+
+
+ def _runner(self, run_dir, flowcell, conf_info):
+ # retrieve config step
+ cfg_filepath = os.path.abspath('config32auto.txt')
+ status_retrieve_cfg = retrieve_config(ci,
+ flowcell,
+ cfg_filepath,
+ self.genome_dir)
+ if status_retrieve_cfg:
+ logging.info("Runner: Retrieve config: success")
+ else:
+ logging.error("Runner: Retrieve config: failed")
+
+
+ # configure step
+ if status_retrieve_cfg:
+ status = configure(ci)
+ if status:
+ logging.info("Runner: Configure: success")
+ else:
+ logging.error("Runner: Configure: failed")
+
+ #if successful, continue
+ if status:
+ # Setup status cmdline status monitor
+ #startCmdLineStatusMonitor(ci)
+
+ # running step
+ print 'Running pipeline now!'
+ run_status = run_pipeline(ci)
+ if run_status is True:
+ logging.info('Runner: Pipeline: success')
+ self.piplineFinished(run_dir)
+ else:
+ logging.info('Runner: Pipeline: failed')
+
+
+ def launchJob(self, run_dir, flowcell, conf_info):
+ """
+ Starts up a thread for running the pipeline
+ """
+ t = threading.Thread(target=self._runner,
+ args=[run_dir, flowcell, conf_info])
+ t.setDaemon(True)
+ t.start()
+
+