Revision 8492f7ccdde00f73fe3e49a0c6a58f6e5abf6858 authored by Fabien Campagne on 06 April 2013, 19:47:05 UTC, committed by Fabien Campagne on 06 April 2013, 19:47:05 UTC
1 parent 36d2bb8
build.xml
<project name="goby" default="test" basedir="." xmlns:artifact="antlib:org.apache.maven.artifact.ant">
<!-- compiler and javadoc settings -->
<property name="debug" value="on"/>
<property name="optimize" value="on"/>
<property name="deprecation" value="off"/>
<property name="ant.build.javac.source" value="1.6"/>
<property name="ant.build.javac.target" value="1.6"/>
<!-- jar files created in this project -->
<property name="goby-jarfile-name" value="goby.jar"/>
<property name="goby-jarfile" location="${goby-jarfile-name}"/>
<property name="goby-api-jarfile" location="goby-api.jar"/>
<property name="goby-spi-jarfile" location="goby-spi.jar"/>
<property name="goby-io-jarfile" location="goby-io.jar"/>
<property name="goby-io-api-jarfile" location="goby-io-api.jar"/>
<property name="label" value="development"/>
<!-- default memory size for tests -->
<property name="test.max.memory" value="2000m"/>
<!--
* The target named by this task will be called before tests
* are run (but after dependencies are met). If one doesn't
* define "pre-test-task" nothing special will happen.
-->
<property name="pre-test-task" value="pre-test-task"/>
<import file="buildsupport/build.xml"/>
<if>
<os family="windows"/>
<then>
<property name="test.java.library.path" location="${env.R_HOME}/library/rJava/jri"/>
</then>
</if>
<import file="testsupport/build.xml"/>
<path id="compile.classpath">
<fileset dir="${lib}">
<include name="*.jar"/>
</fileset>
</path>
<path id="classpath">
<pathelement location="${classes}"/>
<pathelement location="${config}"/>
<fileset dir="${lib}">
<include name="*.jar"/>
</fileset>
</path>
<fileset dir="${src}" id="pmd-fileset">
<include name="**/*.java"/>
<exclude name="edu/cornell/med/icb/goby/alignments/Alignments.java"/>
<exclude name="edu/cornell/med/icb/goby/reads/Reads.java"/>
</fileset>
<fileset dir="${src}" id="checkstyle-fileset">
<include name="**/*.java"/>
<exclude name="**/package-info.java"/>
<exclude name="edu/cornell/med/icb/goby/alignments/Alignments.java"/>
<exclude name="edu/cornell/med/icb/goby/reads/Reads.java"/>
</fileset>
<target name="init" depends="buildsupport.init, testsupport.init"/>
<target name="clean" depends="buildsupport.clean, testsupport.clean" description="Cleans up the directory">
<delete file="${goby-jarfile}"/>
<delete file="${goby-api-jarfile}"/>
<delete file="${goby-spi-jarfile}"/>
</target>
<target name="install" depends="jar" description="install the jar file(s) to maven local repository.">
<artifact:pom id="goby-pom" file="pom.xml"></artifact:pom>
<artifact:install file="goby.jar">
<pom refid="goby-pom"/>
<artifact:attach file="goby-io.jar" classifier="io"/>
<artifact:attach file="goby-api.jar" classifier="api"/>
<artifact:attach file="goby-io-igv.jar" classifier="io-igv"/>
</artifact:install>
<!--artifact:deploy file="goby.jar">
<remoteRepository url="file:///www/repository"/>
<pom refid="mypom"/>
</artifact:deploy-->
</target>
<target name="compile" depends="init,jar-goby-spi" description="compiles the source code">
<javac srcdir="${src}" destdir="${classes}" debug="${debug}" deprecation="${deprecation}">
<classpath refid="compile.classpath"/>
</javac>
<copy todir="${classes}">
<fileset dir="${src}">
<include name="**/*.jsap"/>
<include name="**/jaxb.index"/>
</fileset>
</copy>
</target>
<!--
* Before tests, compile goby-spi jar then place it it in
* test-lib/ - for this target to be called, we've defined
* a property named "pre-test-task" that points to this target.
