If you wish to distribute jobs across a cluster you will need to install the appropriate snakemake executor plugin. For example, to use SLURM you can install the snakemake-executor-slurm plugin using pip:
pixi shell
pip install snakemake-executor-plugin-slurm
We recommend adding a snakemake conda prefix to your bashrc, e.g. in the Stergachis lab add:
export SNAKEMAKE_CONDA_PREFIX=/mmfs1/gscratch/stergachislab/snakemake-conda-envs
export APPTAINER_CACHEDIR=/mmfs1/gscratch/stergachislab/snakemake-conda-envs/apptainer-cacheThen snakemake installs all the additional requirements as conda envs in that directory.