I got my local instance of Galaxy running and most tools work properly.
Unfortunately I seem not to understand how to implement cufflinks within
Galaxy, in particular I do not know how to inform Galaxy about the location
of GTF annotation files.

I searched the archives for this and was not successful. Furthermore I
cannot find a preference file holding cufflinks specific information nor a
general place to keep annotation data.

Who can point me there?

Best regards and thanks for your effort!
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