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-99e0c68a2fe11e32a592e36abd1f2c38' to '/mnt/galaxyTools/galaxy-central/universe_wsgi.ini'. * 19:01:25 - Retrieved file 'tool_conf.xml.cloud' from bucket 'cm-99e0c68a2fe11e32a592e36abd1f2c38' to '/mnt/galaxyTools/galaxy-central/tool_conf.xml'. * 19:01:25 - Retrieved file 'tool_data_table_conf.xml.cloud' from bucket 'cm-99e0c68a2fe11e32a592e36abd1f2c38' 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 [eafgan@emory.edu] Sent: Tuesday, June 28, 2011 11:46 AM To: Joseph Hargitai Cc: 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.hargitai@einstein.yu.edu<mailto:joseph.hargitai@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 ___________________________________________________________ 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>. 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/

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 [eafgan@emory.edu] Sent: Tuesday, June 28, 2011 3:30 PM To: Joseph Hargitai Cc: 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.hargitai@einstein.yu.edu<mailto:joseph.hargitai@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-99e0c68a2fe11e32a592e36abd1f2c38' to '/mnt/galaxyTools/galaxy-central/universe_wsgi.ini'. * 19:01:25 - Retrieved file 'tool_conf.xml.cloud' from bucket 'cm-99e0c68a2fe11e32a592e36abd1f2c38' to '/mnt/galaxyTools/galaxy-central/tool_conf.xml'. * 19:01:25 - Retrieved file 'tool_data_table_conf.xml.cloud' from bucket 'cm-99e0c68a2fe11e32a592e36abd1f2c38' 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 [eafgan@emory.edu<mailto:eafgan@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> 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.hargitai@einstein.yu.edu<mailto:joseph.hargitai@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 ___________________________________________________________ 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>. 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/

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_...). 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.hargitai@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 [eafgan@emory.edu] Sent: Tuesday, June 28, 2011 3:30 PM

To: Joseph Hargitai Cc: 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.hargitai@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-99e0c68a2fe11e32a592e36abd1f2c38' to '/mnt/galaxyTools/galaxy-central/universe_wsgi.ini'. • 19:01:25 - Retrieved file 'tool_conf.xml.cloud' from bucket 'cm-99e0c68a2fe11e32a592e36abd1f2c38' to '/mnt/galaxyTools/galaxy-central/tool_conf.xml'. • 19:01:25 - Retrieved file 'tool_data_table_conf.xml.cloud' from bucket 'cm-99e0c68a2fe11e32a592e36abd1f2c38' 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 [eafgan@emory.edu] Sent: Tuesday, June 28, 2011 11:46 AM To: Joseph Hargitai Cc: 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.hargitai@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

___________________________________________________________ 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/

___________________________________________________________ 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/

-- Research Scientist Department of Biostatistics Associate Director Bioinformatics Core Harvard School of Public Health Skype: ohofmann Phone: +1 (617) 365 0984

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 <ohofmann@hsph.harvard.edu <mailto:ohofmann@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_...). 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.hargitai@einstein.yu.edu <mailto:joseph.hargitai@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 [eafgan@emory.edu <mailto:eafgan@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> > 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.hargitai@einstein.yu.edu <mailto:joseph.hargitai@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-99e0c68a2fe11e32a592e36abd1f2c38' to '/mnt/galaxyTools/galaxy-central/universe_wsgi.ini'. > • 19:01:25 - Retrieved file 'tool_conf.xml.cloud' from bucket 'cm-99e0c68a2fe11e32a592e36abd1f2c38' to '/mnt/galaxyTools/galaxy-central/tool_conf.xml'. > • 19:01:25 - Retrieved file 'tool_data_table_conf.xml.cloud' from bucket 'cm-99e0c68a2fe11e32a592e36abd1f2c38' 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 [eafgan@emory.edu <mailto:eafgan@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> > 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.hargitai@einstein.yu.edu <mailto:joseph.hargitai@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 > > > ___________________________________________________________ > 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>. 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/ > > > > ___________________________________________________________ > 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>. 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/

