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.
chmod +x galaxytocummerbund.sh
./galaxytocummerbund.sh