Hi Maxim:

I think you have to load your annotations into your history to do this.
I keep ours in the shared data area and have users import and provide it as 
input to our workflows.


Brad
On Feb 21, 2013, at 6:53 AM, Maxim 
<deeeperso...@googlemail.com<mailto:deeeperso...@googlemail.com>> wrote:

Hi,

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!
Maxim
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