sub_file

class gwas_tools.helpers.sub_file.SubFile(name, universe='vanilla', description='')

Class to create a .sub file to be submitted with condor_submit.

Parameters:

• name (str) – name of the .sub file

• universe (str, optional) – universe (default : vanilla)

• description (str, optional) – description string of the sub file (default : empty)

add_blank_line()

Add blank line to .sub file.

add_executable(exec_name)

Add executable to .sub file.

Parameters:

exec_name (str) – executable name

add_arguments(args)

Add arguments to .sub file.

Parameters:

args (str) – arguments as a single string

add_accounting_group_info(group, user)

Add accounting_group and accounting_group_user to .sub file.

Parameters:

• group (str) – accounting group

• user (str) – accounting group user

add_specs(ncpu, memory, disk=None)

Add request_cpus, request_memory, and optional request_disk to .sub file.

Parameters:

• ncpu (int) – number of cpus

• memory (int) – requested memory in Mb

• disk (int) – requested disk space (default : None)

add_logs(output, error, to_append=None)

Add output and error to .sub file.

Parameters:

• output (str) – path to the output folder

• error (str) – path to the error folder

• to_append (list[str], optional) – str to be appended to output and error file names

add(line)

Add custom line to .sub file.

Parameters:

line (str) – line to add

save()

Save .sub file to name.