updated graphite submodule to c3cea89
updated getopt-complete submodule to 95e944c
Make fix_alt_and_gt optional so things are not broken.
Merge branch 'master' into gb_master
Switch the queue these land in so they don't compete with their parent.
Updated `genome` tab completion.
Updated `gmt` tab completion.
updated ur submodule to 926b226
Reduce our tmp space request. RT#92318

It is believed that newer tophat versions and improvements to SX both
contribute to reduced tmp space requirements.  This change should be
sufficient to schedule two jobs simultaneously [on our current systems].
Output bam file paths that are missing
Merge branch 'master' into gb_master
SX: external command base will run the underlying command in back ticks
Make ModelSummary have more flexible def of failed builds

Useful for models with say one unstartable and one succeeded, the
unstartable build should be cleaned up but since I wasn't flagged as a
failed build the model had 0 failed builds and therefore the unstartable
was not set to clean up.
Strengthen interface of DifferentialExpression command
Remove incorrect comment
Disable some tests (blocking the model tests from being run)
Reactivate tests and update test results to account for correction of ALL1 sample common names
OK the ref.align diff.
added option to remove scaffolds by min_length
Updated `genome` tab completion.