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Proteobench / ProteoBench

ProteoBench is an open and collaborative platform for community-curated benchmarks for proteomics data analysis pipelines. Our goal is to allow a continuous, easy, and controlled comparison of proteomics data analysis workflows.
https://proteobench.readthedocs.io
Apache License 2.0
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Error during submission of FragPipe output/FragPipe - MSFragger version number #285

Closed brvpuyve closed 1 month ago

brvpuyve commented 2 months ago

Hi all,

When I tried to submit the output of FragPipe, I received an error message: image (2) It seems the issue is specifically related to the parameter files as the submission succeeded once I removed the parameter files.

In addition, it seems there is an issue when extracting the version of the software module and the search engine. If I am correct, the software module should be FragPipe (v.21.1) and the search engine should be MSFragger (v4.0).

Best, Bart

enryH commented 2 months ago

At least during testing the search engine is correctly specified. Did you use the public deployed app?

brvpuyve commented 1 month ago

Hi Henry,

I was just checking the MSFragger interface within Proteobench and I did spot one minor issue that we preferably want to resolve.

More specifically, I noticed that it gives back the same version number for both FragPipe and MSFragger: 'search_engine': 'MSFragger', 'search_engine_version': '21.1', 'software_name': 'FragPipe', 'software_version': '21.1',

In reality, the version number for MSFragger should be 4.0.

Sorry that I only spot this error just now.

Bart

mlocardpaulet commented 1 month ago

related to the previous somment: see https://github.com/Proteobot/Results_quant_ion_DDA/pull/193 it is the pull request that Bart generated. @enryH I think that this was an issue that was corrected... I don't know where it went wrong.

enryH commented 1 month ago

I indeed corrected it. Maybe it's just no present on the deployed version atm?

mlocardpaulet commented 1 month ago

I indeed corrected it. Maybe it's just no present on the deployed version atm?

Do you think that we should try to make a new version now?

enryH commented 1 month ago

You can. You will just need to update the Change Log file, then it should be automatically updated.

https://github.com/Proteobench/ProteoBench/blame/main/CHANGELOG.md

enryH commented 1 month ago

And for Bart: In the main branch, the parsing is correct, see the fragger_extracted_params file.

mlocardpaulet commented 1 month ago

@enryH I tried locally with the main. It still does not parse well the search_engine_version: ProteoBench parsing: image fragpipe.workflow: image The search engine (MSFragger) version should be 4.0

enryH commented 1 month ago

Can you send me the .workflow file? Could be due to the fact that Bart has Windows paths...

mlocardpaulet commented 1 month ago

I'll send you asap by email.

enryH commented 1 month ago

So... As I am developing on Windows, locally Bart's Windows Path is interpreted correctly, but then it produces errors on the UNIX server. So note: We should collect test for all major platforms people run stuff on...