> 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
> Any other suggestions?
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