Harald Barsnes

Would it be a viable alternative to add a new specific path option called, for example, -config_folder that allows you to set the config folder via the SearchCLI or PathCLI...

> I just thought that an env variable was easyer on your part, because you don't need to pass it from the cli programs, all the way down to every...

I've deployed a beta version of SearchGUI that supports the config_folder option here: https://genesis.ugent.be/archiva/repository/maven2/eu/isas/searchgui/SearchGUI/4.2.10-beta/. However, as far as I can tell the conf folder is not used when using the...

I agree that treating each file as a single fraction is not ideal. However, we sadly not not have the manpower to implement new features at the moment. But we’ll...

If PeptideShaker is stuck at that particular step for long, you can cancel the process and have a look at the PeptideShaker log file. You can find it from the...

I don't see any errors in the log file related to the progress halting when importing the PSMs. Would it be possible for you to share the SearchGUI output file...

Thanks for sharing the SearchGUI zip file! However, in order to try loading the data I will also need the spectrum and FASTA files. Any chance you could share those...

Thanks again! Any chance you can share the mgf file C:\Gui\MS\Glutenmgf.mgf instead of the raw file? (As I'm having some issues with the spectrum titles not matching yours if I...

Your data initially loaded fine on my end without any issues. However, when I downgraded my Java version to the same as the one you are using, I was finally...

Great to hear that you can now load the Comet data! As for the MS Amanda issue, I don't see any explanations for this in the log file. Would you...