1224 lines
56 KiB
XML
1224 lines
56 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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<property name="build.sysclasspath" value="first" />
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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="contract.dump.dir" value="dump" />
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<property name="pipelinetest.dir" value="pipelinetests" />
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<property name="lib.dir" value="lib" />
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<property name="external.dir" value="external" />
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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="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.classes" value="${build.dir}/java/classes" />
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<property name="R.public.scripts.dir" value="${public.dir}/R/scripts" />
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<property name="R.private.scripts.dir" value="${private.dir}/R/scripts" />
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<property name="R.public.src.dir" value="${public.dir}/R/src" />
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<!-- Legacy: Installing libraries back into the source directory
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instead of the build or dist directory... intentionally avoids ant clean?? -->
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<property name="R.library.dir" value="${public.dir}/R" />
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<property name="R.tar.dir" value="${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="resource.file" value="StingText.properties" />
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<property name="resource.path" value="${java.classes}/StingText.properties" />
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<property name="scala.public.source.dir" value="${public.dir}/scala/src" />
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<property name="scala.private.source.dir" value="${private.dir}/scala/src" />
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<property name="scala.classes" value="${build.dir}/scala/classes" />
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<property name="queue-extensions.source.dir" value="${build.dir}/queue-extensions/src" />
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<property name="javadoc.dir" value="javadoc" />
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<property name="scaladoc.dir" value="scaladoc" />
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<!-- Contracts for Java -->
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<!-- By default, enabled only for test targets -->
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<!-- To disable for test targets, run with -Duse.contracts=false -->
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<!-- To enable for non-test targets, run with -Duse.contracts=true -->
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<property name="java.contracts" value="${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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<!-- where to find 'findbugs', which you must set if you plan to use 'ant findbugs' -->
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<property name="findbugs.home" value="./findbugs"/>
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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?
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false means it goes to the screen (default) true to file -->
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<property name="usefile" value="false" />
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<!-- If running the 'package' task, this property controls the name of the xml file to package -->
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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="executable" value="GenomeAnalysisTK" />
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<property environment="env"/>
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<patternset id="java.source.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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</patternset>
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<fileset id="java.source.files" dir="${basedir}">
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<patternset refid="java.source.pattern" />
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</fileset>
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<!-- terrible hack to get gatkdocs to see all files -->
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<patternset id="all.java.source.pattern">
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<include name="${java.public.source.dir}/**/*.java" />
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<include name="${java.private.source.dir}/**/*.java" />
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</patternset>
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<fileset id="all.java.source.files" dir="${basedir}">
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<patternset refid="all.java.source.pattern" />
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</fileset>
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<fileset id="external.source.files" dir="${external.dir}" erroronmissingdir="false">
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<include name="**/*.java" />
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</fileset>
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<fileset id="java.class.files" dir="${java.classes}" erroronmissingdir="false">
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<include name="**/*.class"/>
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</fileset>
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<!-- 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="${java.private.source.dir}/**/templates/*" if="include.private" />
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</fileset>
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</path>
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<patternset id="dependency.mask" includes="*.jar">
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<exclude name="testng*.jar" />
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<exclude name="bcel*.jar" />
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</patternset>
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<path id="external.dependencies">
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<fileset dir="${lib.dir}">
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<patternset refid="dependency.mask" />
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</fileset>
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</path>
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<path id="testng.dependencies">
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<fileset dir="${lib.dir}">
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<include name="jcommander*.jar"/>
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<include name="guice*.jar"/>
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<include name="junit*.jar"/>
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<include name="bsh*.jar"/>
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<include name="snakeyaml*.jar"/>
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</fileset>
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</path>
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<path id="build.results">
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<fileset dir="dist">
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<patternset refid="dependency.mask" />
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</fileset>
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</path>
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<!-- Path to scala dependencies. -->
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<path id="scala.dependencies">
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<path refid="external.dependencies" />
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<pathelement location="${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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<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"
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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="${ivy.jar.dir}/ivy-2.2.0-rc1.jar"/>
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<!--
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An old versions of the ivy-1.4.1.xml does not contain /ivy-module/configuration/conf/@name="compile".
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Easier to upgrade to 1.4.4 than try to deal with xmlproperty and conditional deletion in ant.
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Just in case we remove explicit 1.4.4 and go back to 1.4.1, try to clean out the file for now.
