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.
On Nov 30, 2009, at 12:46 PM, Jordan Mendler wrote:
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.
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