recetox-msfinder not working on usegalaxy.eu

usegalaxy.eu support
,
1

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.

1 Like
2

Update 2

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)

Hi @hechth

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:

  1. Run the earlier version for urgent work
  2. Post back the details about the tool/version, and we can open a ticket to get that one fixed up too.

Thanks!

3

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!

1 Like