[galaxy-dev] where to announce transcript annotation file in local Galaxy install

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