gatk-3.8/public/packages/GenomeAnalysisTK.xml

<?xml version="1.0" encoding="UTF-8"?>
<package name="GenomeAnalysisTK">
  <version file="StingText.properties" property="org.broadinstitute.sting.gatk.version" />
  <executable name="GenomeAnalysisTK">
    <main-class name="org.broadinstitute.sting.gatk.CommandLineGATK" />
    <resource-bundle file="StingText.properties" />
    <modules>
      <module file="GATKEngine.xml"/>
    </modules>
  </executable>
  <modules>
    <module file="AnalyzeCovariates.xml"/>
  </modules>
  <resources>
    <!-- GATK sample code and build scripts -->
    <file name="public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java" />
    <file name="public/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java" />
    <file name="public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java" />
    <file name="public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLociWalker.java" />
    <file name="public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadsWalker.java" />
    <file name="public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java" />
    <file name="public/R/titvFPEst.R" />
  </resources>
  <release>
    <executable directory="/humgen/gsa-hpprojects/GATK/bin" symlink="current" />
    <archive directory="/web/ftp/pub/gsa/GenomeAnalysisTK" symlink="GenomeAnalysisTK-latest.tar.bz2" />
  </release>
</package>
Plumbed packaging support into build.xml and added package for GATK. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1012 348d0f76-0448-11de-a6fe-93d51630548a 2009-06-16 03:41:16 +08:00			`<?xml version="1.0" encoding="UTF-8"?>`
Cleanup and formatting overhaul. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2652 348d0f76-0448-11de-a6fe-93d51630548a 2010-01-22 03:22:56 +08:00			`<package name="GenomeAnalysisTK">`
Autogenerate .tar.bz2 with embedded version number. Misc formatting changes. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2651 348d0f76-0448-11de-a6fe-93d51630548a 2010-01-22 02:32:46 +08:00			`<version file="StingText.properties" property="org.broadinstitute.sting.gatk.version" />`
Cleanup and formatting overhaul. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2652 348d0f76-0448-11de-a6fe-93d51630548a 2010-01-22 03:22:56 +08:00			`<executable name="GenomeAnalysisTK">`
			`<main-class name="org.broadinstitute.sting.gatk.CommandLineGATK" />`
			`<resource-bundle file="StingText.properties" />`
Walkers can now specify a class extending from Gatherer to merge custom output formats. Add @Gather(MyGatherer.class) to the walker @Output. JavaCommandLineFunctions can now specify the classpath+mainclass as an alternative to specifying a path to an executable jar. JCLF by default pass on the current classpath and only require the mainclass be specified by the developer extending the JCLF, relieving the QScript author from having to explicitly specify the jar. Like the Picard MergeSamFiles, GATK engine by default is now run from the current classpath. The GATK can still be overridden via .jarFile or .javaClasspath. Walkers from the GATK package are now also embedded into the Queue package. Updated AnalyzeCovariates to make it easier to guess the main class, AnalyzeCovariates instead of AnalyzeCovariatesCLP. Removed the GATK jar argument from the example QScripts. Removed one of the most FAQ when getting started with Scala/Queue, the use of Option[_] in QScripts: 1) Fixed mistaken assumption with java enums. In java enums can be null so they don't need nullable wrappers. 2) Added syntactic sugar for Nullable primitives to the QScript trait. Any variable defined as Option[Int] can just be assigned an Int value or None, ex: myFunc.memoryLimit = 3 Removed other unused code. Re-fixed dry run function ordering. Re-ordered the QCommandline companion object so that IntelliJ doesn't complain about missing main methods. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5504 348d0f76-0448-11de-a6fe-93d51630548a 2011-03-24 22:03:51 +08:00			`<modules>`
			`<module file="GATKEngine.xml"/>`
			`</modules>`
Update packaging system to produce multiple jars if asked nicely. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2246 348d0f76-0448-11de-a6fe-93d51630548a 2009-12-04 01:11:12 +08:00			`</executable>`
Autogenerate .tar.bz2 with embedded version number. Misc formatting changes. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2651 348d0f76-0448-11de-a6fe-93d51630548a 2010-01-22 02:32:46 +08:00			`<modules>`
Cleanup and formatting overhaul. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2652 348d0f76-0448-11de-a6fe-93d51630548a 2010-01-22 03:22:56 +08:00			`<module file="AnalyzeCovariates.xml"/>`
Autogenerate .tar.bz2 with embedded version number. Misc formatting changes. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2651 348d0f76-0448-11de-a6fe-93d51630548a 2010-01-22 02:32:46 +08:00			`</modules>`
First step in replacing the Hello, World! document. Revamped the HelloWalker and checked it into the source tree, created a special build file for it, and added it to the packaging tool. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1135 348d0f76-0448-11de-a6fe-93d51630548a 2009-07-01 05:59:54 +08:00			`<resources>`
Added support python and R scripts for generating covariate output graphs. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1625 348d0f76-0448-11de-a6fe-93d51630548a 2009-09-15 22:17:36 +08:00			`<!-- GATK sample code and build scripts -->`
Fixes to the packaging system to work with the new directory structure. Also added a few R scripts to the list of files to include in the resources directory of the binary distribution, at Ryan's request. 2011-07-01 06:27:17 +08:00			`<file name="public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java" />`
			`<file name="public/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java" />`
			`<file name="public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java" />`
			`<file name="public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLociWalker.java" />`
			`<file name="public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadsWalker.java" />`
			`<file name="public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java" />`
			`<file name="public/R/titvFPEst.R" />`
First step in replacing the Hello, World! document. Revamped the HelloWalker and checked it into the source tree, created a special build file for it, and added it to the packaging tool. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1135 348d0f76-0448-11de-a6fe-93d51630548a 2009-07-01 05:59:54 +08:00			`</resources>`
Add new 'release' task to push releases into a shared directory and the website. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2695 348d0f76-0448-11de-a6fe-93d51630548a 2010-01-27 06:50:20 +08:00			`<release>`
			`<executable directory="/humgen/gsa-hpprojects/GATK/bin" symlink="current" />`
Give the symlink on the webserver a name that would be a bit more obvious. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2717 348d0f76-0448-11de-a6fe-93d51630548a 2010-01-28 08:40:20 +08:00			`<archive directory="/web/ftp/pub/gsa/GenomeAnalysisTK" symlink="GenomeAnalysisTK-latest.tar.bz2" />`
Add new 'release' task to push releases into a shared directory and the website. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2695 348d0f76-0448-11de-a6fe-93d51630548a 2010-01-27 06:50:20 +08:00			`</release>`
Plumbed packaging support into build.xml and added package for GATK. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1012 348d0f76-0448-11de-a6fe-93d51630548a 2009-06-16 03:41:16 +08:00			`</package>`