-- 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>

-- Research Scientist Department of Biostatistics Associate Director Bioinformatics Core Harvard School of Public Health Skype: ohofmann Phone: +1 (617) 365 0984

throws this: {"updated": false} ________________________________ From: Enis Afgan [eafgan@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 <ohofmann@hsph.harvard.edu<mailto:ohofmann@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 <ohofmann@hsph.harvard.edu<mailto:ohofmann@hsph.harvard.edu> <mailto:ohofmann@hsph.harvard.edu<mailto:ohofmann@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_...). 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.hargitai@einstein.yu.edu<mailto:joseph.hargitai@einstein.yu.edu> <mailto:joseph.hargitai@einstein.yu.edu<mailto:joseph.hargitai@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 [eafgan@emory.edu<mailto:eafgan@emory.edu> <mailto:eafgan@emory.edu<mailto:eafgan@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-user@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.hargitai@einstein.yu.edu<mailto:joseph.hargitai@einstein.yu.edu> <mailto:joseph.hargitai@einstein.yu.edu<mailto:joseph.hargitai@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-99e0c68a2fe11e32a592e36abd1f2c38' to '/mnt/galaxyTools/galaxy-central/universe_wsgi.ini'. > • 19:01:25 - Retrieved file 'tool_conf.xml.cloud' from bucket 'cm-99e0c68a2fe11e32a592e36abd1f2c38' to '/mnt/galaxyTools/galaxy-central/tool_conf.xml'. > • 19:01:25 - Retrieved file 'tool_data_table_conf.xml.cloud' from bucket 'cm-99e0c68a2fe11e32a592e36abd1f2c38' 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 [eafgan@emory.edu<mailto:eafgan@emory.edu> <mailto:eafgan@emory.edu<mailto:eafgan@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-user@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.hargitai@einstein.yu.edu<mailto:joseph.hargitai@einstein.yu.edu> <mailto:joseph.hargitai@einstein.yu.edu<mailto:joseph.hargitai@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 > > > ___________________________________________________________ > 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 > > To manage your subscriptions to this and other Galaxy lists, > 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 > > 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>

where do i find the 'cloudman' bucket? j ________________________________ From: Enis Afgan [eafgan@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.hargitai@einstein.yu.edu<mailto:joseph.hargitai@einstein.yu.edu>> wrote: throws this: {"updated": false} ________________________________ From: Enis Afgan [eafgan@emory.edu<mailto:eafgan@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 <ohofmann@hsph.harvard.edu<mailto:ohofmann@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 <ohofmann@hsph.harvard.edu<mailto:ohofmann@hsph.harvard.edu> <mailto:ohofmann@hsph.harvard.edu<mailto:ohofmann@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_...). 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.hargitai@einstein.yu.edu<mailto:joseph.hargitai@einstein.yu.edu> <mailto:joseph.hargitai@einstein.yu.edu<mailto:joseph.hargitai@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 [eafgan@emory.edu<mailto:eafgan@emory.edu> <mailto:eafgan@emory.edu<mailto:eafgan@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-user@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.hargitai@einstein.yu.edu<mailto:joseph.hargitai@einstein.yu.edu> <mailto:joseph.hargitai@einstein.yu.edu<mailto:joseph.hargitai@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-99e0c68a2fe11e32a592e36abd1f2c38' to '/mnt/galaxyTools/galaxy-central/universe_wsgi.ini'. > • 19:01:25 - Retrieved file 'tool_conf.xml.cloud' from bucket 'cm-99e0c68a2fe11e32a592e36abd1f2c38' to '/mnt/galaxyTools/galaxy-central/tool_conf.xml'. > • 19:01:25 - Retrieved file 'tool_data_table_conf.xml.cloud' from bucket 'cm-99e0c68a2fe11e32a592e36abd1f2c38' 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 [eafgan@emory.edu<mailto:eafgan@emory.edu> <mailto:eafgan@emory.edu<mailto:eafgan@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-user@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.hargitai@einstein.yu.edu<mailto:joseph.hargitai@einstein.yu.edu> <mailto:joseph.hargitai@einstein.yu.edu<mailto:joseph.hargitai@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 > > > ___________________________________________________________ > 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 > > To manage your subscriptions to this and other Galaxy lists, > 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 > > 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>

