submit module

mavis.submit.OPTIONS = WeakMavisNamespace(__name__='~mavis.submit.options', _defns={'queue': 'the queue jobs are to be submitted to', 'memory_limit': 'the maximum number of megabytes (MB) any given job is allowed', 'import_env': 'flag to import environment variables', 'time_limit': 'the time in seconds any given jobs is allowed', 'validation_memory': 'default memory limit (MB) for the validation stage', 'trans_validation_memory': 'default memory limit (MB) for the validation stage (for transcriptomes)', 'annotation_memory': 'default memory limit (MB) for the annotation stage', 'scheduler': 'The scheduler being used'}, _types={'queue': <class 'str'>, 'memory_limit': <class 'int'>, 'import_env': <function cast_boolean>, 'time_limit': <class 'int'>, 'validation_memory': <class 'int'>, 'trans_validation_memory': <class 'int'>, 'annotation_memory': <class 'int'>, 'scheduler': MavisNamespace(SGE='SGE', SLURM='SLURM', __name__='~mavis.submit.SCHEDULER', _defns={}, _types={'SGE': <class 'str'>, 'SLURM': <class 'str'>})}, annotation_memory=12000, import_env=True, memory_limit=16000, queue='', scheduler='SLURM', time_limit=57600, trans_validation_memory=18000, validation_memory=16000)

MavisNamespace – submission options

• queue
• memory_limit
• import_env
• time_limit
• validation_memory
• trans_validation_memory
• annotation_memory
• scheduler

mavis.submit.SCHEDULER = MavisNamespace(SGE='SGE', SLURM='SLURM', __name__='~mavis.submit.SCHEDULER', _defns={}, _types={'SGE': <class 'str'>, 'SLURM': <class 'str'>})

MavisNamespace – scheduler types

• SGE
• SLURM

class mavis.submit.SubmissionScript(content, scheduler, **kwargs)

Bases: object

holds scheduler options and build submissions scripts

build_header()

returns the header line detailing the scheduler-specific submission options

write(filepath)

write a submission script to the input path

mavis.submit.build_dependency_string(command, delim, jobs)