change sample temparory directory from names["sample"] to names["lane"]
fixed STAR juction input for oncofuse with GRCh37
disable tophat input for now
only works for GRCh37/hg19 genome
resume support for tophat-oncofuse
add checks to make sure the junction file exists before running oncofuse
upload oncofuse output to final directory
catch case where no fusion transcripts are loaded
put tophat2 as the default aligner
temporary solution
Merge pull request #407 from tanglingfung/master

Oncofuse bug fixes.

This should be considered pre-alpha, we haven't been able to validate the calls but this should get us started.

Thanks to @tanglingfung for all of his awesome work.