Slurm Singularity

Template ID: slurm_singularity

Quickstart

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:

template:
  id: slurm_singularity

Fields

Optional

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 JanisConfiguration.notifications.email 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