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 <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
>>>
>
>
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