- Forcing user to set the temp directory via -Djava.io.tmpdir to avoid filling up /tmp.
- By default deleting job outputs tagged as intermediate.
- Defaulting pipeline to scatter count 1 (no reads deleted).
- Cleaning up temp classes even when scripting fails.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4573 348d0f76-0448-11de-a6fe-93d51630548a
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
Added ability to skip up-to-date jobs where the outputs are older than the inputs.
Changed -T CountDuplicates --quiet to --quietLocus so that Queue GATK extensions can use both short and full argument names.
Short names can be used to set values on Queue GATK extensions, for example: vf.XL :+= myFile
Moved Hidden from the GATK to StingUtils.
Updated ivy from 2.0.0 to 2.2.0-rc1 to fix sha1 issue: http://bit.ly/aX72w7
Added Queue to javadoc and testing build targets.
Added first Queue unit test.
Another pass at avoiding cycles in the DAG thanks to all function I/O being files.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4017 348d0f76-0448-11de-a6fe-93d51630548a
kshakir