def runfn(*args): fn_name = args[0] dockerconf = args[1] cmd_args = args[2] parallel = args[3] fn_args = args[4:] return run.do_runfn(fn_name, fn_args, cmd_args, parallel, dockerconf)
def runfn(*args): with _setup_logging(args): assert len(args) == 1 fn_name = args[0][0] dockerconf = args[0][1] cmd_args = args[0][2] parallel = args[0][3] fn_args = args[0][4:] return run.do_runfn(fn_name, fn_args, cmd_args, parallel, dockerconf)
def runfn(*args): args = ipython.unzip_args(args) assert len(args) == 1 fn_args = args[0][4:] with _setup_logging(fn_args): fn_name = args[0][0] dockerconf = args[0][1] cmd_args = args[0][2] parallel = args[0][3] return ipython.zip_args(run.do_runfn(fn_name, fn_args, cmd_args, parallel, dockerconf))
def cmd_runfn(args): args = defaults.update_check_args(args, "Could not run bcbio-nextgen function.") with open(args.parallel) as in_handle: parallel = yaml.safe_load(in_handle) with open(args.runargs) as in_handle: runargs = yaml.safe_load(in_handle) cmd_args = {"systemconfig": args.systemconfig, "pack": parallel["pack"]} out = run.do_runfn(args.fn_name, runargs, cmd_args, parallel, DOCKER) out_file = "%s-out" % os.path.splitext(args.runargs) with open(out_file, "w") as out_handle: yaml.safe_dump(out, out_handle, default_flow_style=False, allow_unicode=False)
def cmd_runfn(args): args = defaults.update_check_args(args, "Could not run bcbio-nextgen function.") args = install.docker_image_arg(args) with open(args.parallel) as in_handle: parallel = yaml.safe_load(in_handle) with open(args.runargs) as in_handle: runargs = yaml.safe_load(in_handle) cmd_args = {"systemconfig": args.systemconfig, "image": args.image, "pack": parallel["pack"]} out = run.do_runfn(args.fn_name, runargs, cmd_args, parallel, devel.DOCKER) out_file = "%s-out%s" % os.path.splitext(args.runargs) with open(out_file, "w") as out_handle: yaml.safe_dump(out, out_handle, default_flow_style=False, allow_unicode=False) pack.send_output(parallel["pack"], out_file)
def runfn(*args): fn_name = args[0] dockerconf = args[1] cmd_args = args[2] parallel = args[3] fn_args = args[4:] # Do not run checkpointed jobs externally now, as need to be inside docker # container even if slow. We need a way to run a batch of jobs together. #if parallel.get("checkpointed"): if False: fn = getattr(multitasks, fn_name) return fn(fn_args) else: return run.do_runfn(fn_name, fn_args, cmd_args, parallel, dockerconf)