From 5c307cd08dfc30208ee663e9e450ad3ff1c99fac Mon Sep 17 00:00:00 2001 From: Brandon King Date: Fri, 4 Jan 2008 00:21:22 +0000 Subject: [PATCH] Work towards getting runner to work properly. * Runner can now run one run if launched in the directory of the analysis it should run. * TODO: Allow for running the pipeline without changing directories. --- gaworkflow/runner.py | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/gaworkflow/runner.py b/gaworkflow/runner.py index a465046..ce27d72 100644 --- a/gaworkflow/runner.py +++ b/gaworkflow/runner.py @@ -129,6 +129,7 @@ class Runner(rpc.XmlRpcBot): def _runner(self, run_dir, flowcell, conf_info): + # retrieve config step cfg_filepath = os.path.abspath('config32auto.txt') status_retrieve_cfg = retrieve_config(conf_info, @@ -143,7 +144,7 @@ class Runner(rpc.XmlRpcBot): # configure step if status_retrieve_cfg: - status = configure(ci) + status = configure(conf_info) if status: logging.info("Runner: Configure: success") else: @@ -156,7 +157,7 @@ class Runner(rpc.XmlRpcBot): # running step print 'Running pipeline now!' - run_status = run_pipeline(ci) + run_status = run_pipeline(conf_info) if run_status is True: logging.info('Runner: Pipeline: success') self.piplineFinished(run_dir) @@ -176,7 +177,7 @@ class Runner(rpc.XmlRpcBot): def main(args=None): - bot = Runner() + bot = Runner('demobot') bot.cfg['loglevel'] = 'DEBUG' return bot.main(args) -- 2.30.2