Re: [galaxy-dev] Cannot update Cloudman from a clean install on EC2?
It looks like the update didn't merge correctly and shed_tool_data_table_conf.xml.sample (and potentially others, looking at `hg diff run.sh` on a new instance, after updating to central's tip) got left out of run.sh. To fix this, you can update run.sh to include the files currently left out: shed_tool_data_table_conf.xml.sample data_manager_conf.xml.sample shed_data_manager_conf.xml.sample Or if you'd rather not tweak the startup script you can always just copy those .sample files over to the root names (so, `cp shed_tool_data_table_conf.xml.sample shed_tool_data_table_conf.xml` for instance). On Thu, Mar 21, 2013 at 4:05 PM, Brian Lin wrote: > Hi, no problem at all, I'm still trying to get this to work, so the response > was much appreciated! > I setup a new vanilla instance, updated it, got the same error and then > proceeded to restart it 3 more times. > The galaxy log is pasted below. Any ideas on what might be going wrong? > Thanks again! > Brian > > galaxy.tools.data DEBUG 2013-03-21 18:00:55,518 Loaded tool data table > 'lastz_seqs' > galaxy.tools.data DEBUG 2013-03-21 18:00:55,518 Loaded tool data table > 'perm_base_indexes' > galaxy.tools.data DEBUG 2013-03-21 18:00:55,518 Loaded tool data table > 'perm_color_indexes' > galaxy.tools.data DEBUG 2013-03-21 18:00:55,518 Loaded tool data table > 'sam_fa_indexes' > galaxy.tools.data DEBUG 2013-03-21 18:00:55,519 Loaded tool data table > 'picard_indexes' > galaxy.tools.data DEBUG 2013-03-21 18:00:55,519 Loaded tool data table > 'srma_indexes' > galaxy.tools.data DEBUG 2013-03-21 18:00:55,519 Loaded tool data table > 'tophat_indexes' > galaxy.tools.data DEBUG 2013-03-21 18:00:55,519 Loaded tool data table > 'mosaik_indexes' > galaxy.tools.data DEBUG 2013-03-21 18:00:55,519 Loaded tool data table > 'sam_indexes' > galaxy.tools.data DEBUG 2013-03-21 18:00:55,520 Loaded tool data table > 'twobit' > galaxy.tools.data DEBUG 2013-03-21 18:00:55,520 Loaded tool data table > 'lift_over' > 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 93, in > __init__ > from_shed_config=True ) > File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tools/data/__init__.py", > line 46, in load_from_config_file > tree = util.parse_xml( config_filename ) > File "/mnt/galaxyTools/galaxy-central/lib/galaxy/util/__init__.py", line > 143, in parse_xml > tree = ElementTree.parse(fname) > File > "/mnt/galaxyTools/galaxy-central/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py", > line 859, in parse > tree.parse(source, parser) > File > "/mnt/galaxyTools/galaxy-central/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py", > line 576, in parse > source = open(source, "rb") > IOError: [Errno 2] No such file or directory: > './shed_tool_data_table_conf.xml' > Removing PID file paster.pid > /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/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-
Re: [galaxy-dev] Cannot update Cloudman from a clean install on EC2?
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 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
[galaxy-dev] Cannot update Cloudman from a clean install on EC2?
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_revis
