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build.xml
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build.xml
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<?xml version="1.0"?>
<!--
~ The MIT License
~
~ Copyright (c) 2009 The Broad Institute
~
~ Permission is hereby granted, free of charge, to any person obtaining a copy
~ of this software and associated documentation files (the "Software"), to deal
~ in the Software without restriction, including without limitation the rights
~ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
~ copies of the Software, and to permit persons to whom the Software is
~ furnished to do so, subject to the following conditions:
~
~ The above copyright notice and this permission notice shall be included in
~ all copies or substantial portions of the Software.
~
~ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
~ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
~ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
~ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
~ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
~ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
~ THE SOFTWARE.
-->
<project name="picard-public" basedir="." default="all">
<property name="src" value="src/java"/>
<property name="src.scripts" value="src/scripts"/>
<property name="src.test" value="src/tests"/>
<property name="src.test.java" value="${src.test}/java"/>
<property name="lib" value="lib"/>
<property name="dist" value="dist"/>
<property name="classes" value="classes"/>
<property name="classes.test" value="testclasses"/>
<property name="scripts" value="src/scripts"/>
<property name="reports" value="dist/test"/>
<property name="test.output" value="dist/test"/>
<property name="javac.target" value="1.6"/>
<property name="javac.debug" value="true"/>
<!-- Get SVN revision, if available, otherwise leave it blank. -->
<exec executable="svnversion" outputproperty="repository.revision" failifexecutionfails="false"/>
<property name="repository.revision" value=""/>
<property name="sam-version" value="1.102"/>
<property name="picard-version" value="${sam-version}"/>
<property name="tribble-version" value="${sam-version}"/>
<property name="variant-version" value="${sam-version}"/>
<property name="command_tmp" value=".command_tmp"/>
<property name="command-line-html-dir" value="${dist}/html"/>
<property name="testng.verbosity" value="2"/>
<property name="test.debug.port" value="5005" /> <!-- override on the command line if desired -->
<property environment="env"/>
<property name="java6.home" value="${env.JAVA6_HOME}"/>
<condition property="isUnix">
<os family="unix"/>
</condition>
<target name="set_excluded_test_groups_unix" if="isUnix">
<property name="excludedTestGroups" value="slow, broken"/>
</target>
<target name="set_excluded_test_groups_non_unix" unless="isUnix">
<property name="excludedTestGroups" value="slow, broken, unix"/>
</target>
<target name="set_excluded_test_groups" depends="set_excluded_test_groups_unix,set_excluded_test_groups_non_unix"/>
<!-- INIT -->
<target name="init">
<path id="classpath">
<fileset dir="${lib}">
<include name="**/*.jar"/>
</fileset>
</path>
<path id="metrics.classpath">
<pathelement path="${classpath}"/>
<pathelement location="${classes}"/>
</path>
<path id="java6.lib.ref">
<fileset dir="${java6.home}/lib" includes="*.jar"/>
</path>
</target>
<!-- CLEAN -->
<target name="clean">
<delete dir="${classes}"/>
<delete dir="${classes.test}"/>
<delete dir="${test.output}"/>
<delete dir="${dist}"/>
<delete dir="${command_tmp}"/>
<delete dir="javadoc"/>
</target>
<!-- COMPILE -->
<target name="compile" depends="compile-src, compile-tests"
description="Compile files without cleaning">
</target>
<target name="compile-src" depends="compile-sam-jdk, compile-picard, compile-tribble, compile-variant" description="Compile files without cleaning"/>
<target name="compile-sam-jdk" depends="init" description="Compile sam-jdk files without cleaning">
<compile-src includes="net/sf/samtools/**/*.*"/>
</target>
<target name="compile-picard" depends="init, compile-variant" description="Compile picard files without cleaning">
<compile-src includes="net/sf/picard/**/*.*"/>
</target>
<target name="compile-tribble" depends="init" description="Compile tribble files without cleaning">
