Hi Jordan, There are currently two possibilities. First, one can simulate a web client from a command line script. Galaxy is fairly restful, so this is not too hard in practice, although you probably need to login and do cookie management. Second, all of the programs Galaxy runs are command line programs, so you can run them directly. We're working on the next step, which is closer to what you likely want, of actually being able to run a Galaxy workflow outside of the Galaxy UI, but still registering the jobs and datasets in Galaxy so they are visible through the GUI. Thanks, James On Nov 30, 2009, at 12:46 PM, Jordan Mendler wrote:

Hi all,

I was wondering, is there a way to use Galaxy from the Command Line, or is it all web/point-and-click based? I would like to be able to write scripts to run workflows on new experiments that come off the sequencer, from the command line on Cron, so wondering if anything like this is possible with Galaxy.

Thanks, Jordan _______________________________________________ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user