Set up directory structure.
Added Data Package
Added Processing Package
Added Reports Package
Pruned Enrichements and renamed to pathways.  Now its just dealing with
pathways, might throw the hypergeometic enrichments somewhere else.
Divert R errors to file.  These are usually due to not enough data, I
catch these with python but I don't like mucking up my stddout.
Renamed Notebooks.
Post merge commit.
New script based method for running in parallel.  run_cancer.py is
called by CreateClinicalFeed notebook.
Missed a couple files on the last commit.
Reworked some of the paths used to generate reports.
Turns out last time I didn't find all of the paths to fix, this time all
of the paths in the Reports should work.  Also managed to kill a
parameter in the report section generating functions by sticking to the
report_folder field in the ClinicalObject.
Changed next_cancer and prev_cancer to cancer names rather than cancer
objects.
Tweaked PathwayPathway notebook.
 sd
commit
Added Pathway-Pathway Reports
Added drop_pc option to zero out top global pc.
Added more stuff w/ Pathway-Pathway reports... mostly in the notebook.
Added some code to handle methylation age signatures... desperately need
to clean up.