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,


On Wed, Mar 16, 2011 at 3:07 PM, Dannon Baker <dannonba...@me.com> 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 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 step id expected is actually the workflow step_id, not 
> the "Step 1" "Step 2", etc numbers that you'll see in the run workflow page.
> -Dannon
> On Mar 16, 2011, at 6:01 PM, Darren Brown wrote:
>> 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 <dannonba...@me.com> wrote:
>>> 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-key>  <url>/api/workflows 38247d270c7cb1bb
>>>> 'hist_id=38247d270c7cb1bb' '1=hda=30fc17ce78176bfb'
>>> My hunch is that the step id '1' in this line is probably your issue. To 
>>> list workflow details in the api, you can use the scripts/api/display.py
>>> So, for your workflow there,
>>> python /mnt/galaxy/galaxy_dist/scripts/api/display.py <api_key> 
>>> http://localhost:8080/api/workflows/38247d270c7cb1bb
>>> Check that with the workflow in question and see what it returns as the 
>>> inputs dictionary.
>>> -Dannon

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:


Reply via email to