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MDAnalysis / WorkshopPrace2021

Materials for the 2021 PRACE Workshop @ SurfSARA
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add pdbfixer to environment file #18

Closed orbeckst closed 3 years ago

orbeckst commented 3 years ago

close #17

orbeckst commented 3 years ago

@mnmelo I assume you installed pdbfixer on Lisa, too?

IAlibay commented 3 years ago

@mnmelo I assume you installed pdbfixer on Lisa, too?

Going by discord discussions it seems like it.

mnmelo commented 3 years ago

Indeed! Because the conda install had to be done as a submission job I have the set of commands I actually run as a semi-neat SLURM job. Would that make sense to bring into this repo?

orbeckst commented 3 years ago

In my opinion, this repo will be the primary permanent record so anything that will help us in the future should go here. Just put it into an appropriately directory ("development" or "DO_NOT_TOUCH_EVER_YES_I_MEAN_YOU")

mnmelo commented 3 years ago

On this topic, is there a nice way to specify which jupyter nbextensions to activate for the environment? So far we got 8.

IAlibay commented 3 years ago

@mnmelo I don't think you can do it directly from a yaml file, but we can/should do this: https://github.com/IAlibay/MDAnalysis-talks/tree/main/binder

That way we can just set up binder to run on top of the repo.