Comments (9)
Can you provide some code please? (if it's possible to share the workflow, that would be helpful as well)
Are you able to run the workflow successfully in the UI?
Best wishes,
Simon
from bioblend.
gi = bioblend.galaxy.GalaxyInstance(url=config["galaxyUrl"], key=config["apikey"])
## workflow_args is a generator yielding tuples of history_id and hdca data description
workflow_args = upload_dir(config['datapath'], config['libraryId'], config['folderId'], config['workflow'], gi)
wfdesc = get_workflow_description(gi, config['workflow'])
workflow_id = wfdesc["uuid"]
for hid, data in workflow_args:
inputs = {
'0': {
"src": data['src'],
"id": data['id'],
},
}
res = gi.workflows.invoke_workflow(workflow_id, inputs, history_id=hid, import_inputs_to_history=False)
from bioblend.
Does this link work for you?
https://galaxydev.ohsu.edu/u/strgar/w/crc-r01
Invoking the workflow in the browser successfully completes the entire pipeline.
from bioblend.
I cannot access that link - I get Server Not Found
.
If you can invoke it in the UI, I would suggest looking up the successful invocation id with gi.invocations.show_invocations()
and checking that the inputs
and input_step_parameters
fields match what you are submitting via the API.
from bioblend.
I had previously check input but I'll look at input_step_parameters.
If they differ how can I adjust the invocation to specify step parameters?
from bioblend.
You should be able to add params=input_step_parameters
to gi.workflows.invoke_workflow()
.
from bioblend.
There are no differences in the input fields for jobs invoked from the command line and those invoked from the GUI.
from bioblend.
If you could share the workflow and some test data with me (either via a public Galaxy instance, or a chat like gitter or matrix, or in this issue, whatever you prefer) I can have a look. Not sure what else to suggest right now.
from bioblend.
Sure gitter works. Thanks for your offer. Presumably your handle is gitter.im/simonbray? Message sent.
from bioblend.
Related Issues (20)
- Method to cancel a job
- Add type annotations to BioBlend API HOT 2
- Rebuild docs with sphinx-apidoc
- Add an `invoke()` method to the BioBlend.objects `Workflow` class
- Fix unreliable tests
- Add tests for bioblend.toolshed
- 'GalaxyInstance' raises AttributeError when instantiated with email & password combination HOT 2
- Incorrect PyYAML version for bioblend 0.9.0 - 0.16.0 HOT 1
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- Error when trying to get ids of workflow outputs HOT 13
- Drop cloudlaunch support ? HOT 4
- Add support for parameter "all" in get_histories HOT 2
- Tool search in Toolshed: number total results HOT 6
- File name displayed as Pasted Entry for file uploaded using upload_file_contents HOT 2
- Downloading a file from a shared data library HOT 3
- Extend bioblend to support the new notification API HOT 3
- Bioblend reporting workflow as failed while workflow is running or completed successfully. HOT 6
- workflows.refactor_workflows fails on subworkflows HOT 14
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from bioblend.