<compile-src includes="org/broad/tribble/**/*.*"/>
</target>
<target name="compile-variant" depends="init, compile-tribble" description="Compile variant files without cleaning">
<compile-src includes="org/broadinstitute/variant/**/*.*" compiler.args="-proc:none"/>
</target>
<target name="compile-tests" depends="compile-sam-jdk-tests, compile-picard-tests, compile-tribble-tests, compile-variant-tests" description="Compile test files without cleaning"/>
<target name="compile-sam-jdk-tests" depends="init" description="Compile sam-jdk test files without cleaning">
<compile-tests includes="net/sf/samtools/**/*.*"/>
</target>
<target name="compile-picard-tests" depends="init" description="Compile picard test files without cleaning">
<compile-tests includes="net/sf/picard/**/*.*"/>
<copy todir="${classes.test}/">
<fileset dir="${src.test}/scripts" includes="**/*"/>
</copy>
</target>
<target name="compile-tribble-tests" depends="init" description="Compile tribble test files without cleaning">
<compile-tests includes="org/broad/tribble/**/*.*"/>
</target>
<target name="compile-variant-tests" depends="init" description="Compile variant test files without cleaning">
<compile-tests includes="org/broadinstitute/variant/**/*.*" compiler.args="-proc:none"/>
</target>
<!-- TEST -->
<target name="test" depends="compile, set_excluded_test_groups" description="Run unit tests">
<taskdef resource="testngtasks" classpathref="classpath"/>
<testng suitename="picard-tests" classpathref="classpath" outputdir="${test.output}"
failureproperty="tests.failed" excludedgroups="${excludedTestGroups}" workingDir="${basedir}"
verbose="${testng.verbosity}">
<classpath>
<pathelement path="${classes}"/>
<pathelement path="${classes.test}"/>
<pathelement path="${scripts}"/>
</classpath>
<classfileset dir="${classes.test}">
<include name="**/Test*.class"/>
<include name="**/*Test.class"/>
</classfileset>
<jvmarg value="-Xmx2G"/>
</testng>
<junitreport todir="${dist}/test" >
<fileset dir="${test.output}">
<include name="*.xml"/>
</fileset>
<report format="noframes" todir="${dist}/test" styledir="etc/test"/>
</junitreport>
<copy file="etc/test/testng.css" todir="${dist}/test" overwrite="true"/>
<fail if="tests.failed" message="There were failed unit tests"/>
</target>
<target name="single-test"
depends="compile, compile-tests"
description="Compile and run a single test.">
<taskdef resource="testngtasks" classpathref="classpath"/>
<fail unless="name" message="Please provide input test: -Dname=..." />
<condition property="debug.jvm.args" value="-Xdebug -Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=${test.debug.port}" else="">
<isset property="test.debug" />
</condition>
<testng suitename="samtools-single-test" classpathref="classpath" outputdir="${test.output}"
verbose="${testng.verbosity}">
<jvmarg line="-Xmx512M ${debug.jvm.args}"/>
<classpath>
<pathelement path="${classes}"/>
<pathelement path="${classes.test}"/>
<pathelement path="${scripts}"/>
</classpath>
<classfileset dir="${classes.test}">
<include name="**/${name}.class"/>
</classfileset>
</testng>
</target>
<target name="sam-jar" depends="compile-sam-jdk"
description="Builds sam-${sam-version}.jar for inclusion in other projects">
<mkdir dir="${dist}"/>
<jar destfile="${dist}/sam-${sam-version}.jar" compress="no">
<fileset dir="${classes}" includes ="net/sf/samtools/**/*.*"/>
<manifest>
<attribute name="Implementation-Version" value="${picard-version}(${repository.revision})"/>
<attribute name="Implementation-Vendor" value="Broad Institute"/>
</manifest>
</jar>
</target>
<target name="picard-jar" depends="compile"
description="Builds picard-${picard-version}.jar for inclusion in other projects">
<mkdir dir="${dist}"/>
<jar destfile="${dist}/picard-${picard-version}.jar" compress="no">
<fileset dir="${classes}" includes ="net/sf/picard/**/*.*"/>
<fileset dir="${src.scripts}" includes="**/*.R"/>
<zipfileset src="${lib}/apache-ant-1.8.2-bzip2.jar"/>
<manifest>
<attribute name="Implementation-Version" value="${picard-version}(${repository.revision})"/>
<attribute name="Implementation-Vendor" value="Broad Institute"/>
</manifest>
</jar>
</target>
<target name="tribble-jar" depends="compile"
description="Builds tribble-${tribble-version}.jar for inclusion in other projects">
<mkdir dir="${dist}"/>
<jar destfile="${dist}/tribble-${tribble-version}.jar" compress="no">
