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)