bugs fixed for oncofuse

it's for initial bug fixes for the oncofuse pipeline.

I disabled tophat fusion workflow for now, and star junction output should work fine for GRCh37/hg19 genome. oncofuse output follows hg19 chromosome name though. sorry for the long delays in the fix (for #237)

I haven't handled:
1. The oncofuse fusion gene calls should be saved in the upload directory.
2. checks for an empty fusion file from STAR or Tophat