-->
<target name="pre-test-task" depends="jar-goby-spi">
<copy file="${goby-spi-jarfile}" todir="${test-lib}" overwrite="true" failonerror="true"/>
</target>
<target name="jar" depends="jar-goby, jar-goby-api, jar-goby-spi, jar-goby-io, jar-goby-io-api"
description="Create project jarfiles"/>
<target name="jar-goby" depends="compile"
description="Create the goby.jar file. Gobies are a large species of fish that include some of the smallest fish. Now, isn't that fitting?">
<!-- Standalone jar file. -->
<copy file="${config}/log4j-sample.properties" tofile="${classes}/log4j.properties" overwrite="true"
failonerror="true"/>
<jar jarfile="${goby-jarfile}">
<fileset file="VERSION.txt"/>
<fileset dir="${classes}"/>
<zipgroupfileset dir="${lib}">
<include name="bdval-api.jar"/>
<include name="commons-collections-3.2.1.jar"/>
<include name="commons-configuration-1.6.jar"/>
<include name="commons-exec-1.0.1.jar"/>
<include name="commons-io-1.4.jar"/>
<include name="commons-lang-2.5.jar"/>
<include name="commons-logging-1.1.1.jar"/>
<include name="commons-math-2.1.jar"/>
<include name="commons-pool-1.6.jar"/>
<include name="edu.mssm.crover.cli.jar"/>
<include name="bzip2.jar"/>
<include name="fastutil-6.3.jar"/>
<include name="dsiutils-1.0.12.jar"/>
<include name="icb-utils.jar"/>
<include name="JSAP-2.1.jar"/>
<include name="log4j-1.2.15.jar"/>
<include name="protobuf-java-2.4.1.jar"/>
<include name="sam-1.64.jar"/>
<include name="picard-1.64.jar"/>
<include name="squil.jar"/>
<include name="reflections-0.9.5.jar"/>
<include name="guava-r08.jar"/>
<include name="slf4j-api-1.6.1.jar"/>
<include name="slf4j-nop-1.6.4.jar"/>
<include name="javassist-3.12.1.GA.jar"/>
<include name="tisim-api.jar"/>
<include name="pj*.jar"/>
<include name="JRI.jar"/>
<include name="mg4j-3.0.1.jar"/>
<include name="xstream-1.4.3.jar"/>
<!-- Required by JSAP -->
</zipgroupfileset>
<manifest>
<attribute name="Specification-Title" value="Goby"/>
<attribute name="Specification-Vendor"
value="Institute for Computational Biomedicine (ICB), Weill Medical College of Cornell University"/>
<attribute name="Implementation-Version" value="${label} (${buildstamp})"/>
<attribute name="Implementation-Vendor"
value="Institute for Computational Biomedicine (ICB), Weill Medical College of Cornell University"/>
<attribute name="Main-Class" value="edu.cornell.med.icb.goby.modes.GobyDriver"/>
<attribute name="Built-By" value="${user.name}"/>
</manifest>
<service type="edu.cornell.med.icb.goby.reads.ReadCodec">
<provider classname="edu.cornell.med.icb.goby.reads.ReadCodecImpl"/>
<provider classname="edu.cornell.med.icb.goby.reads.ReadCodec2"/>
</service>
<service type="edu.cornell.med.icb.goby.compression.ChunkCodec">
<provider classname="edu.cornell.med.icb.goby.compression.NullChunkCodec"/>
<provider classname="edu.cornell.med.icb.goby.compression.NotCompressedChunkCodec"/>
<provider classname="edu.cornell.med.icb.goby.compression.GZipChunkCodec"/>
<provider classname="edu.cornell.med.icb.goby.compression.BZip2ChunkCodec"/>
<provider classname="edu.cornell.med.icb.goby.compression.HybridChunkCodec1"/>
<provider classname="edu.cornell.med.icb.goby.compression.HybridChunkCodec2"/>
</service>
<!-- define the implementation of NormalizationMethods as Java ServiceProviders: -->
<service type="edu.cornell.med.icb.goby.stats.NormalizationMethod">
<provider classname="edu.cornell.med.icb.goby.stats.BullardUpperQuartileNormalization"/>
