On Thu, Apr 21, 2011 at 2:40 PM, Dannon Baker <dannonbaker@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.Walton@jax.org> wrote: Is the server below down? I'm trying to get there this morning and having no luck...
_in_a_directory
Dave
On 4/15/11 12:16 PM, "Pieter Neerincx" <pieter.neerincx@gmail.com> wrote:
Hi,
You're not alone with this request! Unfortunately I wasn't able to join
2-day Galaxy Hackathon, but I heard from a colleague who just came back
this was one of the topics they worked on. At the end of the hackathon
had a working prototype:
https://wiki.nbic.nl/index.php/NBIC_Galaxy_Hackathon_project#Loop_over_files...
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
https://wiki.nbic.nl/index.php/NBIC_Galaxy_Hackathon_project#Loop_over_files the that they 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
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