Hi
I tried running Fragpipe tool but I get an error message saying there is a new version of MSFragger. How can I update this tool or any of the other tools like Fragpipe.
Welcome, @Lizex
The messages from the tool are getting passed into the output as a type of log message. You can ignore those when working at a public Galaxy server. We handle all of the technical dependencies server side for you.
We have wrapped the version that is currently available under the license you reference, so it is fine use the one we host.
If you are getting an error, check the logs for why – it won’t be about the tool version, but about your data and the processing error, maybe further down? Job logs from scientific tools can be confusing (anywhere!), so if you need help with that, we can try to help more here to get you going. How to share your work is in the banner at this forum.
Hope this helps to explain what is going on! 