<provider classname="edu.cornell.med.icb.goby.stats.AlignedCountNormalization"/>
</service>
</jar>
<!-- Set executable permissions on the goby wrapper scrip -->
<chmod file="goby" perm="+x"/>
<chmod file="scripts/sge/*.sh" perm="+x"/>
<delete file="${classes}/log4j.properties" failonerror="true"/>
</target>
<target name="jar-goby-api" depends="compile" description="Create the goby-api.jar file">
<!-- Standalone jar file. -->
<jar jarfile="${goby-api-jarfile}">
<fileset dir="${classes}"/>
<manifest>
<attribute name="Specification-Title" value="Goby API"/>
<attribute name="Specification-Vendor"
value="Campagne Laboratory, Institute for Computational Biomedicine, Weill Medical College of Cornell University"/>
<attribute name="Implementation-Version" value="${label} (${buildstamp})"/>
<attribute name="Implementation-Vendor"
value="Institute for Computational Biomedicine (ICB), Weill Medical College of Cornell University"/>
<attribute name="Built-By" value="${user.name}"/>
</manifest>
<!-- define the implementation of NormalizationMethods as Java ServiceProviders: -->
<service type="edu.cornell.med.icb.goby.stats.NormalizationMethod">
<provider classname="edu.cornell.med.icb.goby.stats.BullardUpperQuartileNormalization"/>
<provider classname="edu.cornell.med.icb.goby.stats.AlignedCountNormalization"/>
</service>
</jar>
</target>
<target name="jar-goby-spi" description="Creates a manifest only jar file for Goby services">
<jar jarfile="${goby-spi-jarfile}">
<manifest>
<attribute name="Specification-Title" value="Goby"/>
<attribute name="Specification-Vendor"
value="Campagne Laboratory, Institute for Computational Biomedicine, Weill Medical College of Cornell University"/>
<attribute name="Implementation-Version" value="${label} (${buildstamp})"/>
<attribute name="Implementation-Vendor"
value="Institute for Computational Biomedicine (ICB), Weill Medical College of Cornell University"/>
<attribute name="Built-By" value="${user.name}"/>
</manifest>
<!-- define the implementation of NormalizationMethods as Java ServiceProviders: -->
<service type="edu.cornell.med.icb.goby.stats.NormalizationMethod">
<provider classname="edu.cornell.med.icb.goby.stats.BullardUpperQuartileNormalization"/>
<provider classname="edu.cornell.med.icb.goby.stats.AlignedCountNormalization"/>
</service>
<service type="edu.cornell.med.icb.goby.reads.ReadCodec">
<provider classname="edu.cornell.med.icb.goby.reads.ReadCodecImpl"/>
<provider classname="edu.cornell.med.icb.goby.reads.ReadCodec2"/>
</service>
<service type="edu.cornell.med.icb.goby.compression.ChunkCodec">
<provider classname="edu.cornell.med.icb.goby.compression.NullChunkCodec"/>
<provider classname="edu.cornell.med.icb.goby.compression.NotCompressedChunkCodec"/>
<provider classname="edu.cornell.med.icb.goby.compression.GZipChunkCodec"/>
<provider classname="edu.cornell.med.icb.goby.compression.BZip2ChunkCodec"/>
<provider classname="edu.cornell.med.icb.goby.compression.HybridChunkCodec1"/>
<provider classname="edu.cornell.med.icb.goby.compression.HybridChunkCodec2"/>
</service>
</jar>
</target>
<target name="jar-goby-io" depends="compile" description="Create the goby-io.jar file (LGPL code only)">
<!-- Standalone jar file. -->
<jar jarfile="${goby-io-jarfile}">
<fileset dir="${classes}">
<include name="edu/cornell/med/icb/goby/algorithmic/compression/**"/>
<include name="edu/cornell/med/icb/goby/compression/**"/>
<include name="edu/cornell/med/icb/goby/reads/**"/>
