Hi all,

Here’s a mail for heads up and googleable error message in case someone finds a 
similar error and scratches her/his head.

So (some time) after the very nice API class we had at GCC2015 I am now trying 
my hand at running workflows using Bioblend. I had some frustration trying to 
invoke a simple WF, but now found out that the inputs parameter to 
invoke_workflow is not as I thought it would be. I’m on the latest galaxy-dist 
and using Bioblend 0.7 in Python3.4.

So I thought I’d call e.g.:

gi.workflows.invoke_workflow(workflow_id, inputs={‘9678’: {’src’: ‘hda’, ‘id’: 
‘abcdef12345’}} , history_id=‘abc1234’)

Where the keys in inputs dict represent the ids from:

But apparently the new standard is to use the step_order (so 0 for the first 
step) instead of the step_id, as shown in the code at 
So this gave me the HTTP 400 error "Workflow cannot be run because an expected 
input step '84' has no input dataset."

I have reverted to using legacy code with run_workflow and dataset_map, which 
circumvents the problem:
gi.workflows.run_workflow(workflow_id, dataset_map={‘9678’: {’src’: ‘hda’, 
‘id’: ‘abcdef12345’}} , history_id=‘abc1234’)

Is there any way to specify inputs_by in the payload or am I on the wrong 
bioblend version? Otherwise I can file a request on the Bioblend github.

Jorrit Boekel
Proteomics systems developer
BILS / Lehtiö lab
Scilifelab Stockholm, Sweden

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