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>
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