Increase bwamem tmp space lsf resource request
updated ur submodule to 66f7fc1
change some status_message to debug_message

These can be changed back if needed.  We still don't have an easy way to
show debug messages (or to log them).  These messages were switched due
to TCGA reference alignment builds spitting out hundreds of lines of
messages.
make reference_coverage semi-required

reference_coverage is only required if there are
reference_coverage_objects, e.g. a region_of_interest_set_name.
Merge branch 'anti-spam'

CHANGELOG: In an attempt to reduce the amount of information that gets
spammed to the screen when you start a reference alignment model we
have suppressed many messages that really only need to be displayed for
debugging purposes.  Next time you start a reference alignment model you
may feel like something is wrong because you are used to those messages
but we hope that this will provide a better experience.
Make reference-transcripts non-optional.

The params to `gmt annotate transcript-variants` get mangled otherwise.
Updated class browser cache.
Updated `genome` tab completion.
Updated `gmt` tab completion.
Sample Import Manager: initial commit
Sample Import Manager: add load from sample csv
Sample Import Manager: update sample data structure when loading from csv
Sample Import Manager: _load_samples works
Sample Import Manager: move job status into separate method
Sample Import Manager: update get/set sample status method
Sample Import Manager: add inst data and model getting for load samples
Sample Import Manager: require original data path in samples csv
Sample Manager: config file is YAML, is loaded inn _errors__ and has model and job config
Sample Manager: samples are a property that is a hash
Sample Manager: add tests for config file and sample csv existing