<include name="edu/cornell/med/icb/goby/readers/**"/>
<include name="edu/cornell/med/icb/goby/alignments/**"/>
<include name="edu/cornell/med/icb/goby/counts/**"/>
<include name="edu/cornell/med/icb/goby/modes/UpgradeMode*"/>
<include name="edu/cornell/med/icb/goby/modes/AbstractGobyMode*"/>
<include name="edu/cornell/med/icb/goby/modes/AbstractCommandLineMode*"/>
<include name="edu/cornell/med/icb/goby/modes/TabToColumnInfoMode*"/>
<include name="edu/cornell/med/icb/goby/modes/GenericToolsDriver*"/>
<include name="edu/cornell/med/icb/goby/util/**"/>
<include name="edu/cornell/med/icb/goby/exception/**"/>
<include name="edu/cornell/med/icb/goby/identifier/**"/>
<include name="edu/cornell/med/icb/goby/counts/**"/>
<include name="edu/cornell/med/icb/goby/GobyVersion*"/>
</fileset>
<zipgroupfileset dir="${lib}">
<include name="bzip2.jar"/>
<!-- Apache Software License -->
<include name="fastutil-6.3.jar"/>
<!-- LGPL -->
<include name="dsiutils-1.0.12.jar"/>
<!-- LGPL -->
<include name="icb-utils.jar"/>
<!-- LGPL -->
<include name="protobuf-java-2.4.1.jar"/>
<!-- new BSD license, compatible with LGPL? -->
<include name="commons-io-1.4.jar"/>
<!-- Apache version 2 license -->
<include name="commons-lang-2.5.jar"/>
<!-- Apache version 2 license -->
<include name="commons-logging-1.1.1.jar"/>
<!-- Apache version 2 license -->
<include name="bdval-api.jar"/>
<!-- LGPL -->
<include name="JSAP-2.1.jar"/>
<!-- LGPL -->
<include name="xstream-1.4.3.jar"/>
<!-- Required by JSAP, BSD. -->
</zipgroupfileset>
<manifest>
<attribute name="Specification-Title" value="Goby IO (LGPL compatible)"/>
<attribute name="Specification-Vendor"
value="Campagne Laboratory, Institute for Computational Biomedicine, Weill Medical College of Cornell University"/>
<attribute name="Implementation-Version" value="${label} (${buildstamp})"/>
<attribute name="Implementation-Vendor"
value="Institute for Computational Biomedicine (ICB), Weill Medical College of Cornell University"/>
<attribute name="Built-By" value="${user.name}"/>
</manifest>
<service type="edu.cornell.med.icb.goby.compression.ChunkCodec">
<provider classname="edu.cornell.med.icb.goby.compression.NullChunkCodec"/>
<provider classname="edu.cornell.med.icb.goby.compression.GZipChunkCodec"/>
<provider classname="edu.cornell.med.icb.goby.compression.BZip2ChunkCodec"/>
<provider classname="edu.cornell.med.icb.goby.compression.HybridChunkCodec1"/>
</service>
</jar>
<chmod file="scripts/autojar/run-autojar.sh" perm="744"/>
<exec command="scripts/autojar/run-autojar.sh"/>
</target>
<target name="jar-goby-io-api" depends="compile" description="Create the goby-io-api.jar file (LGPL code only)">
<!-- Standalone jar file. -->
<jar jarfile="${goby-io-api-jarfile}">
<fileset dir="${classes}">
<include name="edu/cornell/med/icb/goby/compression/**"/>
<include name="edu/cornell/med/icb/goby/reads/**"/>
<include name="edu/cornell/med/icb/goby/readers/**"/>
<include name="edu/cornell/med/icb/goby/alignments/**"/>
<include name="edu/cornell/med/icb/goby/counts/**"/>
<include name="edu/cornell/med/icb/goby/modes/UpgradeMode*"/>
<include name="edu/cornell/med/icb/goby/modes/AbstractGobyMode*"/>
<include name="edu/cornell/med/icb/goby/modes/AbstractCommandLineMode*"/>
<include name="edu/cornell/med/icb/goby/modes/TabToColumnInfoMode*"/>
<include name="edu/cornell/med/icb/goby/modes/GenericToolsDriver*"/>
<include name="edu/cornell/med/icb/goby/util/**"/>
<include name="edu/cornell/med/icb/goby/exception/**"/>
