`babs submit`: Submit jobs 

Table of Contents

babs submit: Submit jobs

Command-Line Arguments 

Submit jobs to cluster compute nodes.

usage: babs submit [-h] [--count COUNT | --select SELECT [SELECT ...] |
                   --inclusion-file INCLUSION_FILE]
                   [PATH]

Positional Arguments 

PATH: Absolute path to the root of BABS project. For example, '/path/to/my_BABS_project/' (default is current working directory).

Named Arguments 

--count: Submit this many jobs instead of submitting all remaining jobs.
--select: Select specific jobs to submit by subject and optionally session. Use as --select sub-XX [ses-YY] and repeat the flag to submit multiple jobs, or provide multiple values per flag (argparse appends and supports nargs). Examples: --select sub-01, --select sub-01 ses-01, --select sub-01 --select sub-02, --select sub-01 ses-01 --select sub-02 ses-02.
--inclusion-file: Path to a CSV file that lists the subjects (and sessions) to analyze. The file should columns: sub_id and, if session-level processing, ses_id. If this flag is specified, it will override the --select flag.

Warning

Do NOT kill babs submit while it's running! Otherwise, new job IDs may not be captured or saved into the job_status.csv!

Example commands 

Basic use 

If users only provide the required argument project_root, babs submit will only submit one job:

babs submit /path/to/my_BABS_project

Submitting a certain amount of jobs 

babs submit \
    /path/to/my_BABS_project \
    --count N

Change N to the number of jobs to be submitted.

Submit jobs for specific subjects (and sessions)

For single-session datasets, select subjects with --select. You can repeat the flag or pass multiple values in one flag (argparse appends and supports nargs):

babs submit \
    /path/to/my_BABS_project \
    --select sub-01 \
    --select sub-02

For multi-session datasets, include both sub-XX and ses-YY pairs:

babs submit \
    /path/to/my_BABS_project \
    --select sub-01 ses-A \
    --select sub-02 ses-B

You may also pass multiple values per flag:

babs submit \
    /path/to/my_BABS_project \
    --select sub-01 sub-02

Note

If there are jobs currently running, babs submit will refuse to submit new jobs until the running jobs finish or are cancelled. Use babs status to check progress.