<fileset dir="${classes}" includes="org/broad/tribble/**/*.*"/>
</jar>
<copy todir="${dist}">
<fileset dir="lib" includes="*.jar"/>
</copy>
</target>
<target name="variant-jar" depends="compile"
description="Builds variant-${variant-version}.jar for inclusion in other projects">
<mkdir dir="${dist}"/>
<jar destfile="${dist}/variant-${variant-version}.jar" compress="no">
<fileset dir="${classes}" includes="org/broadinstitute/variant/**/*.*"/>
</jar>
<copy todir="${dist}">
<fileset dir="lib" includes="*.jar"/>
</copy>
</target>
<target name="javadoc" depends="init" description="Generates the project javadoc.">
<javadoc
sourcepath="${src}"
destdir="javadoc"
packagenames="net.sf.samtools.*, net.sf.picard.*"
windowtitle="SAM JDK API Documentation"
doctitle="<h1>SAM JDK API Documentation</h1>"
author="true"
protected="true"
use="true"
version="true"
failonerror="true">
<classpath location="${java.home}/../lib/tools.jar"/>
<link href="http://java.sun.com/j2se/1.5.0/docs/api/"/>
</javadoc>
<mkdir dir="${command-line-html-dir}"/>
<javadoc sourcepath="${src}/java"
doclet="net.sf.picard.util.MetricsDoclet"
docletpathref="metrics.classpath"
classpathref="metrics.classpath"
failonerror="true">
<sourcepath path="${src}"/>
<arg line="-f ${command-line-html-dir}/picard-metric-definitions.shtml"/>
</javadoc>
</target>
<target name="package-commands" depends="compile, sam-jar, picard-jar, tribble-jar, variant-jar">
<delete dir="${command_tmp}"/>
<mkdir dir="${command_tmp}"/>
<copy todir="${command_tmp}">
<fileset dir="${classes}" includes="**/*"/>
</copy>
<unzip dest=".command_tmp">
<fileset dir="${lib}">
<include name="*.jar"/>
</fileset>
</unzip>
<delete dir="${command-line-html-dir}"/>
<!-- The order of these elements determines the order they appear in the on-line help -->
<!-- If you don't want to generate on-line doc for a command, use package-command instead of package-and-document-command -->
<package-and-document-command title="AddOrReplaceReadGroups" main-class="net.sf.picard.sam.AddOrReplaceReadGroups"/>
<package-and-document-command title="BamToBfq" main-class="net.sf.picard.fastq.BamToBfq"/>
<package-and-document-command title="BamIndexStats" main-class="net.sf.picard.sam.BamIndexStats"/>
<package-and-document-command title="BuildBamIndex" main-class="net.sf.picard.sam.BuildBamIndex"/>
<package-and-document-command title="CalculateHsMetrics" main-class="net.sf.picard.analysis.directed.CalculateHsMetrics"/>
<package-and-document-command title="CleanSam" main-class="net.sf.picard.sam.CleanSam"/>
<package-and-document-command title="CollectAlignmentSummaryMetrics" main-class="net.sf.picard.analysis.CollectAlignmentSummaryMetrics"/>
<package-and-document-command title="CollectGcBiasMetrics" main-class="net.sf.picard.analysis.CollectGcBiasMetrics"/>
<package-and-document-command title="CollectInsertSizeMetrics" main-class="net.sf.picard.analysis.CollectInsertSizeMetrics"/>
<package-and-document-command title="CollectMultipleMetrics" main-class="net.sf.picard.analysis.CollectMultipleMetrics"/>
<package-and-document-command title="CollectTargetedPcrMetrics" main-class="net.sf.picard.analysis.directed.CollectTargetedPcrMetrics"/>
<package-and-document-command title="CollectRnaSeqMetrics" main-class="net.sf.picard.analysis.CollectRnaSeqMetrics"/>
<package-and-document-command title="CompareSAMs" main-class="net.sf.picard.sam.CompareSAMs"/>
<package-and-document-command title="CreateSequenceDictionary" main-class="net.sf.picard.sam.CreateSequenceDictionary"/>
<package-and-document-command title="DownsampleSam" main-class="net.sf.picard.sam.DownsampleSam"/>
<package-and-document-command title="ExtractIlluminaBarcodes" main-class="net.sf.picard.illumina.ExtractIlluminaBarcodes"/>
<package-and-document-command title="EstimateLibraryComplexity" main-class="net.sf.picard.sam.EstimateLibraryComplexity"/>
<package-and-document-command title="FastqToSam" main-class="net.sf.picard.sam.FastqToSam"/>
<package-and-document-command title="FilterSamReads" main-class="net.sf.picard.sam.FilterSamReads"/>
<package-and-document-command title="FixMateInformation" main-class="net.sf.picard.sam.FixMateInformation"/>
<package-and-document-command title="IlluminaBasecallsToFastq" main-class="net.sf.picard.illumina.IlluminaBasecallsToFastq"/>
