Python prep_system Examples

Example #1

def run(args):
    """Run a CWL preparation pipeline.
    """
    dirs, config, run_info_yaml = run_info.prep_system(args.sample_config,
                                                       args.systemconfig)
    world = run_info.organize(dirs, config, run_info_yaml)
    create.from_world(world, run_info_yaml)

Example #2

File: main.py Project: dlorson/bcbio-nextgen

def run(args):
    """Run a CWL preparation pipeline.
    """
    dirs, config, run_info_yaml = run_info.prep_system(args.sample_config, args.systemconfig)
    integrations = args.integrations if hasattr(args, "integrations") else {}
    world = run_info.organize(dirs, config, run_info_yaml, add_provenance=False, integrations=integrations)
    create.from_world(world, run_info_yaml)

Example #3

File: main.py Project: chapmanb/bcbio-nextgen

def run(args):
    """Run a CWL preparation pipeline.
    """
    dirs, config, run_info_yaml = run_info.prep_system(args.sample_config, args.systemconfig)
    integrations = args.integrations if hasattr(args, "integrations") else {}
    world = run_info.organize(dirs, config, run_info_yaml, is_cwl=True, integrations=integrations)
    create.from_world(world, run_info_yaml, integrations=integrations, add_container_tag=args.add_container_tag)

Example #4

def run(args):
    """Run a CWL preparation pipeline.
    """
    dirs, config, run_info_yaml = run_info.prep_system(args.sample_config, args.systemconfig)
    integrations = args.integrations if hasattr(args, "integrations") else {}
    world = run_info.organize(dirs, config, run_info_yaml, add_provenance=False, integrations=integrations)
    create.from_world(world, run_info_yaml, integrations=integrations)

Example #5

File: multitasks.py Project: rndw/bcbio-nextgen

def prep_system(*args):
    return run_info.prep_system(*args)

Example #6

File: multitasks.py Project: gifford-lab/bcbio-nextgen

def prep_system(*args):
    return run_info.prep_system(*args)

Example #7

File: main.py Project: Cyberbio-Lab/bcbio-nextgen

def run(args):
    """Run a CWL preparation pipeline.
    """
    dirs, config, run_info_yaml = run_info.prep_system(args.sample_config, args.systemconfig)
    world = run_info.organize(dirs, config, run_info_yaml, add_provenance=False)
    create.from_world(world, run_info_yaml)