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
>
>
>
_____________________________________________________________
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>
> To manage your subscriptions to this and other Galaxy
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> 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>