Enis, thanks once again, works like a charm. Updated, the CloudMan interface now has an admin page, and old data made it through the update. Best, Oliver

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.hargitai@einstein.yu.edu <mailto:joseph.hargitai@einstein.yu.edu>> wrote:

where do i find the 'cloudman' bucket?

j

------------------------------------------------------------------------ *From:* Enis Afgan [eafgan@emory.edu <mailto:eafgan@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.hargitai@einstein.yu.edu <mailto:joseph.hargitai@einstein.yu.edu>> wrote:

throws this:

{"updated": false}

------------------------------------------------------------------------ *From:* Enis Afgan [eafgan@emory.edu <mailto:eafgan@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 <ohofmann@hsph.harvard.edu <mailto:ohofmann@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 <ohofmann@hsph.harvard.edu <mailto:ohofmann@hsph.harvard.edu> <mailto:ohofmann@hsph.harvard.__edu <mailto:ohofmann@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/2... <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.hargitai@einstein.yu.__edu <mailto:joseph.hargitai@einstein.yu.edu> <mailto:joseph.hargitai@__einstein.yu.edu <mailto:joseph.hargitai@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 [eafgan@emory.edu <mailto:eafgan@emory.edu> <mailto:eafgan@emory.edu <mailto:eafgan@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-user@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.hargitai@einstein.yu.__edu <mailto:joseph.hargitai@einstein.yu.edu> <mailto:joseph.hargitai@__einstein.yu.edu <mailto:joseph.hargitai@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 [eafgan@emory.edu <mailto:eafgan@emory.edu> <mailto:eafgan@emory.edu <mailto:eafgan@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-user@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.hargitai@einstein.yu.__edu <mailto:joseph.hargitai@einstein.yu.edu> <mailto:joseph.hargitai@__einstein.yu.edu <mailto:joseph.hargitai@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 > > > _____________________________________________________________ > 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/ > > > > _____________________________________________________________ > 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>

-- Research Scientist Department of Biostatistics Associate Director Bioinformatics Core Harvard School of Public Health Skype: ohofmann Phone: +1 (617) 365 0984

The masthead on the web browser does not have an update option I can see. Is this option in a config file somewhere on the server? We used the AIM since October/ and started a new version about two weeks ago. Of course the overall idea of an upgrade is an interesting one. Eventually you want to rely on AIM, but once you start updating your configuration you move away from the gold-standard with every step. joe ________________________________ From: Enis Afgan [eafgan@emory.edu] Sent: Tuesday, June 28, 2011 3:57 PM To: Joseph Hargitai Cc: galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] cloud instance drops settings on reboot 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_...). 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. Glad you got the configuration to work, Enis On Tue, Jun 28, 2011 at 3:45 PM, Joseph Hargitai <joseph.hargitai@einstein.yu.edu<mailto:joseph.hargitai@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 [eafgan@emory.edu<mailto:eafgan@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> 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.hargitai@einstein.yu.edu<mailto:joseph.hargitai@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-99e0c68a2fe11e32a592e36abd1f2c38' to '/mnt/galaxyTools/galaxy-central/universe_wsgi.ini'. * 19:01:25 - Retrieved file 'tool_conf.xml.cloud' from bucket 'cm-99e0c68a2fe11e32a592e36abd1f2c38' to '/mnt/galaxyTools/galaxy-central/tool_conf.xml'. * 19:01:25 - Retrieved file 'tool_data_table_conf.xml.cloud' from bucket 'cm-99e0c68a2fe11e32a592e36abd1f2c38' 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 [eafgan@emory.edu<mailto:eafgan@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> 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.hargitai@einstein.yu.edu<mailto:joseph.hargitai@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 ___________________________________________________________ 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>. 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/