Hi Oliver,
A message in the masthead/top of the page main CloudMan console page
offering to update CloudMan should show up automatically on page refresh
when a version of CloudMan newer than the one currently running one exists
in the default cloudman bucket. This functionality was added a few months
ago now so if your instance is older, it won't work like that. In that case,
it should be fine to manually download cm.tar.gz from 'cloudman' bucket and
upload it to your cluster's bucket (replacing the current file there -
although make a copy of the current file in case things don't work out as
expected) and restart the instance.

Enis

On Tue, Jun 28, 2011 at 4:28 PM, Oliver Hofmann
<ohofm...@hsph.harvard.edu>wrote:

> Enis,
>
> > 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.
>
> is there a way to update CloudMan through the older admin page as well
> (/cloud/admin)? It already has the Update Galaxy button and passes on the
> galaxy-central bitbucket URL to an 'update_galaxy' script, but doesn't seem
> to trigger anything beyond that (whether Galaxy itself is running or not).
>
> Best, Oliver
>
>
>
> >
> > Glad you got the configuration to work,
> > Enis
> >
> > On Tue, Jun 28, 2011 at 3:45 PM, Joseph Hargitai <
> 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]
> > Sent: Tuesday, June 28, 2011 3:30 PM
> >
> > To: Joseph Hargitai
> > Cc: 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> 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]
> > 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.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
> >
> >
> > ___________________________________________________________
> > 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/
> >
> >
> >
> > ___________________________________________________________
> > 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/
>
> --
> Research Scientist    Department of Biostatistics
> Associate Director    Bioinformatics Core
>                      Harvard School of Public Health
> Skype: ohofmann       Phone: +1 (617) 365 0984
>
>
___________________________________________________________
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