def _add_run_reference_dataset_report(p): opts = [add_log_debug_option, U.add_report_output, U.add_ds_reference_input] f = compose(*opts) return f(p)
def get_parser(): desc = "Run multiple testkit.cfg files in parallel" p = get_default_argparser(__version__, desc) fs = [ TU.add_debug_option, TU.add_override_chunked_mode, TU.add_override_distribute_option ] f = compose(*fs) p = f(p) p.add_argument( 'testkit_cfg_fofn', type=validate_testkit_cfg_fofn, help= "File of butler.cfg file name relative to the current dir (e.g., RS_Resquencing/testkit.cfg" ) p.add_argument('-n', '--nworkers', type=int, default=1, help="Number of jobs to concurrently run.") p.set_defaults(func=_args_run_multi_testkit_cfg) return p
def add_task_parser_options(p): funcs = [ TU.add_override_chunked_mode, TU.add_override_distribute_option, _add_webservice_config, _add_rc_preset_xml_option, _add_preset_xml_option, _add_output_dir_option, _add_entry_point_option, _add_task_id_option, TU.add_debug_option ] f = compose(*funcs) return f(p)
def __add_pipeline_parser_options(p): """Common options for all running pipelines or tasks""" funcs = [ TU.add_override_chunked_mode, TU.add_override_distribute_option, _add_webservice_config, _add_rc_preset_xml_option, _add_preset_xml_option, _add_output_dir_option, _add_entry_point_option, TU.add_debug_option ] f = compose(*funcs) return f(p)
def __add_pipeline_parser_options(p): """Common options for all running pipelines or tasks""" funcs = [TU.add_override_chunked_mode, TU.add_override_distribute_option, _add_webservice_config, _add_rc_preset_xml_option, _add_preset_xml_option, _add_output_dir_option, _add_entry_point_option, add_log_debug_option] f = compose(*funcs) return f(p)
def add_task_parser_options(p): funcs = [ TU.add_override_chunked_mode, TU.add_override_distribute_option, _add_webservice_config, _add_rc_preset_xml_option, _add_preset_xml_option, _add_output_dir_option, _add_entry_point_option, _add_task_id_option, add_log_debug_option] f = compose(*funcs) return f(p)
def get_parser(): desc = "Run multiple testkit.cfg files in parallel" p = get_default_argparser(__version__, desc) fs = [TU.add_debug_option, TU.add_override_chunked_mode, TU.add_override_distribute_option] f = compose(*fs) p = f(p) p.add_argument('testkit_cfg_fofn', type=validate_testkit_cfg_fofn, help="File of butler.cfg file name relative to the current dir (e.g., RS_Resquencing/testkit.cfg") p.add_argument('-n', '--nworkers', type=int, default=1, help="Number of jobs to concurrently run.") p.set_defaults(func=_args_run_multi_testkit_cfg) return p
def get_parser(): desc = "Testkit Tool to run pbsmrtpipe jobs." p = get_default_argparser(__version__, desc) funcs = [TU.add_override_chunked_mode, TU.add_override_distribute_option, _add_config_file_option, add_tests_only_option, add_log_level_option, add_log_file_options, TU.add_debug_option] f = compose(*funcs) p = f(p) return p
return testkit_cfgs def testkit_cfg_fofn_to_files(fofn): return _testkit_cfg_fofn_to_files(fofn, os.path.dirname(fofn)) def _validate_testkit_cfg_fofn(path): p = os.path.abspath(path) # files will be relative the supplied fofn dir_name = os.path.dirname(p) _testkit_cfg_fofn_to_files(p, dir_name) return p validate_testkit_cfg_fofn = compose(_validate_testkit_cfg_fofn, validate_file) def _run_testkit_cfg(testkit_cfg, debug=False, misc_opts=""): os.chdir(os.path.dirname(testkit_cfg)) cmd = "{e} --debug {m} {c}".format(c=testkit_cfg, e=_EXE, m=misc_opts) rcode, stdout, stderr, run_time = backticks(cmd) if debug: log.debug(" ".join([str(i) for i in [cmd, rcode, stdout, stderr]])) # Returning the butler cfg is a bit odd, but this is necessary for the # parallelism to work consistently with the serial version return testkit_cfg, rcode, stdout, stderr, run_time