Dear Benoît Meilhac,
In my plugin, I would have to import the workflow, then run it with inputs
listed in the executable command line, and after a successful execution, I would have to retrieve the outputs generated, then delete the created workflow and any files related that exist.
The inputs (datasets) on which the workflow will run have to exist within the Galaxy's system - you can't supply the files to the workflow directly.
Is it currently possible for me, in a short time, to develop such plugin
performing operations previously described using the existing API? If yes, could you please provide me more information on the current API or some help on the different tools I should use?
You might consider the following flow. I believe all steps can be performed via API.
1. Import datasets into Galaxy ( using Tool API of the upload tool you have 2 options: either by linking the files - https://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFilesor by direct uploading - the choice depends mostly on the size of inputs ) 2. Import workflow( https://galaxy-central.readthedocs.org/en/latest/lib/galaxy.webapps.galaxy.a... ) 3. Run workflow on the datasets in Galaxy 4. Download results from history( https://galaxy-central.readthedocs.org/en/latest/lib/galaxy.webapps.galaxy.a... ) 5. Delete histories 6. Delete workflow
Let me know how this works for you.
thank you for using Galaxy!
Martin
On Fri, Feb 28, 2014 at 9:10 AM, Benoit Meilhac <B.Meilhac@westminster.ac.uk
wrote:
Dear Sir or Madam,
I am working for the University of Westminster on the ER-Flow project ( http://www.erflow.eu/home). I'm currently investigating a way to use the galaxy workflow engine with a command line interface in order to support it within our project. The idea would be to develop a plugin that could make a link between our repository, where a galaxy workflow can be specified (workflow and inputs stored and output declared), and a galaxy server.
We have a specific way our existing plugins work. It would be something like: ./executable -w workflow <list of inputs> And then, outputs are retrieved and returned (they don't need to be given as command line parameters).
I had a quick look at the provided API within the galaxy project and I have some questions. I saw this is possible to import the workflow to the server, then to execute it. In my plugin, I would have to import the workflow, then run it with inputs listed in the executable command line, and after a successful execution, I would have to retrieve the outputs generated, then delete the created workflow and any files related that exist.
Is it currently possible for me, in a short time, to develop such plugin performing operations previously described using the existing API? If yes, could you please provide me more information on the current API or some help on the different tools I should use?
Many thanks and kind regards,
Benoît Meilhac
The University of Westminster is a charity and a company limited by guarantee. Registration number: 977818 England. Registered Office: 309 Regent Street, London W1B 2UW.
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