"AlphaPulldown init" or alike

[jkosinski]

As discussed, the need to clone a git repo with workflow files is problematic (needs git, another intimidating step for non-git people, increased complexity, you cannot pull again when you start modifying config.yaml etc.). The suggestion is to have a command like: AlphaPulldown init or if you want to limit to snakemake: snakemake ... AlphaPulldown init that would download the necessary files and create subdirectory structure necessary for running the workflow. Perhaps already at this step you could download the image and set up everything.

[maurerv]

I think downloading the images will not be possible.

However, we could clone the workflow, check if snakemake is installed etc.