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)
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)
