Ahh, for some reason cloudman is thinking Galaxy is not 'running' but still
'starting' and has thus not enabled the given button. To access the
analysis, in your browser, just delete the '/cloud' part of the URL and that
should load Galaxy.

Sorry about the confusion,
Enis

On Tue, Apr 12, 2011 at 9:12 PM, Mike Dufault <dufau...@yahoo.com> wrote:

> Hi Enis,
>
> Thanks for looking into this.
>
> From the Galaxy Cloudman Console, I can see that it was restarted from the
> log (thanks), but the "Access Galaxy" choice is still grayed out and I don't
> know how to access the Analysis window.
>
> Is there a way back into my analysis?
>
> Thanks,
> Mike
>
>
>
> --- On *Tue, 4/12/11, Enis Afgan <eaf...@emory.edu>* wrote:
>
>
> From: Enis Afgan <eaf...@emory.edu>
> Subject: Re: [galaxy-user] Help!!!!!! with Galaxy Cloud!!!!!
> To: "Mike Dufault" <dufau...@yahoo.com>
> Cc: "Anton Nekrutenko" <an...@bx.psu.edu>, galaxy-u...@bx.psu.edu
> Date: Tuesday, April 12, 2011, 8:55 PM
>
>
> Hi Mike,
> Try accessing your Galaxy instance now. It should be ok.
>
> The link in your email contained the IP for your instance so I took the
> liberty of restarting Galaxy and that brought it back up. There seems to
> have been an issue with Galaxy accessing its database and that resulted in
> Galaxy crashing. We'll look into why that happened in the first place but
> should be ok now.
>
> Let me know if you have any more trouble,
> Enis
>
> On Tue, Apr 12, 2011 at 2:49 PM, Mike Dufault 
> <dufau...@yahoo.com<http://mc/compose?to=dufau...@yahoo.com>
> > wrote:
>
> Hello Galaxy Staff,
>
> My data has been running on the Amazon EC2 for just over 24hrs. I have not
> closed any windows and my Exome analysis made it all the way through to
> filter on Pile up. I have two tabs for this instance. One is the Galaxy
> Cloudman Console and the other is the tab where I perform the analysis, load
> data, history etc.
>
> Anyway, I went to add a step to the work flow and the screen "Welcome
> Galaxy to the Cloud" screen along with the information "There is no Galaxy
> instance running on this host, or the Galaxy instance is not responding. To
> manage Galaxy on this host, please use the Cloud 
> Console<http://ec2-67-202-55-176.compute-1.amazonaws.com/cloud>
> ."
>
> What happened???
>
> When I go back to the Galaxy Cloudman Console, it shows that my instance is
> still running along with the four cores, the Cluster log is below. AWS also
> shows that my instance is running.
>
> Will the work flow finish? Can I get my data? How?
>
> I tried to re-access the analysis page by selecting "Access Galaxy" from
> the "Galaxy Cloudman Console" but it sends me to the same "Welcome page."
>
> Is there a way to get back into the analysis page?
>
> Please help!!!
>
> Thanks,
> Mike
>
> The cluster log shows:
>
>    - 13:05:24 - Master starting
>    - 13:05:25 - Completed initial cluster configuration.
>    - 13:05:33 - Starting service 'SGE'
>    - 13:05:48 - Configuring SGE...
>    - 13:05:56 - Successfully setup SGE; configuring SGE
>    - 13:05:57 - Saved file 'persistent_data.yaml' to bucket
>    'cm-a42f040c55e7519eb63bbaf269fa78d3'
>    - 13:05:57 - Saved file 'cm_boot.py' to bucket
>    'cm-a42f040c55e7519eb63bbaf269fa78d3'
>    - 13:05:57 - Saved file 'cm.tar.gz' to bucket
>    'cm-a42f040c55e7519eb63bbaf269fa78d3'
>    - 13:05:57 - Problem connecting to bucket
>    'cm-a42f040c55e7519eb63bbaf269fa78d3', attempt 1/5
>    - 13:05:59 - Saved file 'Fam122261.clusterName' to bucket
>    'cm-a42f040c55e7519eb63bbaf269fa78d3'
>    - 13:06:24 - Initializing a 'Galaxy' cluster.
>    - 13:06:24 - Retrieved file 'snaps.yaml' from bucket 'cloudman' to
>    'cm_snaps.yaml'.
>    - 13:06:41 - Adding 3 instance(s)...
