Hi Mike,
Once the given EBS volume is attached and mounted, all of the data should be
in /mnt/galaxyData/files/000/
This assumes the file system is mounted to /mnt/galaxyData, which is where
it would get mounted to automatically by cloudman on cluster instantiation.

Enis

On Wed, Apr 13, 2011 at 9:00 PM, Mike Dufault <dufau...@yahoo.com> wrote:

>
> Hi Enis,
>
> I started to use the terminal to check to see if the job was running, but
> it stopped successfully at the same time. Thanks again for helping me to
> complete the run.
>
> Now I have an additional issue. I wanted to save my BAM file, but I kept
> getting an error. I think the error was because it was too large to send
> (4.1GB). So I saved what I could to my local HD and terminated the cluster.
> My EBS volume is 200GB and persisted after the cluster was terminated.
>
> I assume that my BAM file resides somewhere in the EBS volume. I started a
> new Unix cluster and "attached" the EBS to that cluster. I also established
> an ssh to the Unis cluster but I do not know where to find the BAM file. Do
> you know how I can access the BAM file so that I can transfer it to my local
> HD?
>
> Thanks,
> Mike
>
> --- On *Wed, 4/13/11, Enis Afgan <eaf...@emory.edu>* wrote:
>
>
> From: Enis Afgan <eaf...@emory.edu>
> Subject: Re: [galaxy-user] Help!!!!!! with Galaxy Cloud!!!!!
> To: "vasu punj" <pu...@yahoo.com>
>
> Cc: galaxy-u...@bx.psu.edu
> Date: Wednesday, April 13, 2011, 10:01 AM
>
>
> Hi Vasu,
> I am not sure I understand your question but the general instructions on
> how to get started and use Galaxy on the cloud (i.e., Cloudman) are
> available at usegalaxy.org/cloud
>
> Let us know if you that page does not answer your questions,
> Enis
>
> On Wed, Apr 13, 2011 at 9:40 AM, vasu punj 
> <pu...@yahoo.com<http://us.mc1137.mail.yahoo.com/mc/compose?to=pu...@yahoo.com>
> > wrote:
>
>   I was wondering if there are instructions how can I run the Galaxy on
> CloudConsole, Indeed  first I want to know how Galaxy is established on
> console? Can someone direct me to the instructions please.
>
> Thanks.
>
> --- On *Tue, 4/12/11, Enis Afgan 
> <eaf...@emory.edu<http://us.mc1137.mail.yahoo.com/mc/compose?to=eaf...@emory.edu>
> >* wrote:
>
>
> From: Enis Afgan 
> <eaf...@emory.edu<http://us.mc1137.mail.yahoo.com/mc/compose?to=eaf...@emory.edu>
> >
> Subject: Re: [galaxy-user] Help!!!!!! with Galaxy Cloud!!!!!
> To: "Mike Dufault" 
> <dufau...@yahoo.com<http://us.mc1137.mail.yahoo.com/mc/compose?to=dufau...@yahoo.com>
> >
> Cc: 
> galaxy-u...@bx.psu.edu<http://us.mc1137.mail.yahoo.com/mc/compose?to=galaxy-u...@bx.psu.edu>
> Date: Tuesday, April 12, 2011, 9:31 PM
>
>
>  Galaxy has the functionality to recover any jobs that were running after
> it's restarted so it is quite possible to for the job to still be running.
> In addition, from the cloudman console, it appears that at least one
> instance is pretty heavily loaded so that can also mean that the job is
> still running. However, without actually accessing the instance through the
> command line and checking the status of the job queue, it is not possible to
> tell if the job is - actually running. Do you know how to do that? It's just
> a few commands in the terminal:
> - access the instance
> [local]$ ssh -i <path to the private key you downloaded from AWS when you
> created a key pair> ubuntu@<instance public DNS>
> - become galaxy user
> [ec2]$ sudo su galaxy
> - list any running jobs
> [ec2]$ qstat
>
> If that command returns a list of jobs and the jobs are in stare 'r'
> (running), the job is still running; otherwise, no.
>
> Let me know how it goes,
> Enis
>
> On Tue, Apr 12, 2011 at 9:49 PM, Mike Dufault 
> <dufau...@yahoo.com<http://us.mc1147.mail.yahoo.com/mc/compose?to=dufau...@yahoo.com>
> > wrote:
>
>   Hi Enis,
>
> THANK YOU!!!
>
> I see that my "filter pileup on data" step is running. Is this the same
> analysis that was running before or did it relauch when you restarted
> Galaxy? I just don't know if the analysis would be compromised.
>
> Thanks again to you and the whole Galaxy team.
>
> Best,
>
> Mike
>
> --- On *Tue, 4/12/11, Enis Afgan 
> <eaf...@emory.edu<http://us.mc1147.mail.yahoo.com/mc/compose?to=eaf...@emory.edu>
> >* wrote:
>
>
> From: Enis Afgan 
> <eaf...@emory.edu<http://us.mc1147.mail.yahoo.com/mc/compose?to=eaf...@emory.edu>
> >
> Subject: Re: [galaxy-user] Help!!!!!! with Galaxy Cloud!!!!!
> To: "Mike Dufault" 
> <dufau...@yahoo.com<http://us.mc1147.mail.yahoo.com/mc/compose?to=dufau...@yahoo.com>
> >
> Cc: "Anton Nekrutenko" 
> <an...@bx.psu.edu<http://us.mc1147.mail.yahoo.com/mc/compose?to=an...@bx.psu.edu>>,
> galaxy-u...@bx.psu.edu<http://us.mc1147.mail.yahoo.com/mc/compose?to=galaxy-u...@bx.psu.edu>
> Date: Tuesday, April 12, 2011, 9:16 PM
>
>
> 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<http://mc/compose?to=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<http://mc/compose?to=eaf...@emory.edu>
> >* wrote:
>
>
> From: Enis Afgan <eaf...@emory.edu <http://mc/compose?to=eaf...@emory.edu>
> >
> Subject: Re: [galaxy-user] Help!!!!!! with Galaxy Cloud!!!!!
> To: "Mike Dufault" 
> <dufau...@yahoo.com<http://mc/compose?to=dufau...@yahoo.com>
> >
> Cc: "Anton Nekrutenko" 
> <an...@bx.psu.edu<http://mc/compose?to=an...@bx.psu.edu>>,
> galaxy-u...@bx.psu.edu <http://mc/compose?to=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
> 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/
>
>
>
>
>
> -----Inline Attachment Follows-----
>
>
> ___________________________________________________________
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> 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/
>
>
>
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>
> ___________________________________________________________
> 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/
>
>
___________________________________________________________
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at usegalaxy.org.  Please keep all replies on the list by
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use the Galaxy Development list:

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