split submit

Usage

Run using mc_script split submit after installation or using ~ndcn0236/bin/mc_script split submit on jalapeno.

Import in python using from mcutils.scripts.split import submit

Documentation

Submits a job using a mask in multiple parts

In command replace the name of the mask with MASK Any output-file should have JOBID appended to it e.g., to submit dtifit in 4 individual jobs run: mc_script split.submit 4 nodif_brain_mask.nii.gz -q short.q “dtifit -m MASK -b bvals -k data -r bvecs -o dtiJOBID”

Functions

get_job_name(cmd)	Gets the name of the submitted job to set when submitting
get_names(cmd)	Given a command iterates through all the mask-dependent outputs
run(njobs, mask_fn, cmd, submit_params)	Submits the cmd multiple times for different parts of the mask

CLI interface

add_to_parser(parser)	Creates the parser of the command line arguments
run_from_args(args)	Runs the script based on a Namespace containing the command line arguments