gatk-3.8

Author	SHA1	Message	Date
kshakir	fd5970fdd4	At chartl's superb suggestion, command line files are now all Files instead of old method of sometimes "has a File". Should be easier when reassigning them. 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	2010-09-02 21:30:48 +00:00
kshakir	4f51a02dea	Changed logging level to default at INFO instead of WARN. Changes to StingUtils command line for use in Queue, replacing Queue's use of property files. Updates to walkers used in existing QScripts to add @Input/@Output. RMD used in @Required/@Allows now has a new default equal to "any" type. New QueueGATKExtensions.jar generator for auto wrapping walkers as Queue CommandLineFunctions. Added hooks to modify the functions that perform the Scattering and Gathering (setting their jar files, other arguments, etc.) Removed dependency on BroadCore by porting LSF job submitter to scala. Ivy now pulls down module dependencies from maven. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3984 348d0f76-0448-11de-a6fe-93d51630548a	2010-08-09 16:42:48 +00:00
rpoplin	87470d5fe5	Checking in a simplistic VR qscript file for posterity's sake git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3705 348d0f76-0448-11de-a6fe-93d51630548a	2010-07-01 18:53:17 +00:00

Author

SHA1

Message

Date

kshakir

At chartl's superb suggestion, command line files are now all Files instead of old method of sometimes "has a File". Should be easier when reassigning them.

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

2010-09-02 21:30:48 +00:00

kshakir

4f51a02dea

Changed logging level to default at INFO instead of WARN.

Changes to StingUtils command line for use in Queue, replacing Queue's use of property files.
Updates to walkers used in existing QScripts to add @Input/@Output.
RMD used in @Required/@Allows now has a new default equal to "any" type.
New QueueGATKExtensions.jar generator for auto wrapping walkers as Queue CommandLineFunctions.
Added hooks to modify the functions that perform the Scattering and Gathering (setting their jar files, other arguments, etc.)
Removed dependency on BroadCore by porting LSF job submitter to scala.
Ivy now pulls down module dependencies from maven.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3984 348d0f76-0448-11de-a6fe-93d51630548a

2010-08-09 16:42:48 +00:00

rpoplin

87470d5fe5

Checking in a simplistic VR qscript file for posterity's sake

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3705 348d0f76-0448-11de-a6fe-93d51630548a

2010-07-01 18:53:17 +00:00

3 Commits (a10b2a00a55ec85d3d4d64249aed060abb9367d4)