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-->
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<delete file="${ivy.home}/cache/javax.mail/mail/ivy-1.4.1.xml"/>
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<delete file="${ivy.home}/cache/javax.mail/mail/ivydata-1.4.1.properties"/>
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<delete file="${ivy.home}/cache/javax.mail/mail/jars/mail-1.4.1.jar"/>
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</target>
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<target name="init.buildall">
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<!-- Set the properties needed to build everything -->
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<property name="gatk.target" value="private"/>
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<property name="scala.target" value="core"/>
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</target>
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<target name="init.buildpublic">
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<!-- Set the properties needed to build public only -->
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<property name="gatk.target" value="core"/>
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<property name="scala.target" value="core"/>
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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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<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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<!-- define some key locations that might change based on how the build is run -->
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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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<!-- Set target based on STING_BUILD_TYPE environment variable -->
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<condition property="sting.target" value="core" else="${env.STING_BUILD_TYPE}">
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<equals arg1="${env.STING_BUILD_TYPE}" arg2="$${env.STING_BUILD_TYPE}" />
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</condition>
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<!-- Get the gatk build target. Default to the STING_BUILD_TYPE. -->
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<condition property="gatk.target" value="${sting.target}" else="${env.GATK_BUILD_TYPE}">
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<equals arg1="${env.GATK_BUILD_TYPE}" arg2="$${env.GATK_BUILD_TYPE}" />
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</condition>
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<!-- Get the queue build target. Default to none. -->
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<condition property="scala.target" value="none" else="${env.QUEUE_BUILD_TYPE}">
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<equals arg1="${env.QUEUE_BUILD_TYPE}" arg2="$${env.QUEUE_BUILD_TYPE}" />
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</condition>
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<!-- If the scala target is set, then include all scala tasks. -->
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<condition property="scala.include">
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<or>
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<not><equals arg1="${scala.target}" arg2="none" /></not>
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</or>
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</condition>
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<echo message="GATK build : ${gatk.target}"/>
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<echo message="Scala build : ${scala.target}"/>
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<echo message="source revision : ${build.version}"/>
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<echo message="build time : ${build.timestamp}" />
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<condition property="include.private">
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<equals arg1="${gatk.target}" arg2="private" casesensitive="false" />
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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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<!-- 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}"/>
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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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</target>
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<target name="init.scala.compile" depends="resolve"
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description="Initializes the scala ant tasks from scala-compiler.jar">
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<path id="scala.classpath">
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<fileset dir="${lib.dir}">
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<include name="scala-compiler-*.jar"/>
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<include name="scala-library-*.jar"/>
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</fileset>
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</path>
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<taskdef resource="scala/tools/ant/antlib.xml">
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<classpath refid="scala.classpath"/>
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</taskdef>
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</target>
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<target name="gatk.compile.public.source" depends="init,resolve">
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<javac fork="true" srcdir="${java.public.source.dir}" memoryMaximumSize="512m" destdir="${java.classes}" debug="true" debuglevel="lines,vars,source" classpathref="external.dependencies" tempdir="${java.io.tmpdir}">
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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.private.source" depends="gatk.compile.public.source" if="include.private">
