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
<ohofm...@hsph.harvard.edu <mailto: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
    <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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     >
     > ___________________________________________________________
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     > using "reply all" in your mail client.  For discussion of
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    --
    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>




--
Research Scientist    Department of Biostatistics
Associate Director    Bioinformatics Core
                      Harvard School of Public Health
Skype: ohofmann       Phone: +1 (617) 365 0984
___________________________________________________________
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