Custom gatherer prints out the class name in the logs.
Try to retrieve mail domain from /etc/mailname before falling back to the hostname.
Building oneoff jars during ant oneoffs.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5540 348d0f76-0448-11de-a6fe-93d51630548a
Added a property to allow generating Queue extensions around an external version of the GATK.
Updated argument order in -help.
Restored the ability to use QScript trait imported annotations in constructors.
Removing line feeds from email password files.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5416 348d0f76-0448-11de-a6fe-93d51630548a
Added an empty wrapper for a GridEngine job runner which is only activated when SGE_ROOT is detected.
Refactored a bit more common code into CommandLineJobRunner / JobRunner / FunctionEdge.
Status for analyisNames now includes the number of functions in state.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5399 348d0f76-0448-11de-a6fe-93d51630548a
- 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
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
kshakir