<package-and-document-command title="IlluminaBasecallsToSam" main-class="net.sf.picard.illumina.IlluminaBasecallsToSam"/>
<package-and-document-command title="CheckIlluminaDirectory" main-class="net.sf.picard.illumina.CheckIlluminaDirectory"/>
<package-and-document-command title="IntervalListTools" main-class="net.sf.picard.util.IntervalListTools"/>
<package-and-document-command title="MakeSitesOnlyVcf" main-class="net.sf.picard.vcf.MakeSitesOnlyVcf"/>
<package-and-document-command title="MarkDuplicates" main-class="net.sf.picard.sam.MarkDuplicates"/>
<package-and-document-command title="MeanQualityByCycle" main-class="net.sf.picard.analysis.MeanQualityByCycle"/>
<package-and-document-command title="MergeBamAlignment" main-class="net.sf.picard.sam.MergeBamAlignment"/>
<package-and-document-command title="MergeSamFiles" main-class="net.sf.picard.sam.MergeSamFiles"/>
<package-and-document-command title="MergeVcfs" main-class="net.sf.picard.vcf.MergeVcfs">
<package-filesets>
<fileset dir=".command_tmp" >
<include name="org/apache/commons/logging/**/*"/>
</fileset>
</package-filesets>
</package-and-document-command>
<package-and-document-command title="NormalizeFasta" main-class="net.sf.picard.reference.NormalizeFasta"/>
<package-and-document-command title="ExtractSequences" main-class="net.sf.picard.reference.ExtractSequences"/>
<package-and-document-command title="QualityScoreDistribution" main-class="net.sf.picard.analysis.QualityScoreDistribution"/>
<package-and-document-command title="ReorderSam" id="" main-class="net.sf.picard.sam.ReorderSam"/>
<package-and-document-command title="ReplaceSamHeader" main-class="net.sf.picard.sam.ReplaceSamHeader"/>
<package-and-document-command title="RevertSam" main-class="net.sf.picard.sam.RevertSam"/>
<package-and-document-command title="SamFormatConverter" main-class="net.sf.picard.sam.SamFormatConverter"/>
<package-and-document-command title="SamToFastq" main-class="net.sf.picard.sam.SamToFastq"/>
<package-and-document-command title="SortSam" main-class="net.sf.picard.sam.SortSam"/>
<package-and-document-command title="VcfFormatConverter" main-class="net.sf.picard.vcf.VcfFormatConverter">
<package-filesets>
<fileset dir=".command_tmp" >
<include name="org/apache/commons/logging/**/*"/>
</fileset>
</package-filesets>
</package-and-document-command>
<package-and-document-command title="MarkIlluminaAdapters" main-class="net.sf.picard.illumina.MarkIlluminaAdapters"/>
<package-and-document-command title="SplitVcfs" main-class="net.sf.picard.vcf.SplitVcfs">
<package-filesets>
<fileset dir=".command_tmp" >
<include name="org/apache/commons/logging/**/*"/>
</fileset>
</package-filesets>
</package-and-document-command>
<package-and-document-command title="ValidateSamFile" main-class="net.sf.picard.sam.ValidateSamFile"/>
<package-and-document-command title="ViewSam" main-class="net.sf.picard.sam.ViewSam"/>
</target>
<!-- ALL -->
<target name="all" depends="compile, sam-jar, picard-jar, tribble-jar, variant-jar, package-commands, document-standard-options" description="Default build target">
<zip zipfile="${dist}/picard-tools-${picard-version}.zip">
<zipfileset dir="${dist}" includes="*.jar" prefix="picard-tools-${picard-version}"/>
<zipfileset dir="${lib}" includes="snappy*.jar"/>
</zip>
</target>
<!-- ************************************************************************************** -->
<!-- ************************************************************************************** -->
<!-- Beginning of taskdefs that are used elsewhere in the build file -->
<!-- ************************************************************************************** -->
<!-- ************************************************************************************** -->
<!-- Create a jar for a command-line class so it can be run java -jar jarfile -->
<macrodef name="package-command">
<attribute name="main-class"/>
<attribute name="title"/>
<element name="filesets" optional="yes"/>
<sequential>
<classfileset dir="${command_tmp}" id="reqdClasses">
<root classname="@{main-class}"/>
</classfileset>
<jar destfile="${dist}/@{title}.jar">
<fileset refid="reqdClasses"/>
<fileset dir="${src.scripts}" includes="**/*.R"/>
<fileset dir="${command_tmp}" includes="org/xerial/snappy/native/Linux/**/*"/>
<fileset dir="${command_tmp}" includes="org/xerial/snappy/VERSION"/>
