On Wed, Apr 9, 2014 at 9:55 AM, Alexandre Defelicibus
wrote:
> Hi all,
>
> I have some doubts about how to configure a LWR server on Linux.
> I have read the LWR documentation, however how to configure the LWR is not
> clear to me.
>
> This is my scenario:
>
> On my Galaxy server I have some tools that I would like to send their jobs
> to the LWR server. These tools are at the same folder (xml and py).
>
> The LWR server is installed on Linux, and it is accessible through the URL.
>
> This is my job_conf.xml:
>
>
>
>
> load="galaxy.jobs.runners.lwr:LwrJobRunner">
>
>
>
>
>
>
>
>
> http://200.144.255.42:8005/
>
>
>
>
>
>
> 2
> 1
> 24:00:00
> 1
>
>
>
> When I execute the tool, I get this error:
>
> ValueError: No JSON object could be decoded
>
>
> At the LWR server, I use a nginx server, and I see on the log file that the
> server receive this URL:
> GET /setup?tool_id=2pg&job_id=24&tool_version=1.0.0
Cool I have never setup LWR behind nginx but it should certainly work.
>
> So, I concluded that the Galaxy server is accessing the LWR server and
> creating a job, but something wrong happens on the LWR side, but I couldn't
> realize what is missing.
How are you running the LWR? There should be a file called paster.log
in the LWR root directory or in the standard out of the terminal
session you started the LWR using if it did not start as a daemon.
That should have a lot of relevant details.
Basically there should be a bunch of lines in Galaxy's log and the LWR
log corresponding to the attempted submission that will hopefully
provide some details related to the error.
>
> So, I have some questions to ask:
>
> - Do I need to have a Galaxy instance running at the same server of LWR?
No this definitely should not be needed.
> - Are there other variables that I should have set on Galaxy or on LWR
> server?
Not really
> - I know it is better if I use the secure LWR, and I will do, but is there
> something wrong on my job_conf.xml file?
Nothing jumps out at me. The logs will make it clear if there is though I think.
The LWR is distributed with a test script to exercise the server
independent of Galaxy - you should target it at your nginx proxy to
determine if the problem is with above the proxy (i.e. in Galaxy's
configuration or the tool itself) or below it (either in the LWR,
nginx, etc...).
>From the LWR root you should be able to just run:
python run_client_tests.py --url http://200.144.255.42:8005/
You could also clone down the LWR code on your Galaxy host and run
this to determine if there is some firewall problem for instance.
Hope this helps and thanks for your interest in the LWR!
-John
>
> I hope I have shown all the needed details about my installation.
>
> Best regards,
>
> Alexandre
>
> --
> Alexandre Defelicibus
> Mestrando em Bioengenharia
> Programa de Pós-Graduação em Bioengenharia
> Universidade de São Paulo - USP
>
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