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
________________________________
This e-mail message (including any attachments) is for the sole use of
the intended recipient(s) and may contain confidential and privileged
information. If the reader of this message is not the intended
recipient, you are hereby notified that any dissemination, distribution
or copying of this message (including any attachments) is strictly
prohibited.
If you have received this message in error, please contact
the sender by reply e-mail message and destroy all copies of the
original message (including attachments).
___________________________________________________________
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:
http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
