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.


Maybe someone with more expertise has something more to say about this.

Brad Langhorst
New England Biolabs

From: Ryan <ngsbioinformat...@gmail.com<mailto:ngsbioinformat...@gmail.com>>
Date: Wed, 4 Jan 2012 14:25:44 -0500
To: Brad Langhorst <langho...@neb.com<mailto:langho...@neb.com>>
Cc: Usha Reddy <usha.reddy...@gmail.com<mailto:usha.reddy...@gmail.com>>, 
Subject: Re: [galaxy-dev] galaxy command line

On Wed, Jan 4, 2012 at 12:04 PM, Langhorst, Brad 
<langho...@neb.com<mailto:langho...@neb.com>> wrote:

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.

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