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<javac fork="true" srcdir="${java.private.source.dir}" memoryMaximumSize="512m" destdir="${java.classes}" debug="true" debuglevel="lines,vars,source" classpathref="external.dependencies" tempdir="${java.io.tmpdir}">
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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.public.source,gatk.compile.private.source">
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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"
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depends="gatk.compile.public.source,gatk.compile.private.source,gatk.compile.external.source"
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description="compile the GATK source" />
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<target name="gatk.contracts.public" depends="gatk.compile.source" if="include.contracts">
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<javac fork="true" memoryMaximumSize="512m" srcdir="${java.public.source.dir}" destdir="${java.contracts}" debug="true" debuglevel="lines,vars,source" tempdir="${java.io.tmpdir}" >
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<classpath>
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<path refid="external.dependencies" />
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<pathelement path="${java.classes}" />
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</classpath>
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<compilerarg value="-Acom.google.java.contract.debug"/>
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<compilerarg value="-Acom.google.java.contract.dump=${contract.dump.dir}"/>
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<compilerarg value="-proc:only"/>
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</javac>
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</target>
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<target name="check.contracts.private" depends="gatk.contracts.public">
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<condition property="include.contracts.private">
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<and>
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<isset property="include.contracts" />
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<isset property="include.private" />
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</and>
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</condition>
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</target>
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<target name="gatk.contracts.private" depends="check.contracts.private" if="include.contracts.private">
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<javac fork="true" memoryMaximumSize="512m" srcdir="${java.private.source.dir}" destdir="${java.contracts}" debug="true" debuglevel="lines,vars,source" tempdir="${java.io.tmpdir}" >
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<classpath>
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<path refid="external.dependencies" />
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<pathelement path="${java.classes}" />
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</classpath>
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<compilerarg value="-Acom.google.java.contract.debug"/>
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<compilerarg value="-Acom.google.java.contract.dump=${contract.dump.dir}"/>
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<compilerarg value="-proc:only"/>
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</javac>
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</target>
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<target name="gatk.contracts" depends="gatk.contracts.public,gatk.contracts.private"
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description="create GATK contracts" if="include.contracts" />
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<target name="gatk.compile" depends="init,resolve,gatk.compile.source,gatk.contracts" />
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<target name="init.queue-extensions.generate" depends="gatk.compile">
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<condition property="uptodate.queue-extensions.generate">
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<or>
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<not>
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<isset property="scala.include"/>
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</not>
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<uptodate targetfile="${queue-extensions.source.dir}">
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<srcfiles refid="java.class.files"/>
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<srcfiles file="${queue-extensions.gatk.jar}"/>
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</uptodate>
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</or>
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</condition>
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</target>
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<!-- NOTE: Extracting help first to avoid "Unable to load help text. Help output will be sparse." warning message. -->
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<target name="queue-extensions.generate" depends="extracthelp,init.queue-extensions.generate" unless="uptodate.queue-extensions.generate" description="generate GATK modules for Queue">
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<mkdir dir="${queue-extensions.source.dir}"/>
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<echo>Generating Queue GATK extensions...</echo>
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<java fork="true" failonerror="true" classname="org.broadinstitute.sting.queue.extensions.gatk.GATKExtensionsGenerator" >
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<arg value="-outDir" />
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<arg path="${queue-extensions.source.dir}" />
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<arg value="-l" />
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<arg value="WARN" />
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<classpath>
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<file file="${queue-extensions.gatk.jar}"/>
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<path refid="scala.dependencies"/>
