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
kshakir