Hello Pieter,
adding a controller to Galaxy's codebase is not possible through the Tool Shed. It would be very unsecure to allow such.
However, reading your code ( https://gist.github.com/martenson/7ce1ddb19c199b2df61c) you should be able to convert this controller into an actual tool (data source tool kind) pretty easily and publishing the tool through the Tool Shed should be straight forward afterwards.
Dave Bouvier will get back to you with some tips in the next message.
Thank you for using Galaxy.
Martin
On Fri Jan 23 2015 at 8:36:44 AM Lukasse, Pieter pieter.lukasse@wur.nl wrote:
Hi Greg,
I would like to deploy my custom controller together with my tool via toolshed. Is there already a way to do this? What should I add to my tool_dependencies.xml?
I tried something like :
<action type=*"shell_command"*>
*cd* $GALAXY_HOME; *wget* http://toolshed.g2.bx.psu.edu/repos/pieterlukasse/nist_
wrapper/raw-file/tip/nist_controller.py;
</action>
But I’m glad this apparently didn’t work ;)
Thanks,
Pieter
*From:* galaxy-dev [mailto:galaxy-dev-bounces@lists.galaxyproject.org] *On Behalf Of *Lukasse, Pieter *Sent:* vrijdag 9 januari 2015 16:10 *To:* 'galaxy-dev@lists.galaxyproject.org' *Subject:* [galaxy-dev] FW: Adding a new web-service or perhaps a "webapp" to Galaxy
Meanwhile I added a new file indeed to <galaxy-dist>/lib/galaxy/ webapps/galaxy/controllers/
and this works for me. If there is a better/easier/standard way of doing this, please let me know!
Attached my file as example.
Best regards,
Pieter
*From:* galaxy-dev [mailto:galaxy-dev-bounces@lists.galaxyproject.org galaxy-dev-bounces@lists.galaxyproject.org] *On Behalf Of *Lukasse, Pieter *Sent:* vrijdag 9 januari 2015 13:55 *To:* galaxy-dev@lists.bx.psu.edu *Subject:* Re: [galaxy-dev] Adding a new web-service or perhaps a "webapp" to Galaxy
I could add a new file to
<galaxy-dist>/lib/galaxy/webapps/galaxy/controllers/
...is that a good way to do it?
*From:* galaxy-dev [mailto:galaxy-dev-bounces@lists.galaxyproject.org galaxy-dev-bounces@lists.galaxyproject.org] *On Behalf Of *Lukasse, Pieter *Sent:* vrijdag 9 januari 2015 13:28 *To:* galaxy-dev@lists.bx.psu.edu *Subject:* [galaxy-dev] Adding a new web-service or perhaps a "webapp" to Galaxy
Hi,
In one of my tools I generate a HTML report which I would like to enhance with some ajax functionality. I would like the possibility to do some backend computations based on the ajax requests.
My question is: is there an easy way to add a new web-service to my Galaxy server? The web-service implementation would be in python. Ideally I would like to be able to ship this python file together with my tool via tool shed (and when installing from toolshed, the necessary configurations are applied to the server to enable this python code as a local web-service on the respective Galaxy server).
Thanks!
Pieter Lukasse
Wageningen UR, Plant Research International
Department of Bioinformatics (Bioscience)
Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
T: +31-317481122; M: +31-628189540; skype: pieter.lukasse.wur
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