possibility to have readable envs?

maxplanck-ie / snakepipes

Customizable workflows based on snakemake and python for the analysis of NGS data

http://snakepipes.readthedocs.io

MIT License

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possibility to have readable envs? #918

Closed sunta3iouxos closed 11 months ago

sunta3iouxos commented 11 months ago

to use some environments for custom work, for example bedtools in DNA mapping I need to run the snakePipes envInfo command to find the appropriate environment. mamba env list provides no usable information

envs/shared.yaml is in:
    mambaforge/envs/27f2773ffdbc97941318f72b021070d6
envs/createIndices.yaml is in:
    mambaforge/envs/12f227c63319d49227b7c24df8b9f896
envs/rna_seq.yaml is in:
    mambaforge/envs/b4493075523163bb007302e91dbab003

katsikora commented 11 months ago

What would you like to obtain? E.g. if you're after the list of packages inside each env, you can run mamba list -p $PATH_TO_ENV, the path to the environment being what's returned by snakePipes envInfo. You can then mamba activate $PATH_TO_ENV and use the env for any custom work. If you want to read the env yamls to see what's specified in there, the paths should be return by snakePipes info.

Hope this helps,

Best,

Katarzyna