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</classpath>
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</java>
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<touch>
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<file file="${queue-extensions.source.dir}"/>
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</touch>
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</target>
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<!-- Scala depends on the java compile -->
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<target name="scala.compile.public" depends="init,resolve,gatk.compile,queue-extensions.generate,init.scala.compile" if="scala.include">
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<mkdir dir="${scala.classes}"/>
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<echo>Building Scala...</echo>
|
|
<scalac fork="true" jvmargs="-Xmx512m" destdir="${scala.classes}" classpathref="scala.dependencies" deprecation="yes" unchecked="yes">
|
|
<src path="${scala.public.source.dir}" />
|
|
<src path="${queue-extensions.source.dir}" />
|
|
<include name="**/*.scala"/>
|
|
</scalac>
|
|
</target>
|
|
|
|
<target name="check.scala.private" depends="scala.compile.public">
|
|
<condition property="include.scala.private">
|
|
<and>
|
|
<isset property="include.private" />
|
|
<isset property="scala.include" />
|
|
</and>
|
|
</condition>
|
|
</target>
|
|
|
|
<target name="scala.compile.private" depends="check.scala.private" if="include.scala.private">
|
|
<scalac fork="true" jvmargs="-Xmx512m" destdir="${scala.classes}" classpathref="scala.dependencies" deprecation="yes" unchecked="yes">
|
|
<src path="${scala.private.source.dir}" />
|
|
<include name="**/*.scala"/>
|
|
</scalac>
|
|
</target>
|
|
|
|
<target name="scala.compile" depends="scala.compile.public,scala.compile.private" if="scala.include" description="compile Scala" />
|
|
|
|
<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.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="${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>
|
|
|
|
<target name="clean.gatkdocs">
|
|
<delete dir="gatkdocs"/>
|
|
</target>
|
|
|
|
<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>
|
|
<union>
|
|
<fileset refid="all.java.source.files"/>
|
|
</union>
|
|
</sourcefiles>
|
|
</javadoc>
|
|
</target>
|
|
|
|
<target name="sting.compile" depends="gatk.compile, scala.compile" />
|
|
|
|
<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="init.jar" depends="sting.compile,extracthelp">
|
|
<mkdir dir="${dist.dir}"/>
|
|
<copy todir="${dist.dir}">
|
|
<fileset dir="${lib.dir}" includes="*.jar"/>
|
|
</copy>
|
|
</target>
|
|
|
|
<target name="sting-utils.jar" depends="gatk.compile, init.jar, R.public.tar">
|
|
<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/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.public.scripts.dir}">
|
|
<include name="**/utils/**/*.R"/>
|
|
</fileset>
|
|
<fileset dir="${R.private.scripts.dir}" erroronmissingdir="false">
|
|
<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/variantcontext/**/*.class"/>
|
|
<include name="org/broadinstitute/sting/gatk/refdata/SelfScopingFeatureCodec.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"
|
|
description="generate the GATK distribution">
|
|
<jar jarfile="${dist.dir}/GenomeAnalysisTK.jar">
|
|
<path refid="gatk.resources"/>
|
|
<fileset dir="${java.contracts}" />
|
|
<fileset dir="${java.classes}">
|
|
<include name="${resource.file}" />
|
|
<include name="**/gatk/**/*.class" />
|
|
<include name="**/alignment/**/*.class"/>
|
|
</fileset>
|
|
<fileset dir="${R.public.scripts.dir}">
|
|
<include name="**/gatk/**/*.R"/>
|
|
<include name="**/alignment/**/*.R"/>
|
|
</fileset>
|
|
<fileset dir="${R.private.scripts.dir}" erroronmissingdir="false">
|
|
<include name="**/gatk/**/*.R"/>
|
|
<include name="**/alignment/**/*.R"/>
|
|
</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>
|
|
|
|
<jar jarfile="${dist.dir}/AnalyzeCovariates.jar" whenmanifestonly="skip">
|
|
<fileset dir="${java.classes}">
|
|
<include name="**/analyzecovariates/**/*.class" />
|
|
<include name="**/gatk/walkers/recalibration/*.class" />
|
|
</fileset>
|
|
<fileset dir="${R.public.scripts.dir}">
|
|
<include name="**/analyzecovariates/**/*.R"/>
|
|
<include name="**/gatk/walkers/recalibration/**/*.R"/>
|
|
</fileset>
|
|
<fileset dir="${R.private.scripts.dir}" erroronmissingdir="false">
|
|
<include name="**/analyzecovariates/**/*.R"/>
|
|
<include name="**/gatk/walkers/recalibration/**/*.R"/>
|
|
</fileset>
|
|
<manifest>
|
|
<attribute name="Main-Class" value="org.broadinstitute.sting.analyzecovariates.AnalyzeCovariates" />
|
|
</manifest>
|
|
</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="scala.include">
|
|
<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" if="scala.include">
|
|
<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.public.scripts.dir}">
|
|
<include name="org/broadinstitute/sting/queue/**/*.R"/>
|
|
</fileset>
|
|
<fileset dir="${R.private.scripts.dir}" erroronmissingdir="false">
|
|
<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>
|
|
|
|
<jar jarfile="${dist.dir}/AnalyzeCovariates.jar" update="true" whenmanifestonly="skip">
|
|
<manifest>
|
|
<attribute name="Class-Path" value="${jar.classpath}" />
|
|
</manifest>
|
|
</jar>
|
|
|
|
</target>
|
|
|
|
<target name="queue.manifests" depends="queue.jar, init.manifests" if="scala.include">
|
|
<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" />
|
|
|
|
<target name="dist" depends="sting.manifests" />
|
|
|
|
<target name="core" description="force a build of the Sting core code">
|
|
<antcall target="dist" inheritAll="false">
|
|
<param name="sting.target" value="core" />
|
|
</antcall>
|
|
</target>
|
|
|
|
<target name="private" description="force a build of the Sting private code">
|
|
<antcall target="dist" inheritAll="false">
|
|
<param name="sting.target" value="private" />
|
|
</antcall>
|
|
</target>
|
|
|
|
<target name="queue" description="force a build of Queue">
|
|
<!--
|
|
inheritAll is false so that 'ant queue' does not accidentally import
|
|
params if the build was called with 'ant clean oneoffs queue'.
|
|
Instead this task resets the parameters and is just like running
|
|
a fresh 'ant dist -Dscala.target=core'.
