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@tdido tdido commented May 20, 2024

People don't like to read, so by linking my cluster's usage docs to the plugins catalog I consistently get people installing this via pip instead of mamba, which is not ideal in our case.

Hope it's acceptable to add an explicit mamba example which should help people realise there's another option.

@tdido tdido requested a review from johanneskoester May 20, 2024 13:39
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Sure, good idea. Three things:

  1. we should check whether the plugin is really there before rendering this into the docs. Some plugins might not or not yet be available via mamba.
  2. One should at least mention envs and link out to them in order to avoid that people accidentally install it outside of their snakemake env. But the same holds for the pip command.
  3. The same should be done for all plugins, hence maybe use a jinja include for the entire installation section?

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