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 :-).



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?




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Geert Vandeweyer, Ph.D.
Department of Medical Genetics
University of Antwerp
Prins Boudewijnlaan 43
2650 Edegem
Tel: +32 (0)3 275 97 56
E-mail: geert.vandeweyer@ua.ac.be