gatk-3.8

Commit Graph

Author	SHA1	Message	Date
kshakir	8211cee0b2	Queue UI Improvements: - 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	2010-10-26 19:49:08 +00:00
kshakir	e9c6f681a4	Instead of the pipeline's cleaner only writing BAMs with the target intervals, now pulling the list of contigs from the target intervals and outputing reads in those contigs. 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	2010-10-22 22:22:30 +00:00

Author

SHA1

Message

Date

kshakir

8211cee0b2

Queue UI Improvements:

- 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

2010-10-26 19:49:08 +00:00

kshakir

e9c6f681a4

Instead of the pipeline's cleaner only writing BAMs with the target intervals, now pulling the list of contigs from the target intervals and outputing reads in those contigs.

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

2010-10-22 22:22:30 +00:00

2 Commits (8101f8f301d2fc86fbf652a791ac7d9cdcb210df)