Re: [galaxy-user] Help!!!!!! with Galaxy Cloud!!!!!
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. 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 starting13:05:25 - Completed initial cluster configuration.13:05:33 - Starting service 'SGE'13:05:48 - Configuring SGE...13:05:56 - Successfully setup SGE; configuring SGE13:05:57 - 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 1/513:05:59 - 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 application13:08:05 - 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 alive13:08:28 - 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 alive13:08:28 - Sent master public key to worker instance 'i-e26f0a8d'.13:08:33 - Instance 'i-e06f0a8f' reported alive13:08:33 - Sent master public key to worker instance 'i-e06f0a8f'.13:08:33 - Adding instance i-e46f0a8b to SGE Execution Host list13:08:44 - Successfully added instance 'i-e46f0a8b' to SGE13:08:44 - Waiting on worker instance 'i-e46f0a8b' to configure itself...13:08:44 - Instance 'i-e26f0a8d' already in SGE's @allhosts13:08:44 - Waiting on worker instance 'i-e26f0a8d' to configure itself...13:08:45 - Instance 'i-e06f0a8f' already in SGE's @allhosts13:08:45 - Waiting on worker instance 'i-e06f0a8f' to configure itself...13:08:50 - Instance 'i-e46f0a8b' ready13:09:27 - 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'
[galaxy-user] Reload .loc files without restarting the Galaxy server?
Hi all, I am wondering if it's possible to to reload a .loc file without restarting the Galaxy server? Thanks, Luobin ___ 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/
Re: [galaxy-user] Help!!!!!! with Galaxy Cloud!!!!!
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 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 Consolehttp://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
Re: [galaxy-user] Help!!!!!! with Galaxy Cloud!!!!!
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 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. 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 starting13:05:25 - 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 1/513:05:59 - 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 application13:08:05 - 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'
Re: [galaxy-user] Help!!!!!! with Galaxy Cloud!!!!!
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 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, 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 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 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. 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 starting13:05:25 - 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 1/513:05:59 - 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
Re: [galaxy-user] Help!!!!!! with Galaxy Cloud!!!!!
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 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* 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, 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.comhttp://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.eduhttp://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.comhttp://mc/compose?to=dufau...@yahoo.com Cc: Anton Nekrutenko an...@bx.psu.eduhttp://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.comhttp://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 Consolehttp://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
