The masthead on the web browser does not have an update option I can see. Is 
this option in a config file somewhere on the server?

We used the AIM since October/ and started a new version about two weeks ago.

Of course the overall idea of an upgrade is an interesting one. Eventually you 
want to rely on AIM, but once you start updating your configuration you move 
away from the gold-standard with every step.

joe

________________________________
From: Enis Afgan [eaf...@emory.edu]
Sent: Tuesday, June 28, 2011 3:57 PM
To: Joseph Hargitai
Cc: galaxy-user@lists.bx.psu.edu
Subject: Re: [galaxy-user] cloud instance drops settings on reboot

The admin interface is something that I added just last week. It's not related 
to an AMI but to Cloudman itself. When was it you created the given cluster? If 
it's been in the last 5 days, the link should be there (take a look at the most 
recent newsbrief - there is a snapshot of the admin link & interface there: 
https://bitbucket.org/galaxy/galaxy-central/wiki/Features/DevNewsBrief/2011_06_23).
 If your cluster was older than that, Cloudman should have a option in the 
masthead to update it automatically. If you are to update, the link should show 
up. Let me know if neither is the case and we'll work on it more.

Glad you got the configuration to work,
Enis

On Tue, Jun 28, 2011 at 3:45 PM, Joseph Hargitai 
<joseph.hargi...@einstein.yu.edu<mailto:joseph.hargi...@einstein.yu.edu>> wrote:
Yeap,

grabbed a new one from the tar file in the bucket and allowed Mac formatting to 
prevail. Unicode was the culprit.


I am missing however the Cloudman Admin tab you are referring to. Is this a 
version issue?
we use: galaxy-cloudman-2011-03-22 (ami-da58aab3)

I do have the Admin tab in galaxy itself, but I do not think that is what you 
are referring to.

joe


________________________________
From: Enis Afgan [eaf...@emory.edu<mailto:eaf...@emory.edu>]
Sent: Tuesday, June 28, 2011 3:30 PM

To: Joseph Hargitai
Cc: galaxy-user@lists.bx.psu.edu<mailto:galaxy-user@lists.bx.psu.edu>
Subject: Re: [galaxy-user] cloud instance drops settings on reboot

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.hargi...@einstein.yu.edu<mailto:joseph.hargi...@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 [eaf...@emory.edu<mailto:eaf...@emory.edu>]
Sent: Tuesday, June 28, 2011 11:46 AM
To: Joseph Hargitai
Cc: galaxy-user@lists.bx.psu.edu<mailto: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.hargi...@einstein.yu.edu<mailto:joseph.hargi...@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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___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/

Reply via email to