On Jan 4, 2012, at 2:34 PM, Langhorst, Brad wrote:
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
Hi All, It is indeed possible to run workflows from the command line via the API. Have a look at the sample script galaxy-dist/scripts/api/workflow_execute.py to see how it's done. Sorry for the lack of documentation, although this is finally in progress. --nate
-- 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 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: