Running snakemake workflows on octopus

Here's how you run snakemake workflows on our octopus cluster.

First, drop into a guix shell with snakemake and the slurm plugin.

guix shell snakemake python python-snakemake-executor-plugin-slurm python-snakemake-executor-plugin-slurm-jobstep

Assuming you are in the directory with the Snakefile, run it on slurm like so:

snakemake --executor slurm --jobs 8

Feel free to play around with the --jobs parameter.

Running on a specific partition

You can run some rules on a non-default partition using something like

snakemake --executor slurm --jobs 8 --set-resources myrule:slurm_partition=allnodes

Here, we run the rule named "myrule" on the allnodes partition. You can also specify this in a config file instead of on the command-line. Please refer to the snakemake manual.