[galaxy-dev] LWR Support

9 Apr 2014

      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:

<?xml version="1.0"?>
<job_conf>
    <plugins workers="4">
        <plugin id="lwr" type="runner"
load="galaxy.jobs.runners.lwr:LwrJobRunner">
        </plugin>
    </plugins>
    <handlers default="handlers">
        <handler id="handler0" tags="handlers"/>
    </handlers>
    <destinations default="local">
        <destination id="local" runner="local"/>
        <destination id="lwr" runner="lwr">
            <param id="url">http://200.144.255.42:8005/</param>
        </destination>
    </destinations>
    <tools>
        <tool id="2pg" destination="lwr"/>
    </tools>
    <limits>
        <limit type="registered_user_concurrent_jobs">2</limit>
        <limit type="unregistered_user_concurrent_jobs">1</limit>
        <limit type="job_walltime">24:00:00</limit>
        <limit type="concurrent_jobs" id="local">1</limit>
    </limits>
</job_conf>

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

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.

So, I have some questions to ask:

- Do I need to have a Galaxy instance running at the same server of LWR?
- Are there other variables that I should have set on Galaxy or on LWR
server?
- 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?

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