On Wed, Jan 4, 2012 at 2:25 PM, Ryan <ngsbioinformat...@gmail.com> wrote:
> On Wed, Jan 4, 2012 at 12:04 PM, Langhorst, Brad <langho...@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
>

I think Ryan is right and I think that's exactly the niche for the API.

Usha you could take a look into:
http://wiki.g2.bx.psu.edu/Learn/API

It seems there is very limited documentation, but it might help you to
see if what you want is already possible.

Regards,
Carlos

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