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gatk-3.8/public/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"?>
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
<!--
~ Copyright (c) 2011, The Broad Institute
~
~ Permission is hereby granted, free of charge, to any person
~ obtaining a copy of this software and associated documentation
~ files (the "Software"), to deal in the Software without
~ restriction, including without limitation the rights to use,
~ copy, modify, merge, publish, distribute, sublicense, and/or sell
~ copies of the Software, and to permit persons to whom the
~ Software is furnished to do so, subject to the following
~ conditions:
~
~ The above copyright notice and this permission notice shall be
~ included in all copies or substantial portions of the Software.
~ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
~ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
~ OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
~ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
~ HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
~ WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
~ FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
~ OTHER DEALINGS IN THE SOFTWARE.
-->
Build system round 2: finished preparing the packaging system for dual protected/lite releases * Targets to package and release lite/protected versions of the GATK/Queue * Still TODO: -determine the actual directories where the protected releases should go -update the Bamboo release plan -fix a bug in the binary release test targets
2012-05-25 00:05:14 +08:00
<!-- The full release of Queue contains both public and protected tools (but nothing from private) -->
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 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" />
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>
Build system round 2: finished preparing the packaging system for dual protected/lite releases * Targets to package and release lite/protected versions of the GATK/Queue * Still TODO: -determine the actual directories where the protected releases should go -update the Bamboo release plan -fix a bug in the binary release test targets
2012-05-25 00:05:14 +08:00
<module file="QueueEngine.xml"/>
Fixed inclusion of GATKEngine into the Queue package. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5552 348d0f76-0448-11de-a6fe-93d51630548a
2011-04-02 01:45:46 +08:00
<module file="GATKEngine.xml"/>
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>
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>
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>
Inserted final paths for binaries.
2012-07-24 02:29:10 +08:00
<executable directory="/humgen/gsa-hpprojects/Queue/bin" symlink="current" />
<archive directory="/humgen/gsa-hpprojects/Queue/bin" symlink="Queue-latest.tar.bz2" />
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>
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>