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Rappsilber-Laboratory / AlphaLink2

AlphaLink2: Integrating crosslinking MS data into Uni-Fold-Multimer
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Streamlining installation using a conda environment file #10

Open multimeric opened 11 months ago

multimeric commented 11 months ago

Hi, I was recently trying to set up this pipeline on our HPC, and it occurred to me that we could streamline all the conda install, pip install and python setup.py install commands by exporting a conda environment definition file, so that users would only need to clone the repo, then conda env create -f=/path/to/environment.yml and everything should work.

Would you be interested in me contributing something like that?

lhatsk commented 11 months ago

Hi, Yes, that would great! I guess the only manual step that will remain is to copy stereo_chemical_props.txt?

Thanks!

multimeric commented 11 months ago

Yeah so conda won't be able to handle data files like that, but I wonder if that file could be obtained within the AlphaLink2 code, either during setup or at runtime, so users don't have to manually install it?

lhatsk commented 10 months ago

Hm, where would you include it? E.g., download/ copy at the beginning of run_alphalink.sh if it doesn't exist yet?

multimeric commented 10 months ago

I don't know if it's subject to any license issues that prevent it, but what I would do is include it in the package as package data: https://setuptools.pypa.io/en/latest/userguide/datafiles.html. To do that all you need to do is commit it to the git repository and ensure the project metadata is configured correctly. It's only ~ 9 kilobytes so I doubt anyone would really mind.

lhatsk commented 9 months ago

I don't know about the licensing, my guess is there is some issue, otherwise Deepmind would have also packaged it. I'll check it out. I guess just doing a quick check and downloading if necessary isn't too bad.