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 langhorst@neb.com From: Ryan <ngsbioinformatics@gmail.com<mailto:ngsbioinformatics@gmail.com>> Date: Wed, 4 Jan 2012 14:25:44 -0500 To: Brad Langhorst <langhorst@neb.com<mailto:langhorst@neb.com>> Cc: Usha Reddy <usha.reddy.pa@gmail.com<mailto:usha.reddy.pa@gmail.com>>, "galaxy-dev@bx.psu.edu<mailto:galaxy-dev@bx.psu.edu>" <galaxy-dev@bx.psu.edu<mailto: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<mailto: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