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- Include the fasta index builder in the package. 

- Unit/integration  test against the jars built to the dist directory, so that 
  the tests reveal classes that don't exist in the final jars.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4234 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2010-09-08 20:37:54 +00:00
parent ce031b2f05
commit 6c27a9bfc6
1 changed files with 16 additions and 11 deletions
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27
build.xml
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@ -54,21 +54,27 @@
<exclude name="bcel*.jar" />
</patternset>
<path id="runtime.dependencies">
<path id="external.dependencies">
<fileset dir="lib">
<patternset refid="dependency.mask" />
</fileset>
</path>
<path id="build.results">
<fileset dir="dist">
<patternset refid="dependency.mask" />
</fileset>
</path>
<!-- Path to queue dependencies. -->
<path id="queue.dependencies">
<path refid="runtime.dependencies" />
<path refid="external.dependencies" />
<pathelement location="${java.classes}" />
</path>
<!-- Path to queue-extendsions dependencies. -->
<path id="queue-extensions.dependencies">
<path refid="runtime.dependencies" />
<path refid="external.dependencies" />
<pathelement location="${java.classes}" />
<pathelement location="${queue.classes}" />
<!-- Need the resources as we will be running a command line program which needs the help text. -->
@ -190,7 +196,7 @@
<target name="gatk.compile" depends="tribble,init,resolve"
description="compile the source">
<!-- Compile the java code from ${src} into build -->
<javac srcdir="${java.source.dir}" destdir="${java.classes}" debug="true" debuglevel="lines,vars,source" classpathref="runtime.dependencies">
<javac srcdir="${java.source.dir}" destdir="${java.classes}" debug="true" debuglevel="lines,vars,source" classpathref="external.dependencies">
<exclude name="**/examples/**" />
<exclude name="**/playground/**" unless="include.playground"/>
<exclude name="**/oneoffprojects/**" unless="include.oneoffs"/>
@ -230,12 +236,12 @@
description="Extract help key/value pair file from the JavaDoc tags."
unless="disable.help">
<path id="doclet.classpath">
<path refid="runtime.dependencies" />
<path refid="external.dependencies" />
<pathelement location="${java.classes}" />
</path>
<javadoc doclet="org.broadinstitute.sting.utils.help.ResourceBundleExtractorDoclet"
docletpathref="doclet.classpath"
classpathref="runtime.dependencies"
classpathref="external.dependencies"
additionalparam="-build-timestamp &quot;${build.timestamp}&quot; -version-suffix .${build.version} -out ${basedir}/${resource.path}">
<packageset refid="java.source.files"/>
</javadoc>
@ -254,6 +260,7 @@
<jar jarfile="${dist.dir}/StingUtils.jar">
<fileset dir="${java.classes}" includes="**/utils/**/*.class"/>
<fileset dir="${java.classes}" includes="**/commandline/**/*.class"/>
<fileset dir="${java.classes}" includes="net/sf/picard/**/*.class"/>
<manifest>
<attribute name="Premain-Class" value="org.broadinstitute.sting.utils.instrumentation.Sizeof" />
</manifest>
@ -390,7 +397,7 @@
<javac destdir="${java.test.classes}" debug="true" optimize="on">
<src path="${java.test.sources}"/>
<classpath>
<path refid="runtime.dependencies" />
<path refid="external.dependencies" />
<pathelement location="${java.classes}"/>
<pathelement location="lib/junit-4.4.jar"/>
</classpath>
@ -469,10 +476,8 @@
<formatter type="brief" usefile="false" />
<formatter type="xml"/>
<classpath>
<path refid="runtime.dependencies"/>
<pathelement location="${java.classes}"/>
<path refid="build.results"/>
<pathelement location="${java.test.classes}"/>
<pathelement location="${queue.classes}"/>
<pathelement location="${queue.test.classes}"/>
<pathelement location="lib/junit-4.4.jar"/>
</classpath>
@ -549,7 +554,7 @@
<target name="javadoc" depends="init.buildall,resolve,queue-extensions.generate" description="generates javadoc">
<mkdir dir="javadoc"/>
<javadoc destdir="javadoc"
classpathref="runtime.dependencies">
classpathref="external.dependencies">
<packageset refid="java.source.files"/>
</javadoc>