throws this:
{"updated": false}
________________________________
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.
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
Enis,
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
<joseph.hargitai@einstein.yu.edu<mailto:joseph.hargitai@einstein.yu .edu="">
formatting to prevail. Unicode was the culprit.
Is this a version issue?
is what you are referring to.
<mailto:galaxy-user@lists.bx.psu.edu<mailto:galaxy- user@lists.bx.psu.edu="">>
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.
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.
<joseph.hargitai@einstein.yu.edu<mailto:joseph.hargitai@einstein.yu .edu="">
admin user. I uploaded the file back into the bucket but now the
galaxy part is not starting. It is throwing an error:
bucket 'cm-99e0c68a2fe11e32a592e36abd1f2c38' to
'/mnt/galaxyTools/galaxy-central/universe_wsgi.ini'.
bucket 'cm-99e0c68a2fe11e32a592e36abd1f2c38' to
'/mnt/galaxyTools/galaxy-central/tool_conf.xml'.
'tool_data_table_conf.xml.cloud' from bucket
'cm-99e0c68a2fe11e32a592e36abd1f2c38' to
'/mnt/galaxyTools/galaxy-central/tool_data_table_conf.xml.cloud'.
'/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' '
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.
<mailto:galaxy-user@lists.bx.psu.edu<mailto:galaxy- user@lists.bx.psu.edu="">>
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.
at top right of the Cloudman console page) that gives you an option
to restart Cloudman (as well as individual application-level
services).
<joseph.hargitai@einstein.yu.edu<mailto:joseph.hargitai@einstein.yu .edu="">
galaxy - ./runs.sh
Amazon console) the setting reverted to original.
reboot?
on the list by
on the list by
--
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>
