Merge pull request #18 from spacepod/develop

collecting env var warnings
removed hard-coded path from script
Merge branch 'develop' of https://github.com/cancerregulome/gidget into develop to update wget_ALL_parse_biotab_untar.sh to push
added new tumor types and changed RPPA platform design file
added error message in case input FMx is empty
fixed a bug in how the new feature names for indicator features are generated
based on the parent feature name
fixed bug in how days relative to sample-submission or sample-procurement are computed
added new tumor types to list(s)
changed one line so that output of addDiscreteFeat.py is dumped to a log file
modified _addGeneName so that if the place where it expects to find a single
gene symbol actually contains a list of genes, it will take just the first
one (eventually we need to modify this so that multiple features will be
generated in this case)
Merge branch 'develop' of https://github.com/cancerregulome/gidget into develop
for CNVR features, never annotate with gene symbol, always with locus
no change
modified how pathway GNAB features are generated -- particularly y_del and
y_amp features which now fall back on the y_n feature for a gene if the
y_del/amp feature is not available
fixed typo, duh
added ucs tumor type
added new tumor type: ucs
Update README.md
added warning to usage text that this script takes a LONG time to run
Merge branch 'develop' of https://github.com/cancerregulome/gidget into develop