Added a brute force -retry <count> option to Queue for transient errors.
Waiting up to 2 minutes for the LSF logs to appear before trying to display the errors from the logs.
Updates to the local job runner error logging when a job fails.
Refactored QGraph's settings as duplicate code was getting out of control.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4563 348d0f76-0448-11de-a6fe-93d51630548a
Queue GATK generated .intervals is now a List(File) again removing special case handling in the generator.
Instead of using @Scatter annotation, using ScatterFunction instance to determine if a job can be scattered.
Implemented special VcfGatherFunction which only uses the header from the first file, even if the other files differ in their headers.
Added a -deleteIntermediates to Queue to delete the outputs from intermediate commands after a successful run.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4536 348d0f76-0448-11de-a6fe-93d51630548a
Re-logging the failed jobs and the path to their log files at the end of a run.
Added a parameter -bigMemQueue for the fullCallingPipeline.q instead of hardcoding gsa (gsa was backed up and it was actually faster to run on week).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4520 348d0f76-0448-11de-a6fe-93d51630548a
On -run cleaning up .done and .fail files for jobs that will be run.
Added detection to Firehose YAML generator shell script for (g)awk versions that ignore "\n" in patterns.
Removed obsolete mergeText and splitIntervals shell scripts.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4452 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
kshakir