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galaxyproject / tools-iuc

Tool Shed repositories maintained by the Intergalactic Utilities Commission
https://galaxyproject.org/iuc
MIT License
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Add Sage (search engine) on usegalaxy.eu #5960

Closed sciordia closed 7 months ago

sciordia commented 7 months ago

I was wondering if it would be possible to add a new proteomics tool (link below) to the public usegalaxy.eu server that is associated with the protein identification using a FASTA Database?.

SageAdapter

Sage: The fastest search engine 1

Sage is well-integrated into the open-source proteomics ecosystem, e.g. in the OpenMS package (which is already partly integrated in useGalaxy).

It would be great if you could add it to the public server.

Thank you very much.

Bests, Sergio

bernt-matthias commented 7 months ago

This should come with https://github.com/galaxyproteomics/tools-galaxyp/pull/697 which is unfortunately delayed...

sciordia commented 7 months ago

Thank you very much @bernt-matthias for including my request. I really appreciate it.

Could you let me know when you release the next release of OpenMS, please?.

Thanks again.

Best regards, Sergio

bernt-matthias commented 7 months ago

Will try, but you could also subscribe to the linked PR.

sciordia commented 7 months ago

Thank you @bernt-matthias , you are right it is easier if I subscribe. Done.

Since I have your attention, hehe, I wanted to make a second suggestion. The SAGE data output can be processed (re-scoring) by both the percolator tool (already included in galaxyp) and mokapot. The latter re-scoring tool is becoming fashionable in proteomics.

Here is the link: https://mokapot.readthedocs.io/en/latest/

Do you think you could also include it in the next release, please?. If necessary I could create a new post.

That would be great but obviously I leave it up to you.

Thanks again for everything.

Best regards, Sergio

bernt-matthias commented 7 months ago

This is not part of OpenMS. But it definitely looks interesting. Would be good if you create a new issue, ideally at https://github.com/galaxyproteomics/tools-galaxyp/

I would close this issue, since it will be covered by https://github.com/galaxyproteomics/tools-galaxyp/pull/697