3.9 years ago by
The reference genome is not coming up or do you mean the reference annotation dataset? This is a GTF/GFF3 dataset. It is not provided within Galaxy and must be obtained from a source such as iGenomes (if available), UCSC, Ensembl, and others.
iGenomes is the best source due to specific attributes included in the annotation. I double check and we are in luck - canFam3 is supported.
Download the .tar file for the build = UCSC and genome canFam3. Uncompress the tarball, locate the "genes.gtf" dataset, upload just that to Galaxy, and double check the metadata assignments (datatype and database - use the "Edit Attributes" functions found by clicking on the pencil icon in the upper right corner for the dataset once loaded. You can set these upon upload, but it is always good to do the metadata double check to avoid problems later on.
Galaxy does not uncompress and load multi-file tar archives through the Upload tool. If you unsure about how to download the data from iGenomes, please see the instructions there. The commands needed to uncompress a tar archive can be found with a google search. This one is a good one to follow, with clear, specific commands listed for various OS systems and specific extensions. But the others that come up in the search are also good to review if you have issues.
I perhaps added more detail here than you yourself require, but it may help others with a similar need. I will also add these instructions to my list of advanced topic to update/include during the help resource updates we are working on over the next month or so (these will be published to our wiki and here in Biostar for reference).
Hopefully this helps! Jen, Galaxy team