def cmd_ipython(args):
args = defaults.update_check_args(args, "Could not run IPython parallel analysis.")
args = install.docker_image_arg(args)
parallel = clargs.to_parallel(args, "bcbiovm.docker")
parallel["wrapper"] = "runfn"
with open(args.sample_config) as in_handle:
ready_config, _ = mounts.normalize_config(yaml.load(in_handle), args.fcdir)
work_dir = os.getcwd()
ready_config_file = os.path.join(work_dir, "%s-ready%s" %
(os.path.splitext(os.path.basename(args.sample_config))))
with open(ready_config_file, "w") as out_handle:
yaml.safe_dump(ready_config, out_handle, default_flow_style=False, allow_unicode=False)
work_dir = os.getcwd()
systemconfig = run.local_system_config(args.systemconfig, args.datadir, work_dir)
cur_pack = pack.shared_filesystem(work_dir, args.datadir, args.tmpdir)
parallel["wrapper_args"] = [devel.DOCKER, {"sample_config": ready_config_file,
"fcdir": args.fcdir,
"pack": cur_pack,
"systemconfig": systemconfig,
"image": args.image}]
# For testing, run on a local ipython cluster
parallel["run_local"] = parallel.get("queue") == "localrun"
from bcbio.pipeline import main
main.run_main(work_dir, run_info_yaml=ready_config_file,
config_file=systemconfig, fc_dir=args.fcdir,
parallel=parallel)
def cmd_ipython(args):
args = defaults.update_check_args(args, "Could not run IPython parallel analysis.")
args = install.docker_image_arg(args)
parallel = clargs.to_parallel(args, "bcbiovm.docker")
parallel["wrapper"] = "runfn"
with open(args.sample_config) as in_handle:
ready_config, _ = mounts.normalize_config(yaml.safe_load(in_handle), args.fcdir)
work_dir = os.getcwd()
ready_config_file = os.path.join(work_dir, "%s-ready%s" %
(os.path.splitext(os.path.basename(args.sample_config))))
with open(ready_config_file, "w") as out_handle:
yaml.safe_dump(ready_config, out_handle, default_flow_style=False, allow_unicode=False)
work_dir = os.getcwd()
systemconfig = run.local_system_config(args.systemconfig, args.datadir, work_dir)
cur_pack = pack.shared_filesystem(work_dir, args.datadir, args.tmpdir)
parallel["wrapper_args"] = [devel.DOCKER, {"sample_config": ready_config_file,
"fcdir": args.fcdir,
"pack": cur_pack,
"systemconfig": systemconfig,
"image": args.image}]
# For testing, run on a local ipython cluster
parallel["run_local"] = parallel.get("queue") == "localrun"
from bcbio.pipeline import main
main.run_main(work_dir, run_info_yaml=ready_config_file,
config_file=systemconfig, fc_dir=args.fcdir,
parallel=parallel)
def cmd_ipython(args):
args = defaults.update_check_args(args, "Could not run IPython parallel analysis.")
args = install.docker_image_arg(args)
parallel = clargs.to_parallel(args, "bcbiovm.docker")
parallel["wrapper"] = "runfn"
with open(args.sample_config) as in_handle:
ready_config, _ = mounts.normalize_config(yaml.load(in_handle), args.fcdir)
work_dir = os.getcwd()
ready_config_file = os.path.join(work_dir, "%s-ready%s" %
(os.path.splitext(os.path.basename(args.sample_config))))
with open(ready_config_file, "w") as out_handle:
yaml.safe_dump(ready_config, out_handle, default_flow_style=False, allow_unicode=False)
parallel["wrapper_args"] = [DOCKER, {"sample_config": ready_config_file,
"fcdir": args.fcdir,
"pack": pack.shared_filesystem(work_dir, args.datadir, args.tmpdir),
"systemconfig": args.systemconfig,
"image": args.image}]
# For testing, run on a local ipython cluster
parallel["run_local"] = parallel.get("queue") == "localrun"
workdir_mount = "%s:%s" % (work_dir, DOCKER["work_dir"])
manage.run_bcbio_cmd(args.image, [workdir_mount],
["version", "--workdir=%s" % DOCKER["work_dir"]])
main.run_main(work_dir, run_info_yaml=ready_config_file,
config_file=args.systemconfig, fc_dir=args.fcdir,
parallel=parallel)
def run(args, docker_config):
work_dir = os.getcwd()
parallel = {
"type": "clusterk",
"queue": args.queue,
"cores": args.numcores,
"module": "bcbiovm.clusterk",
"wrapper": "runfn"
}
with open(args.sample_config) as in_handle:
ready_config, _ = mounts.normalize_config(yaml.safe_load(in_handle),
args.fcdir)
ready_config_file = os.path.join(
work_dir, "%s-ready%s" %
(os.path.splitext(os.path.basename(args.sample_config))))
with open(ready_config_file, "w") as out_handle:
yaml.safe_dump(ready_config,
out_handle,
default_flow_style=False,
allow_unicode=False)
parallel["pack"] = pack.prep_s3(args.biodata_bucket, args.run_bucket,
"runfn_output")
parallel["wrapper_args"] = [{
"sample_config": ready_config_file,
"docker_config": docker_config,
"fcdir": args.fcdir,
"datadir": args.datadir,
"systemconfig": args.systemconfig
}]
workdir_mount = "%s:%s" % (work_dir, docker_config["work_dir"])
manage.run_bcbio_cmd(
args.image, [workdir_mount],
["version", "--workdir=%s" % docker_config["work_dir"]])
from bcbio.pipeline import main
main.run_main(work_dir,
run_info_yaml=ready_config_file,
config_file=args.systemconfig,
fc_dir=args.fcdir,
parallel=parallel)
def run(args, docker_config):
work_dir = os.getcwd()
parallel = {"type": "clusterk", "queue": args.queue, "cores": args.numcores,
"module": "bcbiovm.clusterk", "wrapper": "runfn"}
with open(args.sample_config) as in_handle:
ready_config, _ = mounts.normalize_config(yaml.load(in_handle), args.fcdir)
ready_config_file = os.path.join(work_dir, "%s-ready%s" %
(os.path.splitext(os.path.basename(args.sample_config))))
with open(ready_config_file, "w") as out_handle:
yaml.safe_dump(ready_config, out_handle, default_flow_style=False, allow_unicode=False)
parallel["pack"] = pack.prep_s3(args.biodata_bucket, args.run_bucket, "runfn_output")
parallel["wrapper_args"] = [{"sample_config": ready_config_file,
"docker_config": docker_config,
"fcdir": args.fcdir,
"datadir": args.datadir,
"systemconfig": args.systemconfig}]
workdir_mount = "%s:%s" % (work_dir, docker_config["work_dir"])
manage.run_bcbio_cmd(args.image, [workdir_mount],
["version", "--workdir=%s" % docker_config["work_dir"]])
main.run_main(work_dir, run_info_yaml=ready_config_file,
config_file=args.systemconfig, fc_dir=args.fcdir,
parallel=parallel)
