Yes, there are two things that could be changed (in addition to the original tool correction). Let’s summarize:
Repair the taxonomy fetching tool
I just check and it is not resolved yet. I’ll follow up more about this. Comments will post on the ticket for intermediate updates.
Blast indexes and form options – what’s supported.
The extended taxonomy options have never been supported (intentionally) so far at any of the public Galaxy servers, and the message you noticed in the logs is expected if this is attempted. There were two technical reasons but I’m not certain if both are still relevant or what else could be done to make it happen. I’ll also follow up about this to get some clarity.
- Prior topic discussing the log message Blast issue when trying to add species name: Fetch Taxonomic Ranks - #2 by jennaj
- Wrapper update ticket: (pending!)
Update Blast indexes – agree!
I added in the other database to an existing ticket. This is enough to prompt the whole package to be updated. I’ve contributed to these updates in the past, and maybe can help again this time if someone else can’t pick it up. More feedback will be added to the ticket, plus I’ll be updating back at this topic as each of these items is reviewed.
Then for your comment @SAlves
The taxonomy fetching tool works by using the subject GI identifiers for a look up. The target information is always included in outputs (unless specifically omitted?), and when the target is a database from NCBI, all of the artifacts will have a GI number available.
While the GI is not included in the default 25 tables, this can be toggle into an output in the extended tabular options as sgi = Subject GI. Maybe this helps you? I have an example in my testing history linked to the Github ticket for the taxonomy tool correction above. Please ask if you need to do this and are not sure how – sharing a screenshot of your current options would be a good place to start!
More soon! 