Cannot configure DRMAA

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Cannot configure DRMAA

Patel, Viren
Hello. I have installed Galaxy and run it successfully. Now I am trying to configure it to use DRMAA job runner. I created a job_conf.xml file as explained in the Galaxy wiki:

<?xml version="1.0"?>
<job_conf>
    <plugins>
        <plugin id="sge" type="runner" load="galaxy.jobs.runners.drmaa:DRMAAJobRunner" workers="4"/>
    </plugins>
    <destinations default="sge_default">
        <destination id="sge_default" runner="drmaa"/>
    </destinations>
</job_conf>

The galaxy user has the necessary environment variable:

$ echo $DRMAA_LIBRARY_PATH
/opt/sge/lib/lx-amd64/libdrmaa.so

But then Galaxy does not start. Here are the final log messages:

galaxy.jobs DEBUG 2013-06-17 17:32:27,715 Loading job configuration from ./job_conf.xml
Traceback (most recent call last):
  File "/mnt/FSS2/data/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py", line 35, in app_factory
    app = UniverseApplication( global_conf = global_conf, **kwargs )
  File "/mnt/FSS2/data/home/galaxy/galaxy-dist/lib/galaxy/app.py", line 97, in __init__
    self.job_config = jobs.JobConfiguration(self)
  File "/mnt/FSS2/data/home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 109, in __init__
    self.__parse_job_conf_xml(tree)
  File "/mnt/FSS2/data/home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 159, in __parse_job_conf_xml
    self.default_handler_id = self.__get_default(handlers, self.handlers.keys())
  File "/mnt/FSS2/data/home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 288, in __get_default
    rval = parent.get('default')
AttributeError: 'NoneType' object has no attribute 'get'
Removing PID file galaxy-web1.pid

I am using the following to start Galaxy:

/bin/sh run.sh --pid-file galaxy.pid --log-file galaxy.log

I have updated my Galaxy install to the latest stable version, but the problem persists. Any help will be much appreciated. Please note that Galaxy runs ok without the job_conf.xml file. Is there some configuration I am missing? Thanks.

Viren




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Re: Cannot configure DRMAA

cjav
On Mon, Jun 17, 2013 at 5:44 PM, Patel, Viren <[hidden email]> wrote:

> Hello. I have installed Galaxy and run it successfully. Now I am trying to
> configure it to use DRMAA job runner. I created a job_conf.xml file as
> explained in the Galaxy wiki:
>
> <?xml version="1.0"?>
> <job_conf>
>     <plugins>
>         <plugin id="sge" type="runner"
> load="galaxy.jobs.runners.drmaa:DRMAAJobRunner" workers="4"/>
>     </plugins>
>     <destinations default="sge_default">
>         <destination id="sge_default" runner="drmaa"/>
>     </destinations>
> </job_conf>
>

I think you are missing the handlers configuration section. Assuming
you are using only one server called main([server:main] in
'universe_wsgi.ini') you should use something like this:

<?xml version="1.0"?>
<job_conf>
    <plugins>
        <plugin id="sge" type="runner"
load="galaxy.jobs.runners.drmaa:DRMAAJobRunner" workers="4"/>
    </plugins>
    <handlers default="handlers">
        <!-- Additional job handlers - the id should match the name of a
             [server:<id>] in universe_wsgi.ini.
         -->
        <handler id="main" tags="handlers"/>
    </handlers>
    <destinations default="sge_default">
        <destination id="sge_default" runner="drmaa"/>
    </destinations>
</job_conf>

The wiki[1] doesn't include the 'handlers' section in the examples. I
personally prefer starting from the supplied sample
file('job_conf.xml.sample_advanced').

[1]http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster

Hope it helps,
Carlos
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