-----Original Message-----
From: jmchil...@gmail.com [mailto:jmchil...@gmail.com] On Behalf Of John Chilton
Sent: Thursday, February 28, 2013 11:27 PM
To: Marc Logghe
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] blend4j
This is not a blend4j issue, it is more of a Galaxy API issue. I think
it is essentially a known problem that you cannot specify runtime
parameters for workflow, only data inputs. Here the relevant piece of
Galaxy code:
inputs = {}
for step in latest_workflow.steps:
if step.type == 'data_input':
inputs[step.id] = {'label':step.tool_inputs['name'], 'value':""}
else:
pass
# Eventually, allow regular tool parameters to be
inserted and modified at runtime.
# p = step.get_required_parameters()
I think the meantime, the work around is not define these are workflow
parameters but instead hard code some values, and then pull down,
rewrite, and reupload a new workflow for each execution:
WorkflowsClient client = galaxyInstance.getWorkflowsClient();
String workflowJson = client.exportWorkflow(originalWorkflowId);
// modify workflow json
Workflow importedWorkflow = client.importWorkflow(workflowJson);
String importedWorkflowId = importedWorkflow.getId();
It is not pretty obviously. They are pretty good about responding to
API pull requests so if you have the time to fix the Galaxy code
itself I think everyone would appreciate that fix.
-John
Hi John
Thanks for the quick answer; I'll give it a try.
Regarding the fix: you need to give me some time, started with a python
tutorial only 2 days ago ;-)
Regards,
Marc
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