|
|
-->
|
|
<antcall target="dist" inheritAll="false">
|
|
<param name="scala.target" value="core" />
|
|
</antcall>
|
|
</target>
|
|
|
|
<!-- new scala target -->
|
|
|
|
<target name="scala" description="build the scala directory">
|
|
<antcall target="scala.jar" inheritAll="false">
|
|
<param name="scala.target" value="core" />
|
|
</antcall>
|
|
</target>
|
|
|
|
<!-- ***************************************************************************** -->
|
|
<!-- *********** Tests and associated tasks ********* -->
|
|
<!-- ***************************************************************************** -->
|
|
<!-- where to put reports and tests-->
|
|
<property name="report" value="${build.dir}/report"/>
|
|
<property name="test.output" value="${dist.dir}/test"/>
|
|
<property name="java.test.classes" value="${build.dir}/java/testclasses"/>
|
|
<property name="java.public.test.classes" value="${java.test.classes}/public"/>
|
|
<property name="java.private.test.classes" value="${java.test.classes}/private"/>
|
|
<property name="java.public.test.sources" value="${public.dir}/java/test"/>
|
|
<property name="java.private.test.sources" value="${private.dir}/java/test"/>
|
|
<property name="scala.test.classes" value="${build.dir}/scala/testclasses"/>
|
|
<property name="scala.public.test.classes" value="${scala.test.classes}/public"/>
|
|
<property name="scala.private.test.classes" value="${scala.test.classes}/private"/>
|
|
<property name="scala.public.test.sources" value="${public.dir}/scala/test"/>
|
|
<property name="scala.private.test.sources" value="${private.dir}/scala/test"/>
|
|
<property name="testng.jar" value="${lib.dir}/testng-5.14.1.jar"/>
|
|
<!-- provide a ceiling on the memory that unit/integration tests can consume. -->
|
|
<property name="test.maxmemory" value="4g"/>
|
|
|
|
<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.public.compile" depends="dist,test.init.compile">
|
|
<mkdir dir="${java.public.test.classes}"/>
|
|
<echo message="Sting: Compiling public test cases!"/>
|
|
<javac fork="true" memoryMaximumSize="512m" destdir="${java.public.test.classes}" debug="true" optimize="on" tempdir="${java.io.tmpdir}">
|
|
<src path="${java.public.test.sources}"/>
|
|
<classpath>
|
|
<path refid="external.dependencies" />
|
|
<pathelement location="${java.classes}"/>
|
|
<pathelement location="${java.contracts}"/>
|
|
<pathelement location="${testng.jar}"/>
|
|
</classpath>
|
|
<compilerarg value="-proc:none"/>
|
|
</javac>
|
|
</target>
|
|
|
|
<target name="test.java.private.compile" depends="dist,test.init.compile,test.java.public.compile" if="include.private">
|
|
<mkdir dir="${java.private.test.classes}"/>
|
|
<echo message="Sting: Compiling private test cases!"/>
|
|
<javac fork="true" memoryMaximumSize="512m" destdir="${java.private.test.classes}" debug="true" optimize="on" tempdir="${java.io.tmpdir}">
|
|
<src path="${java.private.test.sources}"/>
|
|
<classpath>
|
|
<path refid="external.dependencies" />
|
|
<pathelement location="${java.public.test.classes}"/>
|
|
<pathelement location="${java.classes}"/>
|
|
<pathelement location="${java.contracts}"/>
|
|
<pathelement location="${testng.jar}"/>
|
|
</classpath>
|
|
<compilerarg value="-proc:none"/>
|
|
</javac>
|
|
</target>
|
|
|
|
<target name="test.java.compile" depends="test.java.public.compile, test.java.private.compile"/>
|
|
|
|
<target name="test.scala.public.compile" depends="test.java.compile,scala.compile" if="scala.include">
|
|
<mkdir dir="${scala.public.test.classes}"/>
|
|
<echo message="Scala: Compiling public test cases!"/>
|
|
<scalac fork="true" jvmargs="-Xmx512m" destdir="${scala.public.test.classes}" deprecation="yes" unchecked="yes">
|
|
<src path="${scala.public.test.sources}" />
|
|
<classpath>
|
|
<path refid="scala.dependencies"/>
|
|
<pathelement location="${java.public.test.classes}"/>
|
|
<pathelement location="${testng.jar}"/>
|
|
</classpath>
|
|
</scalac>
|
|
</target>
|
|
|
|
<target name="test.scala.private.compile" depends="test.java.compile,scala.compile,test.scala.public.compile" if="include.scala.private">
|
|
<mkdir dir="${scala.private.test.classes}"/>
|
|
<echo message="Scala: Compiling private test cases!"/>
|
|
<scalac fork="true" jvmargs="-Xmx512m" destdir="${scala.private.test.classes}" deprecation="yes" unchecked="yes">
|
|
<src path="${scala.private.test.sources}" />
|
|
<classpath>
|
|
<path refid="scala.dependencies"/>
|
|
