MSFragger Path not found

[Julie-Cardin]

When trying to run FragPipe with apptainer

error message:
PATH not found for MSFragger

I searched in dirs
/fragpipe_bin/fragPipe-22.0/fragpipe
tools, bin, lib, workflows
No MSFragger ...

Where the MSFragger is supposed to be ? One could expect that dependencies would be installed in the container ?
Is it normal that it is not there ?

Any suggestions how to fix please?

[fcyu]

First of all, I don't know who created the apptainer container, but we don't support that.

Second, MSFragger should be downloaded by users (you) in additional to FragPipe due to the license constraint.

Best,

Fengchao

[Julie-Cardin]

Right, you are not responsible for container, I mentioned mostly as context of use for FragPipe because I am not root on sever.
And thanks for the answer, I understand, user should download due to license , it is normal it is not already part of FragPipe download.

Thanks for your support and time,
Best

[fcyu]

That's correct. The FragPipe (and the container having FragPipe) won't have MSFragger, IonQuant, and diaTracer due to the license. You need to download them and specify the paths in FragPipe.

Best,

Fengchao