Hi, I was trying to run workflows from the command line using workflow_execute.py in /scripts/api. According to the documentation, the commandline should look like: python workflow_execute.py <api_key> <galaxy_url>/api/workflows f2db41e1fa331b3e 'hist_id=a912e9e5d84530d4' '38=hda=03501d7626bd192f I understand that 'hda' refers to the src of the input data, in this case being the history. However, it is not clear to me what 38 is actually referring to. Is it the step number ? Is it the id shown in the JSON response code of <galaxy_url/api/workflows/<workflow id> ? E.g "535" in: {"url": "/galaxy/api/workflows/f7bb1edd6b95db62", "inputs": {}, "steps": {"535": {"tool_id": "iep", "input_steps": {}, "type": "tool", "id": 535}}, "id": "f7bb1edd6b95db62", "name": "test_workflow"} What is "inputs" and why is its value empty {} ? If a tool step has multiple input parameters, how can you refer to the correct parameter using the 'step=src=id' syntax ? Thanks, Marc ________________________________________ THIS E-MAIL MESSAGE IS INTENDED ONLY FOR THE USE OF THE INDIVIDUAL OR ENTITY TO WHICH IT IS ADDRESSED AND MAY CONTAIN INFORMATION THAT IS PRIVILEGED, CONFIDENTIAL AND EXEMPT FROM DISCLOSURE. If the reader of this E-mail message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify us immediately at ablynx@ablynx.com. Thank you for your co-operation. "NANOBODY" and "NANOCLONE" are registered trademarks of Ablynx N.V. ________________________________________
Hey Marc, Yep, the '38' in this case is the step id shown just after "steps", but it would be an id listed in that 'inputs' dict. The inputs dictionary should be a list of all the "Input Dataset" steps for the workflow -- yours just doesn't have any and you'll need to add these to be able to map input datasets to the correct workflow input steps. Currently there's not a good way to tweak the tool parameter dict at execution time for workflows via the API. Unless you want to create new stored workflows on the fly with the correct parameters (via the API), you'll need to fully define workflows and not leave any 'set at runtime' parameters. The plan *is* to eventually allow both tools and workflows to set arbitrary parameters at execution time, but this functionality isn't available yet. -Dannon On Mon, Apr 1, 2013 at 4:40 PM, Marc Logghe <Marc.Logghe@ablynx.com> wrote:
Hi,****
I was trying to run workflows from the command line using workflow_execute.py in /scripts/api.****
According to the documentation, the commandline should look like:****
python workflow_execute.py <api_key> <galaxy_url>/api/workflows f2db41e1fa331b3e 'hist_id=a912e9e5d84530d4' '38=hda=03501d7626bd192f****
** **
I understand that ‘hda’ refers to the src of the input data, in this case being the history. However, it is not clear to me what 38 is actually referring to. Is it the step number ?****
Is it the id shown in the JSON response code of <galaxy_url/api/workflows/<workflow id> ?****
E.g “535” in:****
{"url": "/galaxy/api/workflows/f7bb1edd6b95db62", "inputs": {}, "steps": {"535": {"tool_id": "iep", "input_steps": {}, "type": "tool", "id": 535}}, "id": "f7bb1edd6b95db62", "name": "test_workflow"}****
** **
What is “inputs” and why is its value empty {} ?****
If a tool step has multiple input parameters, how can you refer to the correct parameter using the ‘step=src=id’ syntax ?****
** **
Thanks,****
Marc****
** **
** ** ________________________________________ THIS E-MAIL MESSAGE IS INTENDED ONLY FOR THE USE OF THE INDIVIDUAL OR ENTITY TO WHICH IT IS ADDRESSED AND MAY CONTAIN INFORMATION THAT IS PRIVILEGED, CONFIDENTIAL AND EXEMPT FROM DISCLOSURE. If the reader of this E-mail message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify us immediately at ablynx@ablynx.com. Thank you for your co-operation. "NANOBODY" and "NANOCLONE" are registered trademarks of Ablynx N.V. ________________________________________
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Hi Dannon, Thanks for the reply. From: Dannon Baker [mailto:dannon.baker@gmail.com] Sent: Monday, April 