>    - 13:07:02 - Saved file 'persistent_data.yaml' to bucket
>    'cm-a42f040c55e7519eb63bbaf269fa78d3'
>    - 13:07:38 - Saved file 'persistent_data.yaml' to bucket
>    'cm-a42f040c55e7519eb63bbaf269fa78d3'
>    - 13:07:38 - Saved file 'universe_wsgi.ini.cloud' to bucket
>    'cm-a42f040c55e7519eb63bbaf269fa78d3'
>    - 13:07:38 - Saved file 'tool_conf.xml.cloud' to bucket
>    'cm-a42f040c55e7519eb63bbaf269fa78d3'
>    - 13:07:48 - Error mounting file system '/mnt/galaxyData' from
>    '/dev/sdg3', running command '/bin/mount /dev/sdg3 /mnt/galaxyData' 
> returned
>    code '32' and following stderr: 'mount: you must specify the filesystem 
> type
>    '
>    - 13:07:52 - Saved file 'persistent_data.yaml' to bucket
>    'cm-a42f040c55e7519eb63bbaf269fa78d3'
>    - 13:07:52 - Starting service 'Postgres'
>    - 13:07:52 - PostgreSQL data directory '/mnt/galaxyData/pgsql/data'
>    does not exist (yet?)
>    - 13:07:52 - Configuring PostgreSQL with a database for Galaxy...
>    - 13:08:05 - Saved file 'persistent_data.yaml' to bucket
>    'cm-a42f040c55e7519eb63bbaf269fa78d3'
>    - 13:08:05 - Starting service 'Galaxy'
>    - 13:08:05 - Galaxy daemon not running.
>    - 13:08:05 - Galaxy service state changed from 'Starting' to 'Error'
>    - 13:08:05 - Setting up Galaxy application
>    - 13:08:05 - Retrieved file 'universe_wsgi.ini.cloud' from bucket
>    'cm-a42f040c55e7519eb63bbaf269fa78d3' to
>    '/mnt/galaxyTools/galaxy-central/universe_wsgi.ini'.
>    - 13:08:05 - Retrieved file 'tool_conf.xml.cloud' from bucket
>    'cm-a42f040c55e7519eb63bbaf269fa78d3' to
>    '/mnt/galaxyTools/galaxy-central/tool_conf.xml'.
>    - 13:08:05 - Retrieved file 'tool_data_table_conf.xml.cloud' from
>    bucket 'cloudman' to
>    '/mnt/galaxyTools/galaxy-central/tool_data_table_conf.xml.cloud'.
>    - 13:08:05 - Starting Galaxy...
>    - 13:08:09 - Galaxy service state changed from 'Error' to 'Starting'
>    - 13:08:09 - Saved file 'persistent_data.yaml' to bucket
>    'cm-a42f040c55e7519eb63bbaf269fa78d3'
>    - 13:08:09 - Saved file 'tool_data_table_conf.xml.cloud' to bucket
>    'cm-a42f040c55e7519eb63bbaf269fa78d3'
>    - 13:08:28 - Instance 'i-e46f0a8b' reported alive
>    - 13:08:28 - Successfully generated root user's public key.
>    - 13:08:28 - Sent master public key to worker instance 'i-e46f0a8b'.
>    - 13:08:28 - Instance 'i-e26f0a8d' reported alive
>    - 13:08:28 - Sent master public key to worker instance 'i-e26f0a8d'.
>    - 13:08:33 - Instance 'i-e06f0a8f' reported alive
>    - 13:08:33 - Sent master public key to worker instance 'i-e06f0a8f'.
>    - 13:08:33 - Adding instance i-e46f0a8b to SGE Execution Host list
>    - 13:08:44 - Successfully added instance 'i-e46f0a8b' to SGE
>    - 13:08:44 - Waiting on worker instance 'i-e46f0a8b' to configure
>    itself...
>    - 13:08:44 - Instance 'i-e26f0a8d' already in SGE's @allhosts
>    - 13:08:44 - Waiting on worker instance 'i-e26f0a8d' to configure
>    itself...
>    - 13:08:45 - Instance 'i-e06f0a8f' already in SGE's @allhosts
>    - 13:08:45 - Waiting on worker instance 'i-e06f0a8f' to configure
>    itself...
