Initial commit
initial submission
Added GeneSet class and tests
Lots of additions
moved system to scripts folder
added more options for SGE job submission and controlling the tvc/qc analysis wrapper
test
test
remove temp files
add Jeff's scripts
fixed qsub command line call
updated json status update script process
fixed template writer json path
lots of small changes to tri_driver.py
various updates
test

Conflicts:
	scripts/runner.pyc
	scripts/template_writer.pyc
	scripts/tri_driver.py
added status check and a few parameter chagnes
added logging class to update_json.py
fixed bug in template writer on sample path for QC
add log to find jobs