01, 2013 11:02 PM To: Marc Logghe Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] REST API Hey Marc, Yep, the '38' in this case is the step id shown just after "steps", but it would be an id listed in that 'inputs' dict. The inputs dictionary should be a list of all the "Input Dataset" steps for the workflow -- yours just doesn't have any and you'll need to add these to be able to map input datasets to the correct workflow input steps. I am afraid I don't quite understand. In my case, the single step workflow accepts fasta as input. If you say that it is currently not possible to pass 'set-at-runtime' parameters how do you pass the fasta then ? I mean, what changes to the workflow need to be done in order to make it possible to pass a command line argument like '38=hda=03501d7626bd192f' ? I'am pretty much confused ... Think I keep on missing something crucial here. Regards, Marc ________________________________________ THIS E-MAIL MESSAGE IS INTENDED ONLY FOR THE USE OF THE INDIVIDUAL OR ENTITY TO WHICH IT IS ADDRESSED AND MAY CONTAIN INFORMATION THAT IS PRIVILEGED, CONFIDENTIAL AND EXEMPT FROM DISCLOSURE. If the reader of this E-mail message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify us immediately at ablynx@ablynx.com. Thank you for your co-operation. "NANOBODY" and "NANOCLONE" are registered trademarks of Ablynx N.V. ________________________________________
Hi, I just knew I was missing something crucial here ... Finally I found at the bottom of the Tools list (when you are in workflow editing mode) a section called 'Workflow control' having a single entry: 'Inputs'. Thought it could be useful to share my 'Aha-Erlebnis' :) Now it is perfectly possible to run a workflow using the CLI. Cheers, Marc From: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of Marc Logghe Sent: Monday, April 01, 2013 11:25 PM To: Dannon Baker Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] REST API Hi Dannon, Thanks for the reply. From: Dannon Baker [mailto:dannon.baker@gmail.com] Sent: Monday, April 01, 2013 11:02 PM To: Marc Logghe Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] REST API Hey Marc, Yep, the '38' in this case is the step id shown just after "steps", but it would be an id listed in that 'inputs' dict. The inputs dictionary should be a list of all the "Input Dataset" steps for the workflow -- yours just doesn't have any and you'll need to add these to be able to map input datasets to the correct workflow input steps. I am afraid I don't quite understand. In my case, the single step workflow accepts fasta as input. If you say that it is currently not possible to pass 'set-at-runtime' parameters how do you pass the fasta then ? I mean, what changes to the workflow need to be done in order to make it possible to pass a command line argument like '38=hda=03501d7626bd192f' ? I'am pretty much confused ... Think I keep on missing something crucial here. Regards, Marc ________________________________________ THIS E-MAIL MESSAGE IS INTENDED ONLY FOR THE USE OF THE INDIVIDUAL OR ENTITY TO WHICH IT IS ADDRESSED AND MAY CONTAIN INFORMATION THAT IS PRIVILEGED, CONFIDENTIAL AND EXEMPT FROM DISCLOSURE. If the reader of this E-mail message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify us immediately at ablynx@ablynx.com. Thank you for your co-operation. "NANOBODY" and "NANOCLONE" are registered trademarks of Ablynx N.V. ________________________________________ ________________________________________ THIS E-MAIL MESSAGE IS INTENDED ONLY FOR THE USE OF THE INDIVIDUAL OR ENTITY TO WHICH IT IS ADDRESSED AND MAY CONTAIN INFORMATION THAT IS PRIVILEGED, CONFIDENTIAL AND EXEMPT FROM DISCLOSURE. If the reader of this E-mail message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify us immediately at ablynx@ablynx.com. Thank you for your co-operation. "NANOBODY" and "NANOCLONE" are registered trademarks of Ablynx N.V. ________________________________________
participants (2)
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Dannon Baker -
Marc Logghe