run_info_yaml = os.path.abspath(run_info_yaml)
if kwargs.get("workflow"):
kwargs["inputs"] = inputs
kwargs["config_file"] = global_config
kwargs["fc_dir"] = fc_dir
kwargs["run_info_yaml"] = run_info_yaml
return kwargs
if __name__ == "__main__":
kwargs = parse_cl_args(sys.argv[1:])
if "upgrade" in kwargs and kwargs["upgrade"]:
install.upgrade_bcbio(kwargs["args"])
elif "server" in kwargs and kwargs["server"]:
server_main.start(kwargs["args"])
elif "runfn" in kwargs and kwargs["runfn"]:
runfn.process(kwargs["args"])
elif "graph" in kwargs and kwargs["graph"]:
graph.bootstrap(kwargs["args"])
elif "version" in kwargs and kwargs["version"]:
programs.write_versions({"work": kwargs["args"].workdir})
elif "sequencer" in kwargs and kwargs["sequencer"]:
machine.check_and_postprocess(kwargs["args"])
else:
if kwargs.get("workflow"):
setup_info = workflow.setup(kwargs["workflow"], kwargs.pop("inputs"))
if setup_info is None: # no automated run after setup
sys.exit(0)
workdir, new_kwargs = setup_info
os.chdir(workdir)
kwargs.update(new_kwargs)
main(**kwargs)
if kwargs.get("workflow"):
kwargs["inputs"] = inputs
kwargs["config_file"] = global_config
kwargs["fc_dir"] = fc_dir
kwargs["run_info_yaml"] = run_info_yaml
return kwargs
if __name__ == "__main__":
kwargs = parse_cl_args(sys.argv[1:])
if "upgrade" in kwargs and kwargs["upgrade"]:
install.upgrade_bcbio(kwargs["args"])
elif "server" in kwargs and kwargs["server"]:
server_main.start(kwargs["args"])
elif "runfn" in kwargs and kwargs["runfn"]:
runfn.process(kwargs["args"])
elif "graph" in kwargs and kwargs["graph"]:
graph.bootstrap(kwargs["args"])
elif "version" in kwargs and kwargs["version"]:
programs.write_versions({"work": kwargs["args"].workdir})
elif "sequencer" in kwargs and kwargs["sequencer"]:
machine.check_and_postprocess(kwargs["args"])
else:
if kwargs.get("workflow"):
setup_info = workflow.setup(kwargs["workflow"],
kwargs.pop("inputs"))
if setup_info is None: # no automated run after setup
sys.exit(0)
workdir, new_kwargs = setup_info
os.chdir(workdir)
kwargs.update(new_kwargs)