<pathelement location="${scala.public.test.classes}"/>
|
|
<pathelement location="${java.public.test.classes}"/>
|
|
<pathelement location="${java.private.test.classes}"/>
|
|
<pathelement location="${testng.jar}"/>
|
|
</classpath>
|
|
</scalac>
|
|
</target>
|
|
|
|
<target name="test.scala.compile" depends="test.scala.public.compile,test.scala.private.compile"/>
|
|
|
|
<target name="test.compile" depends="init.usecontracts,test.java.compile,test.scala.compile" />
|
|
|
|
|
|
<path id="testng.default.classpath">
|
|
<pathelement location="${java.classes}" />
|
|
<pathelement location="${scala.classes}" />
|
|
<pathelement location="${java.contracts}" />
|
|
<pathelement location="${java.public.test.classes}" />
|
|
<pathelement location="${java.private.test.classes}" />
|
|
<pathelement location="${scala.public.test.classes}" />
|
|
<pathelement location="${scala.private.test.classes}" />
|
|
<pathelement location="${R.tar.dir}" />
|
|
<pathelement location="${R.public.scripts.dir}" />
|
|
<pathelement location="${R.private.scripts.dir}" />
|
|
<path refid="external.dependencies" />
|
|
</path>
|
|
|
|
<path id="testng.gatk.releasetest.classpath">
|
|
<path refid="testng.dependencies" />
|
|
<path>
|
|
<fileset dir="${package.output.dir}">
|
|
<include name="**/${executable}.jar" />
|
|
</fileset>
|
|
</path>
|
|
<pathelement location="${java.contracts}" />
|
|
<pathelement location="${java.public.test.classes}" />
|
|
<pathelement location="${scala.public.test.classes}" />
|
|
<pathelement location="${scala.classes}" />
|
|
<path>
|
|
<fileset dir="${lib.dir}">
|
|
<include name="scala*.jar"/>
|
|
<include name="jna*.jar"/>
|
|
</fileset>
|
|
</path>
|
|
</path>
|
|
|
|
<path id="testng.queue.releasetest.classpath">
|
|
<path refid="testng.dependencies" />
|
|
<path>
|
|
<fileset dir="${package.output.dir}">
|
|
<include name="**/${executable}.jar" />
|
|
</fileset>
|
|
</path>
|
|
<pathelement location="${java.contracts}" />
|
|
<pathelement location="${java.public.test.classes}" />
|
|
<pathelement location="${scala.public.test.classes}" />
|
|
</path>
|
|
|
|
<!-- TEST -->
|
|
<macrodef name="run-test">
|
|
<attribute name="testtype"/>
|
|
<attribute name="outputdir"/>
|
|
<attribute name="classpath"/>
|
|
<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:${cofoja.jar} -Dcom.google.java.contract.log.contract=false" else="">
|
|
<isset property="include.contracts" />
|
|
</condition>
|
|
|
|
<mkdir dir="@{outputdir}"/>
|
|
<echo message="Sting: Running @{testtype} test cases!"/>
|
|
<taskdef resource="testngtasks" classpath="${testng.jar}"/>
|
|
<testng outputDir="@{outputdir}"
|
|
classpathref="@{classpath}"
|
|
haltOnFailure="false" failureProperty="test.failure"
|
|
verbose="2"
|
|
workingDir="${basedir}"
|
|
useDefaultListeners="false"
|
|
listeners="org.testng.reporters.FailedReporter,org.testng.reporters.JUnitXMLReporter,org.broadinstitute.sting.StingTextReporter">
|
|
<jvmarg value="-Xmx${test.maxmemory}" />
|
|
<jvmarg value="-Djava.awt.headless=true" />
|
|
<jvmarg value="-Dpipeline.run=${pipeline.run}" />
|
|
<jvmarg value="-Djava.io.tmpdir=${java.io.tmpdir}" />
|
|
<jvmarg line="${cofoja.jvm.args}"/>
|
|
<!-- <jvmarg value="-Xdebug"/> -->
|
|
<!-- <jvmarg value="-Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=5005"/> -->
|
|
|
|
<classfileset dir="${java.public.test.classes}" includes="**/@{testtype}.class"/>
|
|
<classfileset dir="${java.private.test.classes}" erroronmissingdir="false">
|
|
<include name="**/@{testtype}.class" if="include.private"/>
|
|
</classfileset>
|
|
<classfileset dir="${scala.public.test.classes}" erroronmissingdir="false">
|
|
<include name="**/@{testtype}*.class" if="scala.include"/>
|
|
</classfileset>
|
|
<classfileset dir="${scala.private.test.classes}" erroronmissingdir="false">
|
|
<include name="**/@{testtype}*.class" if="include.scala.private"/>
|
|
</classfileset>
|
|
|
|
<xmlfileset dir="${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>
|
|
|
|
<fail message="test failed" if="test.failure" />
|
|
</sequential>
|
|
</macrodef>
|
|
|
|
<target name="test.init">
|
|
<property name="testng.classpath" value="testng.default.classpath" />
|
|
</target>
|
|
|
|
<target name="alltests">
|
|
<antcall target="test" inheritAll="false"/>
|
|
<antcall target="integrationtest" inheritAll="false"/>
|
|
<antcall target="pipelinetest" inheritAll="false"/>
|
|
</target>
|
|
|
|
<target name="alltests.public">
