generate-slurm-partition-config - Man Page

generate-slurm-partition-config – Generate SLURM partition configuration for Snakemake

Synopsis

generate-slurm-partition-config [-h] [-o OUTPUT] [clusters]

Options

Positional Arguments

clusters: Comma-separated list of cluster names for multi-cluster setups. If omitted, queries the current/default cluster.

Optional Arguments

-h, --help: Show a help message and exit
-o, --output OUTPUT: Output file path. If not specified, writes to stdout.

Examples

# Query current cluster and output to stdout
generate-slurm-partition-config

# Query specific cluster
generate-slurm-partition-config cluster1

# Query multiple clusters
generate-slurm-partition-config cluster1,cluster2

# Save to file
generate-slurm-partition-config -o partitions.yaml
generate-slurm-partition-config cluster1,cluster2 -o partitions.yaml

The generated YAML file can be used with:

snakemake --executor slurm --slurm-partition-config partitions.yaml

OR for permanent use, copy the partitions.yaml to a location (e.g. ~/.config/snakemake/ or /etc/xdg/snakemake). Be sure to set $SNAKEMAKE_SLURM_PARTITIONS, accordingly.

Info

February 2026