Maxim, Brad is correct - to supply a reference annotation file to Cufflinks, the file must in the active history at the time the tool is executed. Then when setting the options for "Use Reference Annotation:" on the tool form, the pull-down will select from datasets in the right history panel. If you would like to keep these in a common area, using a "Shared Data -> Data Library" is a good choice. When users later import into a history to use, it would really just be a link to the original, saving disc space. An example is on the public Main Galaxy instance under "Shared Data -> Data Library -> iGenomes": https://main.g2.bx.psu.edu/library You could also put the reference files in a history, perhaps with other data, and then embed the dataset or history objects in a shared Page, along with text, graphics, etc. Importing this way creates links to originals as well, saving disc. An example of this is also on Main, in the RNA-seq tutorial under "Shared Data -> Published Pages -> Galaxy RNA-seq Analysis Exercise": https://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise Hopefully one of these options will work for you! Jen Galaxy team On 2/21/13 4:05 AM, Langhorst, Brad wrote:

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 <deeepersound@googlemail.com <mailto:deeepersound@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 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:

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