Dave,
Most likely within a week. If you wanted to go ahead and try it, the latest
changeset that affects the API is 5223:82f9422864ff. You can snag that now
(the subsequent update from galaxy-dist will still work fine, when it comes
out) with:
% hg pull -u -r 82f9422864ff http://bitbucket.or
When is this functionality expected to make it into galaxy-dist?
Thanks,
Dave
On 3/16/11 6:07 PM, "Dannon Baker" wrote:
> That's not actually what I expected, but I see what's going on here. The
> workflows API expects explicit "Input Dataset" steps for mapping datasets, add
> one of those a
Ah I see what you mean Dannon. I need the id of the step from the
database essentially (or maybe there is a better way to do it
'right'). But anyway, I have been able to run a workflow from the
command-line! Thanks so much for your help,
Darren
On Wed, Mar 16, 2011 at 3:07 PM, Dannon Baker wr
That's not actually what I expected, but I see what's going on here. The
workflows API expects explicit "Input Dataset" steps for mapping datasets, add
one of those and connect it to your fastq step and see if it has inputs showing
up for you to map to at that point.
Do note that the input ste
Ah ok, and you are right there is something wrong there. The inputs
dictionary is empty:
inputs: {}
However this seems kind of odd, because I do need to specify history
inputs for the workflow through the web ui.
On Wed, Mar 16, 2011 at 2:55 PM, Dannon Baker wrote:
> On Mar 16, 2011, at 5:43 P
On Mar 16, 2011, at 5:43 PM, Darren Brown wrote:
> However, when I run a workflow from the command line:
>
> python /mnt/galaxy/galaxy_dist/scripts/api/workflow_execute.py
> /api/workflows 38247d270c7cb1bb
> 'hist_id=38247d270c7cb1bb' '1=hda=30fc17ce78176bfb'
My hunch is that the step id '1' i
Hi Dannon,
I am still just trying to proof of concept the workflow_execute script
and running into a little trouble. I am tracking my issue into
workflows.py in the api. In debugging, I am confident that the
datasets are correctly specified, as I can specify a bad dataset and
get the http workfl
Hi Dannon,
Thanks very much for answering these questions. I think this all I need to
get it going. I'll report back soon.
Darren
On Mar 15, 2011 6:06 PM, "Dannon Baker" wrote:
___
Please keep all replies on the list by using "reply all"
in
On Mar 15, 2011, at 7:03 PM, Darren Brown wrote:
> But I am kinda stuck at what these guys actually mean.
The execute_workflow.py command line inputs are indeed a little clunky for all
the information that has to go into each dataset mapping parameter. I didn't
imagine that this script would a
Hi Dannon,
workflow
I am finally getting around to the workflow api. I am having trouble
with a couple things. First, I am trying to get the
workflow_execute.py functioning for a workflow that I have here. I
think I have everything down but how to define the dataset.
Basically, I am trying to re
Hello Dannon,
This looks exactly like how I would like to run a workflow. I'll be
trying this out next week and will let you know how it goes. Thanks
much!
Darren
On Sat, Mar 5, 2011 at 1:51 PM, Dannon Baker wrote:
> Darren,
>
> A first pass at adding workflows to the Galaxy API is now availa
Darren,
A first pass at adding workflows to the Galaxy API is now available. For an
example of how to execute a basic workflow, see
scripts/api/execute_workflow.py. An example of how this might integrate into a
slightly more complex script using library uploads is available at
scripts/api/ex
Hello Dannon,
That is surprising and excellent! Can't wait to hear more.
Take care,
Darren
On Wed, Mar 2, 2011 at 11:38 AM, Dannon Baker wrote:
> Darren,
>
> While this is not currently possible, I'm currently finishing up a first pass
> on a workflow API that will allow this sort of interac
Darren,
While this is not currently possible, I'm currently finishing up a first pass
on a workflow API that will allow this sort of interaction and hope to have an
early version available by the end of this week. I can update you when that
has been committed.
-Dannon
On Feb 24, 2011, at 9:2
Hello folks,
I am using a workflow that needs to be run many times on many
different inputs. I have hacked around and figured out how to pull
multiple inputs from a history, but I am a little baffled on how to
run a galaxy workflow programatically. I have searched around fairly
exhaustively and
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