Re: [galaxy-user] cloud instance drops settings on reboot

28 Jun 2011

      throws this:

{"updated": false}

________________________________
From: Enis Afgan [eafgan@emory.edu]
Sent: Tuesday, June 28, 2011 6:02 PM
To: Oliver Hofmann; Joseph Hargitai
Cc: galaxy-user
Subject: Re: [galaxy-user] cloud instance drops settings on reboot

Well, now that I looked into it, about a week ago I did fix a bug with version checking so that's probably why it's not triggering. To manually invoke the update, you can paste this into your address bar and magic should happen :)
http://ec2-<rest of ip>/cloud/root/update_users_CM

Enis

P.S. Once the auto-checking is working, the attached screenshot shows what the masthead is supposed to look like.

On Tue, Jun 28, 2011 at 5:25 PM, Oliver Hofmann <ohofmann@hsph.harvard.edu<mailto:ohofmann@hsph.harvard.edu>> wrote:
Enis,

running the default EC2 AMI (2011-03-22), cluster was started for the first time about ten days ago so this is odd. I'll read up on how to manually update CM.

Thanks!

       Oliver

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
<ohofmann@hsph.harvard.edu<mailto:ohofmann@hsph.harvard.edu> <mailto:ohofmann@hsph.harvard.edu<mailto:ohofmann@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_...).
   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.hargitai@einstein.yu.edu<mailto:joseph.hargitai@einstein.yu.edu>
   <mailto:joseph.hargitai@einstein.yu.edu<mailto:joseph.hargitai@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 [eafgan@emory.edu<mailto:eafgan@emory.edu> <mailto:eafgan@emory.edu<mailto:eafgan@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>
   <mailto: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.hargitai@einstein.yu.edu<mailto:joseph.hargitai@einstein.yu.edu>
   <mailto:joseph.hargitai@einstein.yu.edu<mailto: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<mailto:eafgan@emory.edu> <mailto:eafgan@emory.edu<mailto:eafgan@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>
   <mailto: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.hargitai@einstein.yu.edu<mailto:joseph.hargitai@einstein.yu.edu>
   <mailto:joseph.hargitai@einstein.yu.edu<mailto: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
    >
    >
    > ___________________________________________________________
    > The Galaxy User list should be used for the discussion of
    > Galaxy analysis and other features on the public server
    > at usegalaxy.org<http://usegalaxy.org> <http://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<http://usegalaxy.org> <http://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<tel:%2B1%20%28617%29%20365%200984>
   <tel:%2B1%20%28617%29%20365%200984>

--
Research Scientist    Department of Biostatistics
Associate Director    Bioinformatics Core
                     Harvard School of Public Health
Skype: ohofmann       Phone: +1 (617) 365 0984<tel:%2B1%20%28617%29%20365%200984>