
|
<not><isset property="single"/></not>
|
|
</condition>
|
|
<run-test testtype="${itype}" outputdir="${report}/${itype}" runfailed="false"/>
|
|
</target>
|
|
|
|
<target name="largescaletest" depends="test.compile,test.init" description="Run large-scale tests">
|
|
<condition property="ptype" value="*LargeScaleTest" else="${single}">
|
|
<not><isset property="single"/></not>
|
|
</condition>
|
|
<run-test testtype="${ptype}" outputdir="${report}/${ptype}" runfailed="false"/>
|
|
</target>
|
|
|
|
<target name="pipelinetest" depends="test.compile,test.init" description="Run pipeline tests">
|
|
<condition property="pipetype" value="*PipelineTest" else="${single}">
|
|
<not><isset property="single"/></not>
|
|
</condition>
|
|
<run-test testtype="${pipetype}" outputdir="${report}/${pipetype}" runfailed="false"/>
|
|
</target>
|
|
|
|
<target name="pipelinetestrun" depends="test.compile,test.init" description="Run pipeline tests">
|
|
<property name="pipeline.run" value="run"/>
|
|
<condition property="pipetype" value="*PipelineTest" else="${single}">
|
|
<not><isset property="single"/></not>
|
|
</condition>
|
|
<run-test testtype="${pipetype}" outputdir="${report}/${pipetype}" runfailed="false"/>
|
|
</target>
|
|
|
|
<target name="failed-unit" depends="test.compile,test.init">
|
|
<run-test testtype="${report}/*UnitTest/testng-failed.xml" outputdir="${report}/failed_rerun" runfailed="true"/>
|
|
</target>
|
|
|
|
<target name="failed-integration" depends="test.compile,test.init">
|
|
<run-test testtype="${report}/*IntegrationTest/testng-failed.xml" outputdir="${report}/failed_rerun" runfailed="true"/>
|
|
</target>
|
|
|
|
<target name="failed-largescale" depends="test.compile,test.init">
|
|
<run-test testtype="${report}/*LargeScaleTest/testng-failed.xml" outputdir="${report}/failed_rerun" runfailed="true"/>
|
|
</target>
|
|
|
|
<target name="failed-pipeline" depends="test.compile,test.init">
|
|
<run-test testtype="${report}/*PipelineTest/testng-failed.xml" outputdir="${report}/failed_rerun" runfailed="true"/>
|
|
</target>
|
|
|
|
|
|
<!-- Fast test target that cuts major corners for speed. Requires that a full build has been done first. Java-only, single test class only -->
|
|
<!-- Usage: ant fasttest -Dsingle=TestClass -->
|
|
<target name="fasttest" depends="init.javaonly,init,test.init">
|
|
<condition property="not.clean">
|
|
<and>
|
|
<available file="${build.dir}" />
|
|
<available file="${lib.dir}" />
|
|
<available file="${dist.dir}" />
|
|
<available file="${java.test.classes}" />
|
|
<available file="${testng.jar}" />
|
|
</and>
|
|
</condition>
|
|
<fail message="fasttest requires a NON-CLEAN working directory (INCLUDING test classes). Do a full test build using ant test.compile first." unless="not.clean" />
|
|
|
|
<condition property="no.single.test.specified">
|
|
<equals arg1="${single}" arg2="$${single}" />
|
|
</condition>
|
|
<fail message="Must specify a specific test. Usage: ant fasttest -Dsingle=TestClass" if="no.single.test.specified" />
|
|
|
|
<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>
|
|
|
|
<javac fork="true" memoryMaximumSize="512m" destdir="${java.test.classes}" debug="true" optimize="on" tempdir="${java.io.tmpdir}">
|
|
<src refid="java.test.source.path" />
|
|
<classpath>
|
|
<path refid="external.dependencies" />
|
|
<pathelement location="${java.classes}"/>
|
|
<pathelement location="${testng.jar}"/>
|
|
</classpath>
|
|
<compilerarg value="-proc:none"/>
|
|
</javac>
|
|
|
|
<run-test testtype="${single}" outputdir="${report}/${single}" runfailed="false"/>
|
|
</target>
|
|
</project>
|