when I choose ET mode under the GeneMark , there is no option to upload RNA data and still ask for a license. Is this feature imcomplete?
Welcome @Andy_Sun
Some annotation sources are released under academic or other licensing constraints. The Galaxy tool wrappers are generally created in a way that supports incorporating protected or licenced data.
However, due to the way the public servers are hosted (free to everyone with an anonymous email address, not only “confirmed” academics!), this means we cannot offer that data to public users unless the author allows a licence pass-through toggle on the tool form. Some do allow limited access but not Genemark.
The alternative is to create a place where you can use the tool!
The minimal option would be to run the bulk of your analysis on the public server, then transfer data to/from your instance for some steps. A local Galaxy is useful for other reasons, example: backup histories for local queries and browsing! For the compute, you can connect to an academic cloud cluster if your local resources are not enough.
Docker Galaxy (local instance) → Galaxy Docker | Galaxy Hub
Use Galaxy | Galaxy Hub (academic-clouds)
Or, for larger projects, a cloud version of Galaxy can be a solution if funding is available. Galaxy itself is always free, but commercial storage and compute are not.
AnVIL Galaxy (hosted personal cloud) → AnVIL | Galaxy Hub
For either, the last step is to install the tool and index using our managed tool install methods.
Once set up, export your public history archive and load it into your Galaxy, upload your license from the authors, and input it onto the form here. When you are done, do the reverse: export your new results and import it back to the public server.
GTN tutorials for Funannotate Predict
With this context, I’m not sure what you mean by this part. Do you mean the Genemark index? Would you like to explain a bit more? Screenshots or a shared history can also help.
The ES/ET modes both expect a prior model for the Use pre-existing Genemark training file (e.g. gmhmm.mod) option, because the index is not hosted on the public server. When on your own server with the index available, RNA data is still input differently. What is your use case? We can help to get it all set up if you are already on your own server with the index?
We know this is tedious but there isn’t another way. Not all software/data has a licence that allows public user. Followup comments questions welcome! Please let us know if this explains you observations! 