On Wed, Jan 4, 2012 at 1:34 PM, Nate Coraor <nate@bx.psu.edu> wrote:

On Jan 4, 2012, at 2:34 PM, Langhorst, Brad wrote:

> Ryan:
>
> I didn't understand Usha's question the same way you did. I agree that it's useful to run workflows in a more automated way.
>
> I have not run workflows using the Galaxy API yet, but I did see some documentation on it and plan to try it soon.
>
> http://wiki.g2.bx.psu.edu/Learn/API/Examples
>
> Maybe someone with more expertise has something more to say about this.
>
> Brad

Hi All,

It is indeed possible to run workflows from the command line via the API. Have a look at the sample script galaxy-dist/scripts/api/workflow_execute.py to see how it's done. Sorry for the lack of documentation, although this is finally in progress.

--nate

> --
> Brad Langhorst
> New England Biolabs
> langhorst@neb.com
>
>
>
> From: Ryan <ngsbioinformatics@gmail.com>
> Date: Wed, 4 Jan 2012 14:25:44 -0500
> To: Brad Langhorst <langhorst@neb.com>
> Cc: Usha Reddy <usha.reddy.pa@gmail.com>, "galaxy-dev@bx.psu.edu" <galaxy-dev@bx.psu.edu>
> Subject: Re: [galaxy-dev] galaxy command line
>
> On Wed, Jan 4, 2012 at 12:04 PM, Langhorst, Brad <Langhorst@neb.com> wrote:
>> Usha:
>>
>> Galaxy is essentially a wrapper around other command line tools.
>> So, while you could probably extract some of its pieces to run on the command line, I don't know why you would want to.
>>
>
> I would argue it would be beneficial to invoke pipelines from the command line instead of being forced to use the web-based interface. command line is beneficial for large #'s of datasets that need to be analyzed.
>
> Ryan

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