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gatk-3.8/packages/Queue.xml

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Added Queue packages, which must be run with 'ant queue package'. To assist with the above no longer removing jars during a new build, so 'ant queue dist' will still have the Queue.jar. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4020 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-13 01:45:53 +08:00
<?xml version="1.0" encoding="UTF-8"?>
<package name="Queue">
Queue now uses its own version instead of the gatk version. Added a Queue release directory. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4050 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-18 03:34:23 +08:00
<version file="StingText.properties" property="org.broadinstitute.sting.queue.version" />
Added Queue packages, which must be run with 'ant queue package'. To assist with the above no longer removing jars during a new build, so 'ant queue dist' will still have the Queue.jar. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4020 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-13 01:45:53 +08:00
<executable name="Queue">
<main-class name="org.broadinstitute.sting.queue.QCommandLine" />
<resource-bundle file="StingText.properties" />
<dependencies>
<!-- Queue -->
<class name="org.broadinstitute.sting.queue.QCommandLine" />
<package name="org.broadinstitute.sting.queue.function" />
<package name="org.broadinstitute.sting.queue.function.*" />
<package name="org.broadinstitute.sting.queue.util" />
Cleaning up Queue debugging output. -l DEBUG with local programs now prints out the stdout/stderr of the programs as they are run. More documentation in the examples with a new even simpler CountReads example. Took out unused option to build Queue GATK extensions separately. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4025 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-13 23:54:08 +08:00
Created a new playground script for cleaning bams in Firehose. Some refactoring of Queue extensions for reusability in scripts. Putting the extensions into the Queue.jar after building them. More updates to GATK walker arguments specifying @Input and @Output for Queue. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4032 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-14 07:52:24 +08:00
<!-- Queue Extensions -->
<package name="org.broadinstitute.sting.queue.extensions.*" />
Enabling support for any scala used in QScripts. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4052 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-18 06:05:56 +08:00
<!-- Scala -->
<package name="scala.**" />
Added Queue packages, which must be run with 'ant queue package'. To assist with the above no longer removing jars during a new build, so 'ant queue dist' will still have the Queue.jar. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4020 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-13 01:45:53 +08:00
</dependencies>
</executable>
Queue now uses its own version instead of the gatk version. Added a Queue release directory. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4050 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-18 03:34:23 +08:00
<release>
<executable directory="/humgen/gsa-hpprojects/Queue/bin" symlink="current" />
<archive directory="/web/ftp/pub/gsa/Queue" symlink="Queue-latest.tar.bz2" />
</release>
Added Queue packages, which must be run with 'ant queue package'. To assist with the above no longer removing jars during a new build, so 'ant queue dist' will still have the Queue.jar. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4020 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-13 01:45:53 +08:00
</package>