Hello Benoît,

I remember seeing projects trying to do something similar (store workflows
internally and execute on Galaxy), like http://refinery-platform.org/, so
it could be useful to take a look there too.  I've been trying to do
something similar but with the Java interface to the Galaxy API
https://github.com/jmchilton/blend4j.  I have no code to show off right now
though :(.

Aaron


On Fri, Feb 28, 2014 at 11:36 AM, Martin Čech <mar...@bx.psu.edu> wrote:

> 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.api.html#module-galaxy.webapps.galaxy.api.workflows
>    )
>    3. Run workflow on the datasets in Galaxy
>    4. Download results from history(
>    
> https://galaxy-central.readthedocs.org/en/latest/lib/galaxy.webapps.galaxy.api.html#module-galaxy.webapps.galaxy.api.histories
>    )
>    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.meil...@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.
>>
>> This message and its attachments are private and confidential. If you
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>>
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>
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