Hello,
May Galaxy Australia please update the version of PICRUSt2? It is now three years out of date. Additionally, the versions after 2.6.0 now use a new database to generate predicted metagenome output that results in better NSTI values; which means better gene predictions.
I asked this with Galaxy helpdesk directly, and they said to ask in here since the wrapper would need to be updated and they are not in charge of that. Can anyone help, please?
Welcome @lyisrae1
This is a great question! Thanks for posting here for visibility! I’m sure others may want to use an updated wrapper as well.
I found your request to the Picrust author’s at their Github repository.
Since the request is for the Galaxy tool wrapper, I added a comment to the issue ticket above, and created a request that the IUC will see. These are the details.
Note to Galaxy user’s about how tools are hosted at Galaxy servers (from jennaj at Galaxy Help)
The tools hosted in Galaxy have a layer added around the original underlying tool we call a tool wrapper. These can be written by the original authors or others! The IUC is our tool standards group. Community contributions are big part of wrapping tools!
How it works: First a tool wrapper is created (or updated) and is published to the Main ToolShed. Once ready, Galaxy servers can host the tool!
The IUC created the current tool wrapper for PICRUSt2 (based on picrust2 (Version 2.5.3))
- Main ToolShed repository
- Development repository
- Request to update to picrust2-2.6.3 → Request: update picrust2 wrapper for picrust2-2.6.3 galaxyproject/tools-iuc#7677
The IUC will get back to us about a potential update on the ticket. The author will usually get back to us here, too, or I will see it and post back the details. How long this takes can vary! But once ready, the public Galaxy servers, including UseGalaxy.org.au, will update!
If you are comfortable on the command-line, you could run the tool in Jupyter! You’ll be able to use this with your existing Galaxy datasets and histories. The instructions at the original tool repository can be followed for the installation and commands.
I hope this helps to route the request to the correct people who can do the update, and to give you some options for now! Any questions, please ask! 