|
|
<antcall target="test.public" inheritAll="false"/>
|
|
<antcall target="integrationtest.public" inheritAll="false"/>
|
|
<antcall target="pipelinetest.public" inheritAll="false"/>
|
|
</target>
|
|
|
|
<target name="alltests.gatk.packagejar" depends="init.buildpublic,package">
|
|
<antcall target="test.public" inheritAll="false">
|
|
<param name="testng.classpath" value="testng.gatk.releasetest.classpath" />
|
|
</antcall>
|
|
<antcall target="integrationtest.public" inheritAll="false">
|
|
<param name="testng.classpath" value="testng.gatk.releasetest.classpath" />
|
|
</antcall>
|
|
</target>
|
|
|
|
<target name="alltests.queue.packagejar" depends="init.buildpublic,queue">
|
|
<antcall target="package" inheritAll="false">
|
|
<param name="executable" value="Queue" />
|
|
</antcall>
|
|
<antcall target="pipelinetest.public" inheritAll="false">
|
|
<param name="executable" value="Queue" />
|
|
<param name="testng.classpath" value="testng.queue.releasetest.classpath" />
|
|
</antcall>
|
|
</target>
|
|
|
|
<!-- Our four different test conditions: Test, IntegrationTest, LargeScaleTest, PipelineTest -->
|
|
<target name="test" depends="init.buildall,test.compile,vcf.jar,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}" classpath="${testng.classpath}" runfailed="false"/>
|
|
</target>
|
|
<target name="test.public" depends="init.buildpublic,test"/>
|
|
|
|
<target name="integrationtest" depends="init.buildall,test.compile,test.init" description="Run integration tests">
|
|
<condition property="itype" value="*IntegrationTest" else="${single}">
|
|
<not><isset property="single"/></not>
|
|
</condition>
|
|
<run-test testtype="${itype}" outputdir="${report}/${itype}" classpath="${testng.classpath}" runfailed="false"/>
|
|
</target>
|
|
<target name="integrationtest.public" depends="init.buildpublic,integrationtest"/>
|
|
|
|
<target name="largescaletest" depends="init.buildall,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}" classpath="${testng.classpath}" runfailed="false"/>
|
|
</target>
|
|
<target name="largescaletest.public" depends="init.buildpublic,largescaletest" />
|
|
|
|
<target name="pipelinetest" depends="init.buildall,test.compile,test.init" description="Run pipeline tests">
|
|
<condition property="pipetype" value="*PipelineTest" else="${single}">
|
|
<not><isset property="single"/></not>
|
|
</condition>
|
|
<run-test testtype="${pipetype}" outputdir="${report}/${pipetype}" classpath="${testng.classpath}" runfailed="false"/>
|
|
</target>
|
|
<target name="pipelinetest.public" depends="init.buildpublic,pipelinetest" />
|
|
|
|
<target name="pipelinetestrun" depends="init.buildall,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}" classpath="${testng.classpath}" runfailed="false"/>
|
|
</target>
|
|
<target name="pipelinetestrun.public" depends="init.buildpublic,pipelinetestrun" />
|
|
|
|
<target name="failed-test" depends="init.buildall,test.compile,test.init">
|
|
<run-test testtype="${report}/*UnitTest/testng-failed.xml" outputdir="${report}/failed_rerun" classpath="${testng.classpath}" runfailed="true"/>
|
|
</target>
|
|
|
|
<target name="failed-integration" depends="init.buildall,test.compile,test.init">
|
|
<run-test testtype="${report}/*IntegrationTest/testng-failed.xml" outputdir="${report}/failed_rerun" classpath="${testng.classpath}" runfailed="true"/>
|
|
</target>
|
|
|
|
<target name="failed-largescale" depends="init.buildall,test.compile,test.init">
|
|
<run-test testtype="${report}/*LargeScaleTest/testng-failed.xml" outputdir="${report}/failed_rerun" classpath="${testng.classpath}" runfailed="true"/>
|
|
</target>
|
|
|
|
<target name="failed-pipeline" depends="init.buildall,test.compile,test.init">
|
|
<run-test testtype="${report}/*PipelineTest/testng-failed.xml" outputdir="${report}/failed_rerun" classpath="${testng.classpath}" runfailed="true"/>
|
|
</target>
|
|
|
|
<!-- ******************************************************************************** -->
|
|
<!-- Javadoc -->
|
|
<!-- ******************************************************************************** -->
|
|
|
|
<target name="clean.javadoc">
|
|
<delete dir="${javadoc.dir}" />
|
|
</target>
|
|
|
|
<target name="init.javadoc">
|
|
<mkdir dir="${javadoc.dir}" />
|
|
</target>
|
|
|
|
<target name="javadoc" depends="init.buildpublic,generate.javadoc" description="Generates public javadoc" />
|
|
|
|
