same - looks nice and very useful. 

best,
joe

________________________________________
From: Oliver Hofmann [ohofman...@gmail.com] on behalf of Oliver Hofmann 
[ohofm...@hsph.harvard.edu]
Sent: Tuesday, June 28, 2011 7:29 PM
To: Enis Afgan
Cc: Joseph Hargitai; galaxy-user
Subject: Re: [galaxy-user] cloud instance drops settings on reboot

Enis,


thanks once again, works like a charm. Updated, the CloudMan interface
now has an admin page, and old data made it through the update.

Best,

        Oliver


> It's a publicly shared S3 bucket. You can download the file directly
> through your browser too: http://s3.amazonaws.com/cloudman/cm.tar.gz
>
> On Tue, Jun 28, 2011 at 7:03 PM, Joseph Hargitai
> <joseph.hargi...@einstein.yu.edu
> <mailto:joseph.hargi...@einstein.yu.edu>> wrote:
>
>     where do i find the 'cloudman' bucket?
>
>     j
>
>     ------------------------------------------------------------------------
>     *From:* Enis Afgan [eaf...@emory.edu <mailto:eaf...@emory.edu>]
>     *Sent:* Tuesday, June 28, 2011 6:48 PM
>     *To:* Joseph Hargitai
>     *Cc:* Oliver Hofmann; galaxy-user
>
>     *Subject:* Re: [galaxy-user] cloud instance drops settings on reboot
>
>     I apologize for making you go through multiple steps - when I sent
>     my last email, I looked at the controller code and not the actual
>     method but it turns out the method performs the same check as the
>     UI, which fails, and so does the method... Sorry.
>     Now, it's going to have to be done manually but it's quite
>     straightforward. So, just in case, make a copy of cm.tar.gz in your
>     cluster's bucket. Then, download cm.tar.gz from `cloudman` bucket
>     and upload it to your cluster's bucket. Then, in AWS S3 console,
>     select the freshly uploaded file, click Properties and then the
>     Metadata tab. Add a new key value pair setting the following to as
>     the key `x-amz-meta-revision` and `114` as the value. Now, restart
>     the CloudMan instance  and (less) magic should happen - but you
>     should have the most recent version of CloudMan running.
>
>     Hopefully this time it's going to happen :)
>     Thanks for patience.
>     Enis
>
>     On Tue, Jun 28, 2011 at 6:38 PM, Joseph Hargitai
>     <joseph.hargi...@einstein.yu.edu
>     <mailto:joseph.hargi...@einstein.yu.edu>> wrote:
>
>         throws this:
>
>         {"updated": false}
>
>         
> ------------------------------------------------------------------------
>         *From:* Enis Afgan [eaf...@emory.edu <mailto:eaf...@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
>         <ohofm...@hsph.harvard.edu <mailto:ohofm...@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
>                 <ohofm...@hsph.harvard.edu
>                 <mailto:ohofm...@hsph.harvard.edu>
>                 <mailto:ohofmann@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
>                 
> <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>
>                 <mailto:joseph.hargitai@__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> <mailto: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>
>                 <mailto:galaxy-u...@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>
>                 <mailto:joseph.hargitai@__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-__99e0c68a2fe11e32a592e36abd1f2c__38' to
>                 '/mnt/galaxyTools/galaxy-__central/universe_wsgi.ini'.
>                  >       • 19:01:25 - Retrieved file
>                 'tool_conf.xml.cloud' from
>                     bucket 'cm-__99e0c68a2fe11e32a592e36abd1f2c__38' to
>                 '/mnt/galaxyTools/galaxy-__central/tool_conf.xml'.
>                  >       • 19:01:25 - Retrieved file
>                 'tool_data_table_conf.xml.__cloud' from bucket
>                 'cm-__99e0c68a2fe11e32a592e36abd1f2c__38' 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> <mailto: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>
>                 <mailto:galaxy-u...@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>
>                 <mailto:joseph.hargitai@__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
>                  >
>                  >
>                  >
>                 _____________________________________________________________
>                  > 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
>                 <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
>                 <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>
>
>
>
>


--
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