INSTALL.md

Install

You will need snakemake which you can install using conda/mamba, e.g.:

mamba create -c conda-forge -c bioconda -n snakemake 'snakemake>=8.4'

Finally, 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:

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-cache

Then snakemake installs all the additional requirements as conda envs in that directory.