Hi,

I've also thought about that approach, but the problem here is that I don't find a way to request the users api key from a tool-xml. So you would have to hard-code an api key in the tool configuration. Or is there a way to request a user's api key from a galaxy-tool. That would also allow the design of tools that would clean up (delete) datasets after workflow execution.

Geert

On 07/19/2012 09:04 AM, Sascha Kastens wrote:

Hi Geert,

thanks for your reply. Unfortunately it is not feasible for us to use a script

outside Galaxy. As long as no official feature for Galaxy is released I will

work on a script which will execute workflows via the API and add this script

as a tool into Galaxy.

Cheers,

Sascha

Original message:

Hi,

In case you’d be interested: we use a script that creates interlaced
data of paired end data.  We run this outside galaxy on groups of
samples ordered in directories at once. We then import the interlaced
data into galaxy, enabling batch workflow. The first step of the
workflow is a deinterlacing of the datafiles.

The script is available here:
http://geertvandeweyer.zymichost.com/index.php?page=read&id=27

Best Regards,

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
___________________________________________________________
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:

  http://lists.bx.psu.edu/

-- 

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