<target name="javadoc.private" depends="init.buildall,generate.javadoc" description="Generates public and private javadoc" />
|
|
|
|
<target name="generate.javadoc" depends="init.javadoc,resolve">
|
|
<javadoc destdir="${javadoc.dir}" classpathref="external.dependencies">
|
|
<fileset refid="java.source.files" />
|
|
<sourcepath path="${external.dir}" />
|
|
</javadoc>
|
|
</target>
|
|
|
|
<!-- ******************************************************************************** -->
|
|
<!-- Scaladoc -->
|
|
<!-- ******************************************************************************** -->
|
|
|
|
<target name="clean.scaladoc">
|
|
<delete dir="${scaladoc.dir}" />
|
|
</target>
|
|
|
|
<target name="init.scaladoc">
|
|
<mkdir dir="${scaladoc.dir}" />
|
|
</target>
|
|
|
|
<!-- NOTE: the scaladoc targets require that the environment variable ANT_OPTS has been set to "-Xmx1G" -->
|
|
|
|
<target name="scaladoc" depends="init.buildpublic,generate.scaladoc" description="Generates public scaladoc -- set ANT_OPTS to -Xmx1G" />
|
|
|
|
<target name="scaladoc.private" depends="init.buildall,generate.scaladoc" description="Generates public and private scaladoc -- set ANT_OPTS to -Xmx1G" />
|
|
|
|
<target name="generate.scaladoc" depends="resolve,queue-extensions.generate,init.scala.compile,scala.compile,init.scaladoc">
|
|
<scaladoc srcdir="${basedir}" destdir="${scaladoc.dir}" classpathref="scala.dependencies" deprecation="yes" unchecked="yes">
|
|
<include name="${scala.public.source.dir}/**/*.scala" />
|
|
<include name="${queue-extensions.source.dir}/**/*.scala" />
|
|
<include name="${scala.private.source.dir}/**/*.scala" if="include.private" />
|
|
</scaladoc>
|
|
</target>
|
|
|
|
<!-- ******************************************************************************** -->
|
|
<!-- Release-related tasks -->
|
|
<!-- ******************************************************************************** -->
|
|
|
|
<!-- 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 -->
|
|
<target name="package" depends="dist,stage" 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}/${executable}.xml" target="package" />
|
|
</target>
|
|
|
|
<target name="release" depends="package" description="release a build, putting each file in a location specified by the package">
|
|
<ant antfile="${package.output.dir}/${executable}.xml" target="release" />
|
|
</target>
|
|
|
|
<!-- Build a subset of picard with only those classes we need by completely abusing the packaging system -->
|
|
<!-- TODO: Reuse as much as possible of the 'stage' and 'package' targets -->
|
|
<target name="build-picard-private" depends="resolve">
|
|
<!-- Build out a classpath -->
|
|
<pathconvert property="required.picard.jars" pathsep=":">
|
|
<fileset dir="${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>
|
|
|
|
<!-- ******************************************************************************** -->
|
|
<!-- Find bug tasks -->
|
|
<!-- ******************************************************************************** -->
|
|
<path id="findbugs.classpath">
|
|
<fileset dir="${lib.dir}" erroronmissingdir="true" includes="*.jar"/>
|
|
</path>
|
|
<target name="findbugs" depends="dist">
|
|
<antcall target ="resolve">
|
|
<param name ="ivy.conf" value="test"/>
|
|
</antcall>
|
|
<!-- setup the taskdef, telling ant where to find the defined task for ant -->
|
|
<taskdef name="findbugs" classname="edu.umd.cs.findbugs.anttask.FindBugsTask" classpathref="findbugs.classpath"/>
|
|
<!-- what should findbug look at: we want to aim it at the GATK.jar -->
|
|
<findbugs home="${findbugs.home}"
|
|
output="xml"
|
|
outputFile="${build.dir}/findbugs.xml"
|
|
classpathref="findbugs.classpath"
|
|
debug="false">
|
|
<auxClasspath>
|
|
<fileset dir="dist" includes="**/*.jar" excludes="**/GenomeAnalysisTK.jar"/>
|
|
</auxClasspath>
|
|
<sourcePath path="../java/src" />
|
|
<class location="dist/GenomeAnalysisTK.jar" />
|
|
</findbugs>
|
|
</target>
|
|
|
|
<target name="clean" description="clean up" depends="clean.javadoc,clean.scaladoc,clean.gatkdocs">
|
|
<delete dir="${build.dir}"/>
|
|
<delete dir="${lib.dir}"/>
|
|
<delete dir="${contract.dump.dir}"/>
|
|
<delete dir="${staging.dir}"/>
|
|
<delete dir="${dist.dir}"/>
|
|
<delete dir="${pipelinetest.dir}"/>
|
|
</target>
|
|
|
|
<!-- 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>
|
|
|
|
<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>
|
|
</project>
|