Slurm Singularity

Template ID: slurm_singularity


Take note below how to configure the template. This quickstart only includes the fields you absolutely require. This will write a new configuration to ~/.janis.conf. See configuring janis for more information.

janis init slurm_singularity

# or to find out more information
janis init slurm_singularity --help

OR you can insert the following lines into your template:

  id: slurm_singularity



ID Type Default Documentation
container_dir <class ‘str’>   Location where to save and execute containers to, this will also look at the env variables ‘CWL_SINGULARITY_CACHE’, ‘SINGULARITY_TMPDIR’
intermediate_execution_dir <class ‘str’>    
queues typing.Union[str, typing.List[str]]   A single or list of queues that work should be submitted to
mail_program     Mail program to pipe email to, eg: ‘sendmail -t’
send_job_emails <class ‘bool’> False (requires to be set) Send emails for mail types END
catch_slurm_errors <class ‘bool’> True Catch Slurm errors (like OOM or walltime)
build_instructions <class ‘str’> singularity pull $image docker://${docker} Instructions for building singularity, it’s recommended to not touch this setting.
singularity_load_instructions     Ensure singularity with this command executed in shell
max_cores     Maximum number of cores a task can request
max_ram     Maximum amount of ram (GB) that a task can request
max_duration     Maximum amount of time in seconds (s) that a task can request
can_run_in_foreground <class ‘bool’> True  
run_in_background <class ‘bool’> False  
sbatch <class ‘str’> sbatch Override the sbatch command