The tools fails with the log message “mono: command not found”. The tool runs in a docker container with mono.
Unfortunately I can’t share an error log or history as the tool creates a variable number of outputs and in this case it just fails creating an empty list.
Confirmed and ticketed. Thanks for reporting the problem!
How to get job details from collection outputs → Click in the “i” info button in the upper right corner of the collection folder in the history. If the history is also in a shared state, you can copy/paste the job details page back here for feedback.
I’ve done that with my test history here just for clarity about the how-to, and to show why this view is my favorite for troubleshooting!
Update: I found the tool, and there is just one version. I’m reviewing.
REF: RECETOX MsFinder Annotation of fragment peaks in mass spectral libraries.(Galaxy Version v3.5.2+galaxy4)
Could you at least share the full tool name and version? Find that at the top of the tool form.
In general, the tool probably needs a configuration update in the container for that specific error. I found another tool like that yesterday – and the earlier versions were fine, the most current version had a problem. I ticketed it and it is being fixed.
So – your solution could be the same:
- Run the earlier version for urgent work
- Post back the details about the tool/version, and we can open a ticket to get that one fixed up too.
Hi, the tool ID is toolshed.g2.bx.psu.edu/repos/recetox/recetox_msfinder/recetox_msfinder/v3.5.2+galaxy4 - there are no previous versions as we just now added this tool to Galaxy :).
Thanks a lot!