Hello all, The documentation is on my todo list, and is fairly high up on it (and now it's a little higher). However, it is a wiki and everyone is encouraged to create an account and update the doc as you learn things.
Dave C. On Wed, Jan 4, 2012 at 1:34 PM, Nate Coraor <n...@bx.psu.edu> wrote: > 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 > > langho...@neb.com > > > > > > > > From: Ryan <ngsbioinformat...@gmail.com> > > Date: Wed, 4 Jan 2012 14:25:44 -0500 > > To: Brad Langhorst <langho...@neb.com> > > Cc: Usha Reddy <usha.reddy...@gmail.com>, "galaxy-...@bx.psu.edu" < > galaxy-...@bx.psu.edu> > > Subject: Re: [galaxy-dev] galaxy command line > > > > On Wed, Jan 4, 2012 at 12:04 PM, Langhorst, Brad <langho...@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: > > > > http://lists.bx.psu.edu/ > > > ___________________________________________________________ > 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: > > http://lists.bx.psu.edu/ > -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/
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