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galaxyproteomics / tools-galaxyp

Galaxy Tool Shed repositories maintained and developed by the GalaxyP community
MIT License
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Add FragPipe #759

Closed reid-wagner closed 1 month ago

reid-wagner commented 1 month ago

This PR adds a wrapper for the FragPipe tool suite.

A handful of default FragPipe workflows are provided for the user, while more may be added in the future. Most FragPipe parameters are duplicated in the Galaxy tool, many of which are optional to allow the workflow defaults to be used.

Some components have not yet been implemented due to license restrictions (DIA-NN & MSBooster). Other parameters need further work and testing before implementation, and will default to the workflow defaults. The workflow, along with the log file and some other FragPipe outputs are optionally selected as Galaxy outputs.

License keys are hard-coded into the tool, and a required select option and text warnings are in place to ensure a user understands the licenses, as has been discussed with the developers.

bgruening commented 1 month ago

@reid-wagner any help needed or a license issues again?

reid-wagner commented 1 month ago

@bgruening No license issue other than DIA-NN/MSBooster, which are disabled for now. Just working through some problems with the tests.

Sorry, I wasn't sure who I might be spamming with Github action notifications. I closed this PR to debug the actions in my fork, although just marking this WIP might have made more sense.

In any case I've got Galaxy docker planemo testing running locally now, but the FragPipe tests still aren't passing. Of course I did manually run these jobs successfully on our instance.

In the meantime, this tool is ready for review pending whatever tweaks I need to make to get it running here. If you were interested in reviewing, you could take a look at the implementation. Otherwise, I can add the review label once tests pass.

reid-wagner commented 1 month ago

It seems like re-opening a pull request that's been force-pushed is not allowed. I'll create a new PR marked WIP.