> My question is which are the best/appropiate TOPHAT and CUFFDIFF versions?

Galaxy wrapper versions do not match tool versions. The tag 'requirements' will 
eventually be used to specify versions, but this work is not yet complete.

You should use Tophat v1.4.0 or 1.4.1 and Cufflinks v1.3.0 for now.

> The error message I get is TOPHAT not recognized.

To solve this problem, you'll need to install Tophat and add it to your Galaxy 
user's path

> Any other suggestions?

Please send questions about local Galaxy installs to galaxy-dev rather than 
galaxy-user; galaxy-user is for questions about how to use Galaxy for 
bioinformatics analyses.

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