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 workflow interface to return an error.  However, the
input dataset that I am specifying is not being forwarded to the
workflow step.  When I execute the workflow from the web ui, I get a
command like this for the first step:

executing: python /mnt/galaxy/galaxy_dist/tools/fastq/fastq_groomer.py
'/mnt/galaxy/galaxy_dist/database/files/000/dataset_48.dat' 'illumina'
'/mnt/galaxy/galaxy_dist/database/job_working_directory/169/galaxy_dataset_169.dat'
'sanger' 'ascii' 'summarize_input'

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'

this is the command I get for the first step:

executing: python /mnt/galaxy/galaxy_dist/tools/fastq/fastq_groomer.py
'None' 'illumina'
'/mnt/galaxy/galaxy_dist/database/job_working_directory/164/galaxy_dataset_164.dat'
'sanger' 'ascii' 'summarize_input'

So the dataset passes all of the asserts, but is not passed to the
first step of the workflow.  The api key and workflow id are working
because it's not failing right away, and the history id is working
because the failed steps are populated in it.  The dataset seems not
to be throwing any errors.  So I am finding myself very confused!  Is
there something obvious that you see?

Take care,

Darren

On Tue, Mar 15, 2011 at 7:50 PM, Darren Brown <br...@centerspace.net> wrote:
> 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" <dannonba...@me.com> wrote:
>
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