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
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
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:
are you planning or maybe working on an update which enables the
possiblilty to run workflows in batch mode with paired end data?
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:
Geert Vandeweyer, Ph.D.
Department of Medical Genetics
University of Antwerp
Prins Boudewijnlaan 43
Tel: +32 (0)3 275 97 56