A bash script that batch renames all the output files downloaded from the Galaxy server so that it can be used to run cummerbund.

##Eases Pipeline integration

The RNA-seq pipeline for many users consists of cuff-diff on galaxy, downloading the files and then running them on R with CummeRbund.

The files downloaded from galaxy have different names than what galaxy expects.

I wrote a script that converts all the files into the proper format.

Open up a terminal with a bash shell.