<fileset dir="${command_tmp}" includes="META-INF/maven/org.xerial.snappy/snappy-java/pom.properties"/>
<filesets/>
<manifest>
<attribute name="Implementation-Title" value="@{title}"/>
<attribute name="Main-Class" value="@{main-class}"/>
<attribute name="Implementation-Version" value="${picard-version}(${repository.revision})"/>
<attribute name="Implementation-Vendor" value="Broad Institute"/>
</manifest>
</jar>
</sequential>
</macrodef>
<target name="document-standard-options" depends="picard-jar, sam-jar">
<sequential>
<!-- For Sourceforge project website -->
<mkdir dir="${command-line-html-dir}/program_usage"/>
<!-- Generate HTML for each command -->
<java classname="net.sf.picard.cmdline.CreateHtmlDocForStandardOptions"
output="${command-line-html-dir}/program_usage/standard-options.shtml"
failonerror="true">
<classpath>
<pathelement location="${dist}/picard-${picard-version}.jar"/>
<pathelement location="${dist}/sam-${sam-version}.jar"/>
</classpath>
</java>
</sequential>
</target>
<!-- generate HTML documentation for command-line program -->
<macrodef name="document-command">
<attribute name="main-class"/>
<attribute name="title"/>
<element name="filesets" optional="yes"/>
<sequential>
<!-- For Sourceforge project website -->
<mkdir dir="${command-line-html-dir}/program_usage"/>
<!-- Generate HTML for each command -->
<java classname="net.sf.picard.cmdline.CreateHtmlDocForProgram"
output="${command-line-html-dir}/program_usage/@{title}.shtml"
failonerror="true">
<classpath>
<pathelement location="${dist}/picard-${picard-version}.jar"/>
<pathelement location="${dist}/sam-${sam-version}.jar"/>
<pathelement location="${dist}/variant-${variant-version}.jar"/>
</classpath>
<arg value="@{main-class}"/>
</java>
<!-- Generate links to each command -->
<echo file="${command-line-html-dir}/command-line-sidebar.shtml" append="true"
message="<li><a href="command-line-overview.shtml#@{title}">@{title}</a>${line.separator}"/>
<!-- include usage for each command -->
<echo file="${command-line-html-dir}/command-line-usage.shtml" append="true"
message="<!--#include virtual="@{title}.shtml" -->${line.separator}"/>
</sequential>
</macrodef>
<!-- Create a jar for a command-line class so it can be run java -jar jarfile, and generate on-line doc for it. -->
<macrodef name="package-and-document-command">
<attribute name="main-class"/>
<attribute name="title"/>
<element name="package-filesets" optional="yes"/>
<sequential>
<package-command title="@{title}" main-class="@{main-class}">
<filesets>
<package-filesets/>
</filesets>
</package-command>
<document-command title="@{title}" main-class="@{main-class}"/>
</sequential>
</macrodef>
<!-- Compile source files specified by includes, from source root. Can specifically
include or exclude-->
<macrodef name="compile-src">
<attribute name="includes" default=""/>
<attribute name="excludes" default=""/>
<attribute name="destdir" default="${classes}"/>
<attribute name="compile.classpath" default="classpath"/>
<attribute name="compiler.args" default=""/>
<sequential>
<mkdir dir="${classes}"/>
<!-- unset the sourcepath attribute in order to compile only files explicitly specified and disable javac's default searching mechanism -->
<javac destdir="@{destdir}"
optimize="${javac.opt}"
debug="${javac.debug}"
sourcepath=""
srcdir="${src}"
includes="@{includes}"
excludes="@{excludes}"
source="${javac.target}"
target="${javac.target}">
<classpath refid="@{compile.classpath}"/>
<compilerarg line="@{compiler.args}" />
<!-- ensure that Java 6 bootclasspath is used -->
<compilerarg value="-Xbootclasspath/p:${toString:java6.lib.ref}"/>
</javac>
</sequential>
</macrodef>
<macrodef name="compile-tests">
<attribute name="includes" default=""/>
<attribute name="excludes" default=""/>
<attribute name="compiler.args" default=""/>
<sequential>
<mkdir dir="${classes.test}"/>
<javac destdir="${classes.test}"
optimize="${javac.opt}"
debug="${javac.debug}"
srcdir="${src.test.java}"
includes="@{includes}"
excludes="@{excludes}"
source="${javac.target}"
target="${javac.target}">
<classpath>
<path refid="classpath"/>
<pathelement location="${classes}"/>
</classpath>
<compilerarg line="@{compiler.args}"/>
<!-- ensure that Java 6 bootclasspath is used -->
<compilerarg value="-Xbootclasspath/p:${toString:java6.lib.ref}"/>
</javac>
</sequential>
</macrodef>
</project>