<include name="edu/cornell/med/icb/goby/identifier/**"/>
<include name="edu/cornell/med/icb/goby/counts/**"/>
<include name="edu/cornell/med/icb/goby/GobyVersion*"/>
</fileset>
<manifest>
<attribute name="Specification-Title" value="Goby IO-API (LGPL compatible)"/>
<attribute name="Specification-Vendor"
value="Campagne Laboratory, Institute for Computational Biomedicine, Weill Medical College of Cornell University"/>
<attribute name="Implementation-Version" value="${label} (${buildstamp})"/>
<attribute name="Implementation-Vendor"
value="Institute for Computational Biomedicine (ICB), Weill Medical College of Cornell University"/>
<attribute name="Built-By" value="${user.name}"/>
</manifest>
<service type="edu.cornell.med.icb.goby.alignments.AlignmentCodec">
<provider classname="edu.cornell.med.icb.goby.alignments.AlignmentCodecDummy"/>
</service>
<service type="edu.cornell.med.icb.goby.compression.ChunkCodec">
<provider classname="edu.cornell.med.icb.goby.compression.NullChunkCodec"/>
<provider classname="edu.cornell.med.icb.goby.compression.NotCompressedChunkCodec"/>
<provider classname="edu.cornell.med.icb.goby.compression.GZipChunkCodec"/>
<provider classname="edu.cornell.med.icb.goby.compression.BZip2ChunkCodec"/>
<provider classname="edu.cornell.med.icb.goby.compression.HybridChunkCodec1"/>
</service>
</jar>
</target>
<target name="cruisecontrol"
depends="clean, cobertura-setup, findbugs, test, jar, javadocs, pmd, cpd, cobertura-report"
description="Run CruiseControl Build and Tests"/>
<!-- =================================================================== -->
<!-- Creates the API documentation -->
<!-- =================================================================== -->
<target name="javadocs" depends="init" description="generates the API documentation">
<mkdir dir="${javadocs}"/>
<javadoc packagenames="*"
sourcepath="${src}" destdir="${javadocs}" encoding="UTF-8"
author="true" version="true" windowtitle="Goby API ${label} (${buildstamp})"
header="Goby API ${label} (${buildstamp})" overview="overview.html">
<link href="http://java.sun.com/javase/6/docs/api/"/>
<link href="http://fastutil.dsi.unimi.it/docs/"/>
<link href="http://dsiutils.dsi.unimi.it/docs/"/>
<link href="http://commons.apache.org/collections/api-release/"/>
<link href="http://commons.apache.org/configuration/apidocs/"/>
<link href="http://commons.apache.org/exec/apidocs/"/>
<link href="http://commons.apache.org/io/api-release/"/>
<link href="http://commons.apache.org/logging/apidocs/"/>
<link href="http://commons.apache.org/lang/api-release"/>
<link href="http://commons.apache.org/math/api-2.1/"/>
<link href="http://martiansoftware.com/jsap/doc/javadoc/"/>
<link href="http://code.google.com/apis/protocolbuffers/docs/reference/java/"/>
<link href="http://icbtools.med.cornell.edu/javadocs/bdval/"/>
<link href="http://icbtools.med.cornell.edu/javadocs/crover/"/>
<link href="http://icbtools.med.cornell.edu/javadocs/icb-utils/"/>
<link href="http://icbtools.med.cornell.edu/javadocs/squil/"/>
<link href="http://icbtools.med.cornell.edu/javadocs/tissueinfo/"/>
<link href="http://picard.sourceforge.net/javadoc/"/>
<classpath>
<path refid="compile.classpath"/>
<pathelement location="${classes}"/>
</classpath>
<bottom>
<![CDATA[<i>Copyright © 2009-${year} Institute for Computational Biomedicine, All Rights Reserved.</i>]]>
</bottom>
</javadoc>
</target>
</project>
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