except KiveMalformedDataException: fastq2 = kive.find_datasets(name='New fastq file 2')[0] # Get the pipeline by family ID pipeline_family = kive.get_pipeline_family(2) print('Using data:') print(fastq1, fastq2) print('With pipeline:') print(pipeline_family.published_or_latest()) # Create a RunBatch. rb = kive.create_run_batch( name="TestRunBatch", description="Created by Python API", users=["kive"], groups=["Developers"] ) # Run the pipeline. status = kive.run_pipeline( pipeline_family.published_or_latest(), [fastq1, fastq2], name="run1", runbatch=rb ) # Run another one, using only the RunBatch ID. status2 = kive.run_pipeline( pipeline_family.published_or_latest(), [fastq2, fastq1],
def main(): args = parse_args() logger.info('Starting.') kive_server = os.environ.get('KIVE_SERVER', 'http://*****:*****@api_runs', json=params, is_json=True) response_json = response.json() launched_run_ids.add(response_json['id']) except Exception: logger.error('Failed to rerun run id %d: %r.', run['id'], run, exc_info=True) logger.info('Done.')
def main(): args = parse_args() logger.info('Starting.') kive_server = os.environ.get('KIVE_SERVER', 'http://*****:*****@api_runs', json=params, is_json=True) response_json = response.json() launched_run_ids.add(response_json['id']) except Exception: logger.error('Failed to rerun run id %d: %r.', run['id'], run, exc_info=True) logger.info('Done.')
["Everyone"]) except KiveMalformedDataException: fastq2 = kive.find_datasets(name='New fastq file 2')[0] # Get the pipeline by family ID pipeline_family = kive.get_pipeline_family(2) print('Using data:') print(fastq1, fastq2) print('With pipeline:') print(pipeline_family.published_or_latest()) # Create a RunBatch. rb = kive.create_run_batch(name="TestRunBatch", description="Created by Python API", users=["kive"], groups=["Developers"]) # Run the pipeline. status = kive.run_pipeline(pipeline_family.published_or_latest(), [fastq1, fastq2], name="run1", runbatch=rb) # Run another one, using only the RunBatch ID. status2 = kive.run_pipeline(pipeline_family.published_or_latest(), [fastq2, fastq1], name="run2", runbatch=rb.id) # Run another one, with coherent permissions.