While I agree that would work, the tool I’m working with generates tools for web operations in a generic fashion. That is, you provide it a WDSL and a list of operations you want from that WSDL, and then tool XML files are generated for each of those operations.
Sincerely, Michael E. Cotterell
Ph.D. Student in Computer Science, University of Georgia Instructor of Record, Graduate RA & TA, University of Georgia Department Liaison, CS Graduate Student Association, University of Georgia mepcotterell@gmail.com (mailto:mepcotterell@gmail.com) mepcott@uga.edu (mailto:mepcott@uga.edu) mec@cs.uga.edu (mailto:mec@cs.uga.edu) http://michaelcotterell.com/
On Thursday, March 6, 2014 at 9:08 AM, Eric Rasche wrote:
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Hi Michael,
I, too, would love to have conditionals and loops, however may want to consider the following approach:
Instead of splitting the web service submission, check for results, and download of results into three steps, make it a single script.
I believe this would solve your problem completely. It largely simplify your use case, as a single script could
- submit and remember a job's ID
- check periodically using that language's web bindings
- collect the results when done
This would mean it's a long-running task, which is perfectly suited to use in galaxy.
Cheers, Eric
On 03/06/2014 07:51 AM, John Chilton wrote:
Hey Michael,
I know there is a lot of interest in this, but these sorts of things are not possible with Galaxy workflows at this time. If you want the traceibility and UI for viewing results provided by Galaxy - you could consider driving tools externally via the API - at that point though the utility of running these jobs through Galaxy has dropped considerably.
There is a Trello card I would encourage you to vote for - https://trello.com/c/rwSeAwos
I have included a link to this e-mail as a reference for specific use cases to consider if or when this idea gets worked on.
Sorry, -John
On Wed, Mar 5, 2014 at 9:05 PM, Michael E. Cotterell <mepcotterell@gmail.com (mailto:mepcotterell@gmail.com)> wrote:
Is there a way to have conditionals and loops for the various steps in a Galaxy workflow?
For example, a conditional might be used to branch to various steps based on the previous steps. Also, a step may need to be repeated until it produces a particular output.
Here is an actual use case: We are invoking a web service in one of our workflows. The first step returns a unique identifier that you need to use later in order to get the actual results (since the web service operation is asynchronous). Later, using another operation, you can check on the status of the job being performed. Sometimes, this operation/step will inform us that the results are not ready. We would like to be able to loop on that second operation/step until it says the job is done, and then move on to a third operation/step to actually get the results.
Any ideas?
Sincerely, Michael E. Cotterell
Ph.D. Student in Computer Science, University of Georgia Instructor of Record, Graduate RA & TA, University of Georgia Department Liaison, CS Graduate Student Association, University of Georgia mepcotterell@gmail.com (mailto:mepcotterell@gmail.com) mepcott@uga.edu (mailto:mepcott@uga.edu) mec@cs.uga.edu (mailto:mec@cs.uga.edu) http://michaelcotterell.com/
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Eric Rasche Programmer II Center for Phage Technology Texas A&M University College Station, TX 77843 404-692-2048 esr@tamu.edu (mailto:esr@tamu.edu) rasche.eric@yandex.ru (mailto:rasche.eric@yandex.ru) -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.17 (GNU/Linux)
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