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gatk-3.8
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adding Ivy lines for findbug, and adding a build task (to run it locally you need to have installation of findbug). I'll put more information on the wiki when it's up and running. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3744 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2010-07-08 19:10:19 +00:00
parent 12fecc8d8f
commit 7ff6106c14
2 changed files with 40 additions and 4 deletions
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38
build.xml
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@ -1,6 +1,5 @@
<project name="Sting" default="dist" basedir="." xmlns:ivy="antlib:org.apache.ivy.ant">
<description>Compile and distribute the Sting toolkit</description>
<property name="build.sysclasspath" value="first" />
<property name="build.dir" value="build" />
@ -9,6 +8,9 @@
<property name="java.classes" value="${build.dir}/java/classes" />
<property name="resource.file" value="StingText.properties" />
<!-- where to find 'findbugs', which you must set if you plan to use 'ant findbugs' -->
<property name="findbugs.home" value="./findbugs"/>
<!-- do we want to halt on failure of a junit test? default to yes (Bamboo uses 'no') -->
<property name="halt" value="yes" />
@ -266,10 +268,10 @@
<property name="scala.classes" value="build/scala" />
<path id="scala.classpath">
<fileset dir="lib">
<fileset dir="lib">
<include name="scala-compiler-*.jar"/>
<include name="scala-library-*.jar"/>
</fileset>
</fileset>
<fileset dir="${dist.dir}">
<patternset id="scalaStuff">
<include name="*.jar"/>
@ -352,7 +354,7 @@
<junit printsummary="yes" showoutput="yes" maxmemory="${test.maxmemory}" clonevm="yes" haltonfailure="${halt}" failureProperty="test.failure">
<formatter type="brief" usefile="false" />
<formatter type="xml"/>
<classpath>
<pathelement location="${java.classes}"/>
<path refid="runtime.dependencies"/>
@ -449,6 +451,34 @@
</ant>
</target>
<!-- ******************************************************************************** -->
<!-- Find bug tasks -->
<!-- ******************************************************************************** -->
<path id="findbugs.classpath">
<fileset dir="lib" erroronmissingdir="true" includes="*.jar"/>
</path>
<target name="findbugs" depends="dist">
<antcall target ="resolve">
<param name ="ivy.conf" value="findbugs"/>
</antcall>
<!-- setup the taskdef, telling ant where to find the defined task for ant -->
<taskdef name="findbugs" classname="edu.umd.cs.findbugs.anttask.FindBugsTask" classpathref="findbugs.classpath"/>
<!-- what should findbug look at: we want to aim it at the GATK.jar -->
<findbugs home="${findbugs.home}"
output="xml"
outputFile="${build.dir}/findbugs.xml"
classpathref="findbugs.classpath"
debug="false">
<auxClasspath>
<fileset dir="dist" includes="**/*.jar" excludes="**/GenomeAnalysisTK.jar"/>
</auxClasspath>
<sourcePath path="../java/src" />
<class location="dist/GenomeAnalysisTK.jar" />
</findbugs>
</target>
<target name="clean" description="clean up">
<delete dir="out"/>
<delete dir="${build.dir}"/>

6
ivy.xml
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@ -5,6 +5,7 @@
<conf name="default" description="the core dependencies for the GATK"/>
<conf name="scala" extends="default" description="the dependencies for scala"/>
<conf name="queue" extends="scala" description="the dependencies for Queue"/>
<conf name="findbugs" extends="default" description="the dependencies for Findbugs"/>
</configurations>
<dependencies defaultconf="default">
<dependency org="net.sf" name="sam" rev="latest.integration" conf="default"/>
@ -49,5 +50,10 @@
<dependency org="commons-lang" name="commons-lang" rev="2.5" conf="queue->default"/>
<dependency org="edu.mit.broad" name="broad-core-all" rev="2.8" conf="queue->default"/>
<!-- findbug dependencies -->
<dependency org="net.sourceforge.findbugs" name="findbugs" rev="1.3.2" conf="findbugs->default"/>
<dependency org="net.sourceforge.findbugs" name="findbugs-ant" rev="1.3.2" conf="findbugs->default"/>
</dependencies>
</ivy-module>