Problems with Mamba and Conda.

Snakemake currently use mamba as the default conda environment manager, instead of conda. The main reason behind this change is the lack of speed conda has experienced since a couple of times now.

Snakemake still allows to use conda as the package manager, over mamba, with the option --conda-frontend conda, however, this statement is currently not used by subworkflows, even if the user specified it in the main snakemake command.

This issue has been reported to snakemake developers (see here and here), but for now I do not know if this bug is corrected.

If you run an old installation of snakemake, you need to install mamba now, otherwise MAGNETO will neither install nor use conda environments anymore. Install mamba with conda (for instance : conda install -n base -c conda-forge mamba).

DO NOT install mamba with pip, as a complete different package with the same name is listed in PyPi.

You can also install snakemake through mamba, as it is now advised in snakemake documentation (see here).

Because of this problem, mamba will be listed as a mandatory dependency for MAGNETO.