Paths, small bug, and RSEM/EBSeq interface

This revision includes 3 changes.
First, I removed any commands that modified the PATH variable--for portability's sake, we will now assume that the user has set up paths appropriately for their system.
Second, I fixed a small bug in the deseq-run.R file where the output filenames are not built correctly.
Finally, I updated the scripts to utilize the latest RSEM/EBSeq command-line interface.