Issue with feature finding and proteomics_4d.config file on linux

[PatrickvanZalm]

Hi,

Thank you for Alphapept! It looks really good.

Im trying to get it running on a containerized linux environment but run into some issues with feature_finding.py. At line 1761 in feature_finding.py it executes the uff-cmdline2 tool, reading the proteomics_4d.config file. Something seems to go wrong here; it would not read the bool 0 or 1 properly. I did fix that by changing to false/true, respectivly.

Now, it doesnt read the floats properly;

Any idea how I could resolve this? Perhaps a .config file is slightly different between Windows and Linux environments? Or maybe eaiser to get in touch with the Bruker people?

Best,
Patrick

[straussmaximilian]

Hi Patrick,
Thanks for your kind words.
As for the Linux version, this is not heavily tested. We have a work-in-progress draft for containerization in docker for Bruker here.

As I don't have a Linux system at hand, I have just made a quick test on Ubuntu 20.04 LTS on WSL. I used our small Bruker IRT file for testing. When just calling the feature finder, it runs through but gets a permission error writing the file. I tested changing the access rights for the feature finder with chmod but was not successful. Unfortunately, I am not very proficient in Linux and didn't proceed with troubleshooting the access rights. When I call the feature finder in the terminal directly as sudo with the same arguments, it runs through. Therefore I would assume that the config file is okay.

From the bug, I could imagine that might be a parsing error (e.g., different settings for comma separator in system etc.).
Attached are some screenshots. I hope his helps



.

[straussmaximilian]

Closed due to inactivity.