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 <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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