Template ID: molpath

Template for Peter Mac molpath, the primary difference being the initial detatched submission sbatch is changed to . /etc/profile.d/; sbatch to handle the pipeline server.


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 molpath

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

OR you can insert the following lines into your template:

  id: molpath



ID Type Default Documentation
intermediate_execution_dir <class ‘str’>   Computation directory
container_dir <class ‘str’> /config/binaries/singularity/containers_devel/janis/ [OPTIONAL] Override the directory singularity containers are stored in
queues typing.Union[str, typing.List[str]] prod_med,prod The queue to submit jobs to
singularity_version <class ‘str’> 3.4.0 The version of Singularity to use on the cluster
send_job_emails <class ‘bool’> False Send Slurm job notifications using the provided email
catch_slurm_errors <class ‘bool’> True Fail the task if Slurm kills the job (eg: memory / time)
singularity_build_instructions <class ‘str’>   Sensible default for PeterMac template
max_cores <class ‘int’> 40 Override maximum number of cores (default: 32)
max_ram <class ‘int’> 256 Override maximum ram (default 508 [GB])
max_workflow_time <class ‘int’> 20100 The walltime of the submitted workflow “brain”
janis_memory_mb <class ‘int’>    
email_format <class ‘str’>   (null, “molpath”)
log_janis_job_id_to_stdout <class ‘bool’> False This is already logged to STDERR, but you can also log the “Submitted batch job d” to stdout with this option set to true.
submission_sbatch <class ‘str’> . /etc/profile.d/; sbatch Override the ‘sbatch’ command for the initial submission of janis to a compute node.