Hey Brian,

Sorry for the delayed response on this one, what you're seeing is a
consequence of how Galaxy's tool migration scripts work -- all you
should need to do is click restart one more time in the cloudman admin
UI.

-Dannon

On Thu, Mar 14, 2013 at 10:56 PM, Brian Lin <brian....@tufts.edu> wrote:
> Hi guys, I'm running into a problem with updating a completely squeaky clean
> fresh cloudman install using the current ami-da58aab3
> Once it is up and running, I have SSHed in and made sure the sample files in
> run.sh are complete.
> I hit the update button, and 3 or 4 minutes later when the daemon tries to
> restart, I get status= error.
> Is anyone else having this issue?? The only threads and posts I have found
> are from a year ago, and the line is in my run.sh.
> The ultimate goal of all this was just so that I could have a cufflinks
> version that is not 0.5.
>
> Thanks for any help anyone can provide.
>
> Brian
>
>
> Here are the logs:
>
> paster.log:
>
> /mnt/galaxyTools/galaxy-central/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/pysam/__init__.py:1:
> RuntimeWarning: __builtin__.file size changed, may indicate binary
> incompatibility
>   from csamtools import *
> python path is:
> /mnt/galaxyTools/galaxy-central/eggs/numpy-1.6.0-py2.6-linux-x86_64-ucs4.egg,
> /mnt/galaxyTools/galaxy-central/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg,
> /mnt/galaxyTools/galaxy-central/eggs/boto-2.5.2-py2.6.egg,
> /mnt/galaxyTools/galaxy-central/eggs/Fabric-1.4.2-py2.6.egg,
> /mnt/galaxyTools/galaxy-central/eggs/ssh-1.7.14-py2.6.egg,
> /mnt/galaxyTools/galaxy-central/eggs/Whoosh-0.3.18-py2.6.egg,
> /mnt/galaxyTools/galaxy-central/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs4.egg,
> /mnt/galaxyTools/galaxy-central/eggs/pycrypto-2.5-py2.6-linux-x86_64-ucs4.egg,
> /mnt/galaxyTools/galaxy-central/eggs/python_lzo-1.08_2.03_static-py2.6-linux-x86_64-ucs4.egg,
> /mnt/galaxyTools/galaxy-central/eggs/bx_python-0.7.1_7b95ff194725-py2.6-linux-x86_64-ucs4.egg,
> /mnt/galaxyTools/galaxy-central/eggs/amqplib-0.6.1-py2.6.egg,
> /mnt/galaxyTools/galaxy-central/eggs/pexpect-2.4-py2.6.egg,
> /mnt/galaxyTools/galaxy-central/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg,
> /mnt/galaxyTools/galaxy-central/eggs/Babel-0.9.4-py2.6.egg,
> /mnt/galaxyTools/galaxy-central/eggs/MarkupSafe-0.12-py2.6-linux-x86_64-ucs4.egg,
> /mnt/galaxyTools/galaxy-central/eggs/Mako-0.4.1-py2.6.egg,
> /mnt/galaxyTools/galaxy-central/eggs/WebHelpers-0.2-py2.6.egg,
> /mnt/galaxyTools/galaxy-central/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg,
> /mnt/galaxyTools/galaxy-central/eggs/WebOb-0.8.5-py2.6.egg,
> /mnt/galaxyTools/galaxy-central/eggs/Routes-1.12.3-py2.6.egg,
> /mnt/galaxyTools/galaxy-central/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg,
> /mnt/galaxyTools/galaxy-central/eggs/wchartype-0.1-py2.6.egg,
> /mnt/galaxyTools/galaxy-central/eggs/elementtree-1.2.6_20050316-py2.6.egg,
> /mnt/galaxyTools/galaxy-central/eggs/docutils-0.7-py2.6.egg,
> /mnt/galaxyTools/galaxy-central/eggs/PasteDeploy-1.5.0-py2.6.egg,
> /mnt/galaxyTools/galaxy-central/eggs/Paste-1.7.5.1-py2.6.egg,
> /mnt/galaxyTools/galaxy-central/lib, /usr/lib/python2.6/,
> /usr/lib/python2.6/plat-linux2, /usr/lib/python2.6/lib-tk,
> /usr/lib/python2.6/lib-old, /usr/lib/python2.6/lib-dynload
> tool_shed.tool_shed_registry DEBUG 2013-03-15 02:47:27,538 Loading
> references to tool sheds from tool_sheds_conf.xml
> tool_shed.tool_shed_registry DEBUG 2013-03-15 02:47:27,538 Loaded reference
> to tool shed: Galaxy main tool shed
> tool_shed.tool_shed_registry DEBUG 2013-03-15 02:47:27,538 Loaded reference
> to tool shed: Galaxy test tool shed
> galaxy.model.migrate.check DEBUG 2013-03-15 02:47:27,556 psycopg2 egg
