Snakemake: How to force the creation of all conda environments

Question

I am aware that by adding the option --conda-create-envs-only you are able to create the conda environments for the workflow. However, would it be possible to force the creation of all conda environments under workflow/envs/ without knowing the workflow DAG in advance?

The reason is that I am planning to run snakemake on an HPC, and the compute nodes have no internet. As such I have to set up the environment in a build node with internet. The problem is that I can only access my input data in the compute nodes.

Answer 1

Maybe make the creation of the conda environments a target itself? Something like, not tested:

localrules: all, make_envs

rule all:
    input:
        # Maybe not needed:
        expand('{env}.done', env= ['env1', 'env2'])


rule make_envs:
    conda:
        'workflow/envs/{env}.yaml',
    output:
        touch('{env}.done'),


rule one:
    input:
        'env1.done',
    conda:
        'workflow/envs/env1.yaml',
    output: ...
    shell: ...

Rule one will find the conda env created because it needs env1.done as input