On Thu, Apr 21, 2011 at 2:40 PM, Dannon Baker <dannonba...@me.com> wrote:

> Leandro,
>
> I see what you mean, I misunderstood your original goal.  There currently
> isn't a way to execute single tools in this fashion.
>
> It isn't exactly straightforward, but you could construct a workflow that
> consisted of two steps-- an Input Dataset step, and whatever tool you wanted
> to use, and then you'd be able to use the functionality described in this
> thread as long as your instance is at 5386:67a19816034b or higher.
>
> -Dannon
>

Hi Dannon,

Thanks for your replies and advice, this leads me to a quesion... is it
possible to execute a tool job via the Galaxy API just like someone does via
the UI? Could I then have a tool script that wraps this programmatic
execution of X tool jobs via the API?

regards,
Leandro



>
>
>

>
>
> On Apr 21, 2011, at 7:49 AM, Leandro Hermida wrote:
>
> > Hi again,
> >
> > Sorry to maybe not understand how to get started, but I'm trying for
> something even without the added complexity of a workflow.
> >
> > If you could point me into the right direction: how would I have a single
> tool where on the tool form there is a multi-select of certain datasets in
> the user's history.  The user multi selects X datasets in the form and hits
> submit and Galaxy will launch X tool jobs (on for each of the datasets) at
> the same time in the history.
> >
> > How do I go about doing this?
> >
> > Sorry for being daft,
> > Leandro
> >
> >
> > On Tue, Apr 19, 2011 at 4:34 PM, Dave Walton <dave.wal...@jax.org>
> wrote:
> > Is the server below down?  I'm trying to get there this morning and
> having
> > no luck...
> >
> >
> https://wiki.nbic.nl/index.php/NBIC_Galaxy_Hackathon_project#Loop_over_files
> > _in_a_directory
> >
> > Dave
> >
> >
> > On 4/15/11 12:16 PM, "Pieter Neerincx" <pieter.neeri...@gmail.com>
> wrote:
> >
> > > Hi,
> > >
> > > You're not alone with this request! Unfortunately I wasn't able to join
> the
> > > 2-day Galaxy Hackathon, but I heard from a colleague who just came back
> that
> > > this was one of the topics they worked on. At the end of the hackathon
> they
> > > had a working prototype:
> > >
> > >
> https://wiki.nbic.nl/index.php/NBIC_Galaxy_Hackathon_project#Loop_over_files_i
> > > n_a_directory
> > >
> > > Since they had only 2 days, it will need some polish, but I heard this
> hack
> > > already made it into the development branch of Galaxy, so we may see
> something
> > > like this in the near future :)
> > >
> > > Cheers,
> > >
> > > Pi
> > >
> > > On Apr 15, 2011, at 4:28 PM, Dave Walton wrote:
> > >
> > >> I've essentially asked the same question of the list in the past and
> gotten
> > >> no real response.
> > >>
> > >> I have the same interest, but from a workflow perspective.
> > >>
> > >> * A module that allows me to select multiple datafiles (say fastq
> files)
> > >> * Then pass each data file to a separate instance of a workflow that
> runs
> > >> tophat and cufflinks
> > >> * then another module that takes the final outputs of each of the
> workflow
> > >> runs and sends them to a final module that merges results.
> > >>
> > >> I am attempting to implement something like this using the API, though
> the
> > >> API is still pretty green from my perspective.
> > >>
> > >> I think functionality like this built into the workflow editor would
> be a
> > >> great addition.
> > >>
> > >> Dave
> > >>
> > >> On Apr 15, 2011, at 8:14 AM, Leandro Hermida wrote:
> > >>
> > >>> Hi everyone,
> > >>>
> > >>> I was wondering what would be the way in Galaxy to program the
> following:
> > >>>
> > >>> - User clicks on a tool and form is displayed
> > >>> - They use a select multi menu in the form to pick lets say X
> multiple
> > >>> datasets from their history
> > >>> - When they click submit the tool launches X number of jobs in the
> history,
> > >>> on for each of the datasets selected.
> > >>>
> > >>> I have a common use case where users have to manually run the same
> tool over
> > >>> and over again with the same parameters for each dataset of interest
> in
> > >>> their history.  I would be great to be able programmatically or
> otherwise
> > >>> with Galaxy to be able to use one form and multi select the datasets
> and
> > >>> then launch the parallel jobs in one go.
> > >>>
> > >>> regards,
> > >>> Leandro
> > >>>
> > >>> <ATT00001..txt>
> > >>
> > >>
> > >> ___________________________________________________________
> > >> 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/
> > >
> > > -------------------------------------------------------------
> > > mobile: +31 6 143 66 783
> > > e-mail: pieter.neeri...@gmail.com
> > > skype:  pieter.online
> > > -------------------------------------------------------------
> > >
> >
> >
> > ___________________________________________________________
> > Please keep all replies on the list by using "reply all"
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> >
> >  http://lists.bx.psu.edu/
>
>
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