> successfully loaded for postgres dialect
> galaxy.model.migrate.check INFO 2013-03-15 02:47:27,633 At database version
> 114
> tool_shed.galaxy_install.migrate.check DEBUG 2013-03-15 02:47:27,643
> psycopg2 egg successfully loaded for postgres dialect
> Traceback (most recent call last):
>   File
> "/mnt/galaxyTools/galaxy-central/lib/galaxy/webapps/galaxy/buildapp.py",
> line 37, in app_factory
>     app = UniverseApplication( global_conf = global_conf, **kwargs )
>   File "/mnt/galaxyTools/galaxy-central/lib/galaxy/app.py", line 54, in
> __init__
>     verify_tools( self, db_url, kwargs.get( 'global_conf', {} ).get(
> '__file__', None ), self.config.database_engine_options )
>   File
> "/mnt/galaxyTools/galaxy-central/lib/tool_shed/galaxy_install/migrate/check.py",
> line 145, in verify_tools
>     raise Exception( msg )
> Exception:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>
> Console Log:
>
> 02:46:56 - Removing 'Galaxy' service
> 02:46:56 - Shutting down Galaxy...
> 02:47:25 - Starting Galaxy...
> 02:47:25 - Galaxy service state changed from 'Shut down' to 'Starting'
> 02:47:26 - Saved file 'persistent_data.yaml' to bucket
> 'cm-5b0fce1cf71e5f439fc17473dd4dcd1d'
> 02:48:28 - Galaxy daemon not running.
> 02:48:28 - Galaxy service state changed from 'Starting' to 'Error'
> 02:48:29 - Saved file 'persistent_data.yaml' to bucket
> 'cm-5b0fce1cf71e5f439fc17473dd4dcd1d'
> 02:49:30 - Galaxy daemon not running.
>
> pgSQL.log:
>
> LOG:  database system was shut down at 2013-03-15 02:11:48 UTC
> LOG:  autovacuum launcher started
> LOG:  database system is ready to accept connections
> ERROR:  relation "page_revision" does not exist
> STATEMENT:  ALTER TABLE page ADD CONSTRAINT page_latest_revision_id_fk
> FOREIGN KEY(latest_revision_id) REFERENCES page_revision (id)
> ERROR:  relation "visualization_revision" does not exist
> STATEMENT:  ALTER TABLE visualization ADD CONSTRAINT
> visualization_latest_revision_id_fk FOREIGN KEY(latest_revision_id)
> REFERENCES visualization_revision (id)
> LOG:  unexpected EOF on client connection
>
> SGE log:
>
> 03/15/2013 01:12:20|  main|ip-10-149-20-174|I|read job database with 0
> entries in 0 seconds
> 03/15/2013 01:12:20|  main|ip-10-149-20-174|E|error opening file
> "/opt/sge/default/common/./sched_configuration" for reading: No such file or
> directory
> 03/15/2013 01:12:20|  main|ip-10-149-20-174|E|error opening file
> "/opt/sge/default/spool/qmaster/./sharetree" for reading: No such file or
> directory
> 03/15/2013 01:12:20|  main|ip-10-149-20-174|I|qmaster hard descriptor limit
> is set to 8192
> 03/15/2013 01:12:20|  main|ip-10-149-20-174|I|qmaster soft descriptor limit
> is set to 8192
> 03/15/2013 01:12:20|  main|ip-10-149-20-174|I|qmaster will use max. 8172
> file descriptors for communication
> 03/15/2013 01:12:20|  main|ip-10-149-20-174|I|qmaster will accept max. 99
> dynamic event clients
> 03/15/2013 01:12:20|  main|ip-10-149-20-174|I|starting up GE 6.2u5
> (lx24-amd64)
> 03/15/2013 01:12:20|  main|ip-10-149-20-174|W|can't open job sequence number
> file "jobseqnum": for reading: No such file or directory -- guessing next
> number
> 03/15/2013 01:12:20|  main|ip-10-149-20-174|W|can't open ar sequence number
> file "arseqnum": for reading: No such file or directory -- guessing next
> number
> 03/15/2013 01:12:21|worker|ip-10-149-20-174|E|adminhost
> "ip-10-149-20-174.ec2.internal" already exists
> 03/15/2013 01:12:21|worker|ip-10-149-20-174|E|adminhost
> "ip-10-149-20-174.ec2.internal" already exists
> 03/15/2013 02:46:57|listen|ip-10-149-20-174|E|commlib error: got read error
> (closing "ip-10-149-20-174.ec2.internal/drmaa/416")
>
>
> --
> Brian Lin
> cont...@brian-lin.com
> brian....@tufts.edu
>
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