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
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 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
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
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 2650 Edegem Belgium Tel: +32 (0)3 275 97 56 E-mail: geert.vandeweyer@ua.ac.be mailto: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:
galaxy-dev@lists.galaxyproject.org
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Geert Vandeweyer -
Sascha Kastens