cluster_configuration.md

Run on a cluster

cluster configuration: config/cluster.yaml

Here is an example configuration:

__default__:
  queue: queue
  name: {rule}.{wildcards}
  stderr: logs/cluster/{rule}/{wildcards}.stderr
  stdout: logs/cluster/{rule}/{wildcards}.stdout
  threads: {threads}
  resources: span[hosts=1]

cluster command: config/cluster_command.txt

bsub -q {cluster.queue} -J {cluster.name} -e {cluster.stderr} -o {cluster.stdout} -R {cluster.resources} -n {cluster.threads}

Commonly used parameters

Parameter	Description
__default__	Rule name (__default__) for default configuration)
queue	Queue name (required)
name	Job name
stderr	Log file for standard error
stdout	Log file for standard output
threads	Number of parallel threads for a job
resources	Resource requirements. span[hosts=1] prevents parallel jobs from being submitted to different nodes

Refer to the snakemake documentation.