>    - 13:08:50 - Instance 'i-e46f0a8b' ready
>    - 13:09:27 - Galaxy service state changed from 'Starting' to 'Running'
>    - 22:38:18 - Found '3' idle instances; trying to remove '2'
>    - 22:38:18 - Specific termination of instance 'i-e26f0a8d' requested.
>    - 22:38:18 - Removing instance 'i-e26f0a8d' from SGE
>    - 22:38:18 - Successfully updated @allhosts to remove 'i-e26f0a8d'
>    - 22:38:19 - Terminating instance 'i-e26f0a8d'
>    - 22:38:19 - Initiated requested termination of instance. Terminating
>    'i-e26f0a8d'.
>    - 22:38:19 - Specific termination of instance 'i-e46f0a8b' requested.
>    - 22:38:19 - Removing instance 'i-e46f0a8b' from SGE
>    - 22:38:19 - Successfully initiated termination of instance
>    'i-e26f0a8d'
>    - 22:38:19 - Successfully updated @allhosts to remove 'i-e46f0a8b'
>    - 22:38:20 - Terminating instance 'i-e46f0a8b'
>    - 22:38:20 - Initiated requested termination of instance. Terminating
>    'i-e46f0a8b'.
>    - 22:38:20 - Initiated requested termination of instances. Terminating
>    '2' instances.
>    - 22:38:20 - Successfully initiated termination of instance
>    'i-e46f0a8b'
>    - 22:38:41 - Found '1' idle instances; trying to remove '1'
>    - 22:38:41 - Specific termination of instance 'i-e06f0a8f' requested.
>    - 22:38:41 - Removing instance 'i-e06f0a8f' from SGE
>    - 22:38:41 - Successfully updated @allhosts to remove 'i-e06f0a8f'
>    - 22:38:42 - Initiated requested termination of instance. Terminating
>    'i-e06f0a8f'.
>    - 22:38:42 - Initiated requested termination of instances. Terminating
>    '1' instances.
>    - 22:38:42 - Terminating instance 'i-e06f0a8f'
>    - 22:38:42 - Successfully initiated termination of instance
>    'i-e06f0a8f'
>    - 22:38:47 - Instance 'i-e26f0a8d' successfully terminated.
>    - 22:38:49 - Instance 'i-e46f0a8b' successfully terminated.
>    - 22:38:59 - Adding 3 instance(s)...
>    - 22:39:07 - Instance 'i-e06f0a8f' successfully terminated.
>    - 22:41:02 - Instance 'i-fa096e95' reported alive
>    - 22:41:02 - Sent master public key to worker instance 'i-fa096e95'.
>    - 22:41:06 - Adding instance i-fa096e95 to SGE Execution Host list
>    - 22:41:17 - Successfully added instance 'i-fa096e95' to SGE
>    - 22:41:17 - Waiting on worker instance 'i-fa096e95' to configure
>    itself...
>    - 22:41:17 - Instance 'i-fe096e91' reported alive
>    - 22:41:17 - Sent master public key to worker instance 'i-fe096e91'.
>    - 22:41:22 - Adding instance i-fe096e91 to SGE Execution Host list
>    - 22:41:34 - Successfully added instance 'i-fe096e91' to SGE
>    - 22:41:34 - Waiting on worker instance 'i-fe096e91' to configure
>    itself...
>    - 22:41:34 - Instance 'i-fa096e95' ready
>    - 22:41:52 - Instance 'i-fe096e91' ready
>    - 22:42:28 - Instance 'i-fc096e93' reported alive
>    - 22:42:28 - Sent master public key to worker instance 'i-fc096e93'.
>    - 22:42:38 - Adding instance i-fc096e93 to SGE Execution Host list
>    - 22:42:49 - Successfully added instance 'i-fc096e93' to SGE
>    - 22:42:49 - Waiting on worker instance 'i-fc096e93' to configure
>    itself...
>    - 22:43:13 - Instance 'i-fc096e93' ready
>    - 18:29:10 - Failure checking disk usage. [Errno 12] Cannot allocate
>    memory
>    - 18:29:10 - Failure checking disk usage. [Errno 12] Cannot allocate
>    memory
>    - 18:29:10 - Failure checking disk usage. [Errno 12] Cannot allocate
>    memory
>
>
>
> ___________________________________________________________
> The Galaxy User list should be used for the discussion of
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>
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> please use the interface at:
>
>  http://lists.bx.psu.edu/
>
>
>
___________________________________________________________
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at usegalaxy.org.  Please keep all replies on the list by
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