Question: ExpatError upon attempt to run galaxy locally
0
gravatar for lzeglin
4.1 years ago by
lzeglin0
United States
lzeglin0 wrote:

Hello,

I installed galaxy locally today and was successful in uploading files and running basic fastq manipulations.  However after I shut down the program, it cannot re-start.  I entered command sh run.sh and the startup fails here:

Traceback (most recent call last):
  File "/Applications/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py", line 44, in app_factory
    app = UniverseApplication( global_conf = global_conf, **kwargs )
  File "/Applications/galaxy-dist/lib/galaxy/app.py", line 77, in __init__
    self.job_config = jobs.JobConfiguration(self)
  File "/Applications/galaxy-dist/lib/galaxy/jobs/__init__.py", line 119, in __init__
    self.__parse_resource_parameters()
  File "/Applications/galaxy-dist/lib/galaxy/jobs/__init__.py", line 361, in __parse_resource_parameters
    resource_definitions = util.parse_xml( self.app.config.job_resource_params_file )
  File "/Applications/galaxy-dist/lib/galaxy/util/__init__.py", line 174, in parse_xml
    tree = ElementTree.parse(fname)
  File "/Applications/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 859, in parse
    tree.parse(source, parser)
  File "/Applications/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 583, in parse
    parser.feed(data)
  File "/Applications/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 1242, in feed
    self._parser.Parse(data, 0)
ExpatError: not well-formed (invalid token): line 2, column 82

The only advice I can find on this error is development related, and I am not using galaxy at anywhere near a development level, I certainly did nothing in python manually.  I did manually modify config xml files as instructed by Galaxy wiki pages to set up a Data Library (to upload large raw sequence data files) and to add tools as an Admin- but nothing more. 

Thank you for your help in starting galaxy again.  The only solution I can resort to with my limited knowledge is to uninstall and reinstall galaxy, but that does not seem very practical.  Thank you!

 

galaxy • 1.3k views
ADD COMMENTlink modified 4.1 years ago • written 4.1 years ago by lzeglin0
1
gravatar for jmchilton
4.1 years ago by
jmchilton1.1k
United States
jmchilton1.1k wrote:

That is very odd - does your Galaxy folder have a job_resource_params_conf.xml or config/job_resource_params_conf.xml file? If it does please delete these and try to restart Galaxy.

If not - do you have a config/galaxy.ini or a universe_wsgi.ini file in your Galaxy directory? If so are they explicitly defining a value for the option job_resource_params_file?

ADD COMMENTlink written 4.1 years ago by jmchilton1.1k
0
gravatar for lzeglin
4.1 years ago by
lzeglin0
United States
lzeglin0 wrote:

Thanks!!  This sounds like a good track since the third thing I was attempting to modify after the tools and data libraries was the number of jobs to run concurrently and the option to use more than 1 core per job.  I did not think I had figured out the correct way to do this, but I had opened config/job_resource_params_conf.xml as well as config/job_conf.xml (and removed the notes on both options in universe_wsgi.ini) to try...

...So I did have a config/job_resource_params_conf.xml file- but when I went back to look at it this morning I found that it had turned into an alias at some point- original file not found (?) In any case I deleted that file, and I get the same error upon attempting to start up, but with a slight change at the line/column that it's calling the error:

Traceback (most recent call last):
  File "/Applications/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py", line 44, in app_factory
    app = UniverseApplication( global_conf = global_conf, **kwargs )
  File "/Applications/galaxy-dist/lib/galaxy/app.py", line 77, in __init__
    self.job_config = jobs.JobConfiguration(self)
  File "/Applications/galaxy-dist/lib/galaxy/jobs/__init__.py", line 122, in __init__
    tree = util.parse_xml(self.app.config.job_config_file)
  File "/Applications/galaxy-dist/lib/galaxy/util/__init__.py", line 174, in parse_xml
    tree = ElementTree.parse(fname)
  File "/Applications/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 859, in parse
    tree.parse(source, parser)
  File "/Applications/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 583, in parse
    parser.feed(data)
  File "/Applications/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 1242, in feed
    self._parser.Parse(data, 0)
ExpatError: not well-formed (invalid token): line 5, column 97

And yes, I had removed the note on the option job_resource_params_file in universe_wsgi.ini; I replaced it after deleting the file so it now reads

#job_resource_params_file = config/job_resource_params_conf.xml

But I do still get the exact same error as pasted above on startup...

Thanks for the help.

 

ADD COMMENTlink written 4.1 years ago by lzeglin0
2

Okay - so this time it is a problem parsing the XML of the job configuration file (config/job_conf.xml). So here you can remove config/job_conf.xml or modify it so the XML is valid.

XML is not a very forgiving format - I don't know how you are modifying these files but it might be worth editing them with an editor that will indicate XML problems as your modify them. I am not a Mac user so I cannot recommend one - but a web search might come up with something.

I have committed a fix to Galaxy that vastly improves these two error messages you encountered - but unfortunately the next stable release of Galaxy is not for a couple months. https://bitbucket.org/galaxy/galaxy-central/commits/46523237518bb9ec8ed9fa4cf30453c800580c24

Sorry about these problems.

ADD REPLYlink written 4.1 years ago by jmchilton1.1k
0
gravatar for lzeglin
4.1 years ago by
lzeglin0
United States
lzeglin0 wrote:

Great, thanks so much, that worked.  It started up normally after deleting config/job_conf.xml.  I also re-installed the original files and then used Xcode to modify the config/job_conf.xml and config/job_resource_params_conf.xml files instead of text editor, and did not get the odd error message upon startup.  Using a better editor is an easy precaution to take but I obviously didn't think of it before.  Very glad that you all are forgiving of me clumsily bumping around in these files even if xml format is not!  Thanks again!

ADD COMMENTlink written 4.1 years ago by lzeglin0
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