Updated pipeline output structure to current recommendations by Corin.
Directories are now automatically before the function runs.
Fixed several bugs with scatter gather binding when the script author needs to change the directories.
Fixed bug with tracking of log files for CloneFunctions.
More error handling and logging of exceptions (good test environment while LSF was down this early AM!)
Removed cleanup utility for scatter gather. SG Output structure has changed significantly. Will need to discuss and find a better approach for Queue programatically deleting files.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4504 348d0f76-0448-11de-a6fe-93d51630548a
Queue now submits new LSF jobs only after previous functions have completed successfully.
When the Queue process is shutdown (ex: via Control-C) sends a bkill command for any running jobs.
Ported commands like creating directories and scatter/gather interval list to scala functions.
Updates to LSF status tracking by porting the python to internally generated bash scripts.
Temporarily disabled job name submission to LSF. Plus side is that the full command is now available in "bjobs -w". TODO: Put back jobName passing to LSF based on an option?
Changed BaseTest to allow scala to access paths to references.
Changed the extension generator to default the analysis name to the walker "name".
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4442 348d0f76-0448-11de-a6fe-93d51630548a
No longer generating deprecated GATK arguments on the Queue extensions.
Emitting deprecation warnings to Queue compile to help debugging issues.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4195 348d0f76-0448-11de-a6fe-93d51630548a
Added the a CommandLineFunction.jobDependencies that will explicitly force a function to wait for a file, even if the value isn't otherwise listed on an @Input.
More bug fixes and refactoring of functions.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4048 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
kshakir