Added the ability to add a file path to a package.
Checking for missing files when packaging.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5685 348d0f76-0448-11de-a6fe-93d51630548a
Scala type inference for the implicit return types on implicit methods was a little too much for poor IntelliJ IDEA to handle, and it was breaking things like copy/paste, auto-complete, etc.
Also updated the Queue package to include all Sting utils.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5646 348d0f76-0448-11de-a6fe-93d51630548a
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
Fixed initialization of pending counts when using -startFromScratch so the count doesn't start at zero and end at -<#njobs>.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5483 348d0f76-0448-11de-a6fe-93d51630548a
Set the -bigMemQueue in the FullCallingPipelineTest to GSA to avoid waiting for the week queue when it is busy.
Fixed the package definition of PipelineTest so that scalac won't recompile it every time.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4755 348d0f76-0448-11de-a6fe-93d51630548a
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
-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
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
the imminent move of IlluminaUtil into picard public.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3493 348d0f76-0448-11de-a6fe-93d51630548a
Picard patch, including move of some of the Picard private classes we use to Picard public.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3087 348d0f76-0448-11de-a6fe-93d51630548a
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