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 -- Brad Langhorst New England Biolabs langho...@neb.com 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>>, "galaxy-...@bx.psu.edu<mailto:galaxy-...@bx.psu.edu>" <galaxy-...@bx.psu.edu<mailto:galaxy-...@bx.psu.edu>> 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: 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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