Hi Geert,

I did something similar but two things I got stumped on and maybe you found a way to do this through the API.

1) I would like to put some of my results into a datalibrary.  But i can't find the API call for that. Do you know if this is possible? I asked repeatedly here on the dev list but no one seems to know if this is possible...

2) I am trying to pass my workflow some parameters that are defined in the workflow with ther ${NameOfVarible} notation.
It works great in the UI, but I cannot seem to figure out how to pass parameters to a workflow...

Any ideas there?

Bedankt!

Thon

On Nov 02, 2012, at 05:39 AM, Geert Vandeweyer <geert.vandeweyer2@ua.ac.be> wrote:

Hi all,

After some fiddling, I've put together an api-based workflow runner. It allows you to start workflows on batches of paired-end data from the commandline, and if set in the galaxy-config, output results to a different user (making history sharing/cloning obsolete from adminuser to end-user).

Needed input (which workflow, which history, which input datafiles (from history/library) are selected on runtime by fetching the the options using the api. 

I've also put some notes together on the following page, regarding the api-syntax:  http://tinyurl.com/cv6zmz2

It's using urllib to post the sumbission to a remote galaxy-server, so you don't need access to the galaxy-installation to run ./submit.py or ./workflow_execute.py. It's a stand-alone script, with no dependencies on the galaxy-provided code.

I hope this helps some people getting started with the galaxy-api :-).

Best,

Geert



On 07/18/2012 02:38 PM, Sascha Kastens wrote:

Hi Dev-Team,

 

are you planning or maybe working on an update which enables the

possiblilty to run workflows in batch mode with paired end data?

 

Cheers,

Sascha



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-- 

Geert Vandeweyer, Ph.D.
Department of Medical Genetics
University of Antwerp
Prins Boudewijnlaan 43
2650 Edegem
Belgium
Tel: +32 (0)3 275 97 56
E-mail: geert.vandeweyer@ua.ac.be
http://ua.ac.be/cognitivegenetics
http://www.linkedin.com/pub/geert-vandeweyer/26/457/726
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