BALSAMIC.commands.run package

Submodules

BALSAMIC.commands.run.analysis module

BALSAMIC.commands.run.base module

BALSAMIC.commands.run.reference module

BALSAMIC.commands.run.scheduler module

class BALSAMIC.commands.run.scheduler.QsubScheduler[source]

Bases: object

docstring for QsubScheduler

build_cmd()[source]
class BALSAMIC.commands.run.scheduler.SbatchScheduler[source]

Bases: object

Builds sbatch command. Commands map to SLURM sbatch options. Params: —— account - -A/–account dependency - {{dependencies}} error - -e/–error mail_type - –mail-type mail_user - –mail-user ntasks - -n/–ntasks output - -o/–output qos - -q/–qos time - -t/–time

build_cmd()[source]

builds sbatch command matching its options

BALSAMIC.commands.run.scheduler.get_parser()[source]

argument parser

BALSAMIC.commands.run.scheduler.main(args=None)[source]

entry point for scheduler.py

BALSAMIC.commands.run.scheduler.read_sample_config(input_json)[source]

load input sample_config file. Output of balsamic config sample.

BALSAMIC.commands.run.scheduler.submit_job(sbatch_cmd, profile)[source]

subprocess call for sbatch command

BALSAMIC.commands.run.scheduler.write_sacct_file(sacct_file, job_id)[source]

writes a yaml file with job ids

Module contents