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.