Add "micromamba" as an option for --conda-frontend

[magmir71]

Dear Snakemake team,
thanks for an awesome software.
I am using snakemake to run jobs on a HPC cluster with SLURM, and mostly use singularity mode. However, for some rules, I need to install a set of packages, for which no ready-to-use docker or singularity image exists. For such rules, I specify docker://continuumio/miniconda3:latest image and a .yaml file with conda packages, as shown in the "Distribution and Reproducibility" docs. Thus, snakemake activates a conda environment within the image with installed conda. The only issue is that installation with conda is very slow.

As an alternative, one could use an official micromamba image: https://hub.docker.com/r/mambaorg/micromamba
Unfortunately, specifying "mamba" as --conda-frontend does not work with that image.

Describe the solution you'd like
Could you add "micromamba" as an option for --conda-frontend?

Thanks a lot!
Aleksei

[fgvieira]

I started PR #1889 for that but it turned out to be a bit more complicated than I had expected (and I don't have a lot of time now), mostly because the conda/mamba/micromamba sub-commands are not consistent.

But you are more than welcome to contribute to the PR. 😄

[ammaraziz]

@fgvieira could you rerun the checks? They have expired, can't see what the issue was.

[fgvieira]

Just rebased the branch.

[f0t1h]

bump

[mfansler]

This is a duplicate of #1038.

[charmoniumQ]

We've been working on this in PR #2013