Pbs Singularity¶
Template ID: pbs_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 pbs_singularity
# or to find out more information
janis init pbs_singularity --help
OR you can insert the following lines into your template:
template:
id: pbs_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 queue 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_pbs_errors | <class ‘bool’> | True | |
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 |