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

README.md

galaxytocummerbund

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 problem

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

The solution

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

Running it

Open up a terminal with a bash shell.

chmod +x galaxytocummerbund.sh
./galaxytocummerbund.sh
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