dag_file

class gwas_tools.helpers.dag_file.DagFile(name)

Class to create a .dag file to be submitted with condor_submit_dag.

Parameters:

name (str) – name of the .dag file

add_blank_line()

Add blank line to .dag file.

add_job(job_number, sub_file, retry=1, args=None)

Add job block to .dag file.

Parameters:

  • job_number (int) – job number

  • sub_file (str) – path to the .sub file

  • retry (int, optional) – how many times retry the job if it fails (default : 1)

  • args (dict, optional) – variables to be assigned in the .sub file (default : None)

add_post_script(job_number, script, args=None)

Add post block to .dag file.

Parameters:

  • job_number (int) – job number

  • script (str) – path to the script file

  • args (list[str], optional) – script arguments (default : [])

set_parent(parents, children)

List parent jobs to be followed by children jobs.

Parameters:

  • parents (list) – parent jobs

  • children (list) – child jobs

save()

Save .dag file to name.