It seems that the formatting of the file was changed and Galaxy is unable to parse the file. The editor you used to edit the file might have done this once the file was saved. I'd suggest using vi to check the file and make sure it follows the formatting of universe_wsgi.ini.sample for example. Then, try uploading the file again. BTW, it's required for the file to have the .cloud extension.

If all you're trying to do is add Galaxy admin users, the Cloudman Admin interface I mentioned earlier offers this functionality and it handles updating of the universe file. If you want to revert to what you had before, feel free to pull in the default universe_wsgi.ini.cloud file from 'cloudman' bucket on S3 and upload it to your cluster's bucket. 

Enis

On Tue, Jun 28, 2011 at 3:21 PM, Joseph Hargitai <joseph.hargitai@einstein.yu.edu> wrote:
Enis,

thanks! I did edit the file in the bucket as much as adding an admin user. I uploaded the file back into the bucket but now the galaxy part is not starting. It is throwing an error:

  • 19:01:24 - Setting up Galaxy application
  • 19:01:24 - Retrieved file 'universe_wsgi.ini.cloud' from bucket 'cm-99e0c68a2fe11e32a592e36abd1f2c38' to '/mnt/galaxyTools/galaxy-central/universe_wsgi.ini'.
  • 19:01:25 - Retrieved file 'tool_conf.xml.cloud' from bucket 'cm-99e0c68a2fe11e32a592e36abd1f2c38' to '/mnt/galaxyTools/galaxy-central/tool_conf.xml'.
  • 19:01:25 - Retrieved file 'tool_data_table_conf.xml.cloud' from bucket 'cm-99e0c68a2fe11e32a592e36abd1f2c38' to '/mnt/galaxyTools/galaxy-central/tool_data_table_conf.xml.cloud'.
  • 19:01:25 - Starting Galaxy...
  • 19:01:25 - Error invoking Galaxy, running command '/bin/su - galaxy -c "export SGE_ROOT=/opt/sge; sh $GALAXY_HOME/run.sh --daemon"' returned code '1' and following stderr: 'Traceback (most recent call last): File "./scripts/check_eggs.py", line 22, in c = Crate() File "/mnt/galaxyTools/galaxy-central/lib/galaxy/eggs/__init__.py", line 259, in __init__ self.galaxy_config = GalaxyConfig() File "/mnt/galaxyTools/galaxy-central/lib/galaxy/eggs/__init__.py", line 356, in __init__ if self.config.read( GalaxyConfig.config_file ) == []: File "/usr/lib/python2.6/ConfigParser.py", line 286, in read self._read(fp, filename) File "/usr/lib/python2.6/ConfigParser.py", line 482, in _read raise MissingSectionHeaderError(fpname, lineno, line) ConfigParser.MissingSectionHeaderError: File contains no section headers. file: /mnt/galaxyTools/galaxy-central/universe_wsgi.ini, line: 1 '\xff\xfe#\x00\n' Traceback (most recent call last): File "./scripts/fetch_eggs.py", line 27, in c = Crate() File "/mnt/galaxyTools/galaxy-central/lib/galaxy/eggs/__init__.py", line 259, in __init__ self.galaxy_config = GalaxyConfig() File "/mnt/galaxyTools/galaxy-central/lib/galaxy/eggs/__init__.py", line 356, in __init__ if self.config.read( GalaxyConfig.config_file ) == []: File "/usr/lib/python2.6/ConfigParser.py", line 286, in read self._read(fp, filename) File "/usr/lib/python2.6/ConfigParser.py", line 482, in _read raise MissingSectionHeaderError(fpname, lineno, line) ConfigParser.MissingSectionHeaderError: File contains no section headers. file: /mnt/galaxyTools/galaxy-central/universe_wsgi.ini, line: 1 '\xff\xfe#\x00\n' '

Is the edited bucket file causing an issue? How do I get a new one or fix this? I did notice that the first uploaded try omitted the .cloud suffix, but i uploaded it again with the correct suffix.


best,
joe








From: Enis Afgan [eafgan@emory.edu]
Sent: Tuesday, June 28, 2011 11:46 AM
To: Joseph Hargitai
Cc: galaxy-user@lists.bx.psu.edu
Subject: Re: [galaxy-user] cloud instance drops settings on reboot

Hi Joe, 
This is by design. In order to change the settings in universe_wsgi.ini, you should edit file universe_wsgi.ini.cloud in the cluster's bucket on S3. This file get pulled in by Cloudman each time an instance starts. 

As far as restarting Cloudman, there is a (new) Admin panel (link at top right of the Cloudman console page) that gives you an option to restart Cloudman (as well as individual application-level services).

Let us know if you have any more questions,
Enis

On Tue, Jun 28, 2011 at 11:29 AM, Joseph Hargitai <joseph.hargitai@einstein.yu.edu> wrote:

Hi,

setting the admin user in
/mnt/galaxyTools/galaxy-central/universe_wsgi.ini

did work after a simple restart of the galaxy service as user galaxy  -  ./runs.sh

However, when I restarted the cloud instance (rebooted from Amazon console) the setting reverted to original.

Is there perhaps another ini file that overrides this one on a reboot?

Also, is there a proper/other way to restart the service?

best,
joe
 

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