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/
___________________________________________________________
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/

Reply via email to