Hi,
I have some questions about adding new custom tools to my Galaxy instance:
1- How can I reuse workflows?
a. Should I wrap a workflow as a tool?
b. Or can I just add a custom workflow as a workflow step in another workflow?
2- I noticed that option 1.b above seems to copy the complete workflow into my new workflow, so if I have an existing workflow A with N steps and want to use this in workflow B which already has M steps, I end up with a workflow that has M+N steps while I would expect M+1 steps... This behaviour gives me the impression that if I change workflow A, this will not automatically imply a change in workflow B. Is my interpretation correct?
3- If option 1.a above is the way to go for now, what are the steps to do this? E.g. what is the command to run a workflow from the command line?
Thanks and regards,
Pieter Lukasse.
Hi Pieter,
You cannot currently embed on workflow within another, although that has been suggested as a nice extension to Galaxy.
You can for instance start a new history, run workflow #1 with N tool steps, then workflow #2 with M tool steps, and save this history as a new workflow #3 with N+M tool steps. This has the downside that if either workflow #1 or #2 is changed, this does not alter #3 - which is an independent copy.
Peter
Hi Peter,
Thanks for the reply.
Does anyone know how to execute a specific workflow from the command prompt? E.g. run the workflow as a job? Then I could perhaps write a workflow wrapper tool to overcome this shortcoming.
Regards,
Pieter.
-----Original Message----- From: Peter Cock [mailto:p.j.a.cock@googlemail.com] Sent: donderdag 13 oktober 2011 12:34 To: Lukasse, Pieter Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Questions about reusing workflows
Hi Pieter,
You cannot currently embed on workflow within another, although that has been suggested as a nice extension to Galaxy.
You can for instance start a new history, run workflow #1 with N tool steps, then workflow #2 with M tool steps, and save this history as a new workflow #3 with N+M tool steps. This has the downside that if either workflow #1 or #2 is changed, this does not alter #3 - which is an independent copy.
Peter
Lukasse, Pieter wrote:
Hi Peter,
Thanks for the reply.
Does anyone know how to execute a specific workflow from the command prompt? E.g. run the workflow as a job? Then I could perhaps write a workflow wrapper tool to overcome this shortcoming.
Hi Pieter,
Have a look at scripts/api/workflow_execute.py
--nate
Regards,
Pieter.
-----Original Message----- From: Peter Cock [mailto:p.j.a.cock@googlemail.com] Sent: donderdag 13 oktober 2011 12:34 To: Lukasse, Pieter Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Questions about reusing workflows
Hi Pieter,
You cannot currently embed on workflow within another, although that has been suggested as a nice extension to Galaxy.
You can for instance start a new history, run workflow #1 with N tool steps, then workflow #2 with M tool steps, and save this history as a new workflow #3 with N+M tool steps. This has the downside that if either workflow #1 or #2 is changed, this does not alter #3 - which is an independent copy.
Peter
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Lukasse, Pieter -
Nate Coraor -
Peter Cock