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")
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.Lin@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 contact@brian-lin.com brian.lin@tufts.edu
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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-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 2013-03-21 18:03:20,620 Loading references to tool sheds from tool_sheds_conf.xml tool_shed.tool_shed_registry DEBUG 2013-03-21 18:03:20,620 Loaded reference to tool shed: Galaxy main tool shed tool_shed.tool_shed_registry DEBUG 2013-03-21 18:03:20,620 Loaded reference to tool shed: Galaxy test tool shed galaxy.model.migrate.check DEBUG 2013-03-21 18:03:20,640 psycopg2 egg successfully loaded for postgres dialect galaxy.model.migrate.check INFO 2013-03-21 18:03:20,782 At database version 114 tool_shed.galaxy_install.migrate.check DEBUG 2013-03-21 18:03:20,793 psycopg2 egg successfully loaded for postgres dialect tool_shed.galaxy_install.migrate.check INFO 2013-03-21 18:03:20,808 At migrate_tools version 7 galaxy.model.custom_types DEBUG 2013-03-21 18:03:20,812 psycopg2 egg successfully loaded for postgres dialect galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,012 Loading datatypes from datatypes_conf.xml galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,019 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Vcf' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,019 Loaded sniffer for datatype 'galaxy.datatypes.binary:TwoBit' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,019 Loaded sniffer for datatype 'galaxy.datatypes.binary:Bam' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,019 Loaded sniffer for datatype 'galaxy.datatypes.binary:Sff' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,020 Loaded sniffer for datatype 'galaxy.datatypes.xml:Phyloxml' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,020 Loaded sniffer for datatype 'galaxy.datatypes.xml:GenericXml' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,020 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Maf' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,020 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Lav' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,020 Loaded sniffer for datatype 'galaxy.datatypes.sequence:csFasta' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,020 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScoreSOLiD' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,020 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScore454' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,020 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fasta' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,020 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fastq' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,020 Loaded sniffer for datatype 'galaxy.datatypes.interval:Wiggle' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,021 Loaded sniffer for datatype 'galaxy.datatypes.images:Html' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,021 Loaded sniffer for datatype 'galaxy.datatypes.images:Pdf' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,021 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Axt' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,021 Loaded sniffer for datatype 'galaxy.datatypes.interval:Bed' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,021 Loaded sniffer for datatype 'galaxy.datatypes.interval:CustomTrack' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,021 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gtf' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,021 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,021 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff3' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,021 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Pileup' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,022 Loaded sniffer for datatype 'galaxy.datatypes.interval:Interval' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,022 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Sam' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,022 Loaded sniffer for datatype 'galaxy.datatypes.data:Newick' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,022 Loaded sniffer for datatype 'galaxy.datatypes.data:Nexus' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,022 Loaded sniffer for datatype 'galaxy.datatypes.images:Jpg' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,022 Loaded sniffer for datatype 'galaxy.datatypes.images:Png' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,022 Loaded sniffer for datatype 'galaxy.datatypes.images:Tiff' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,022 Loaded sniffer for datatype 'galaxy.datatypes.images:Bmp' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,022 Loaded sniffer for datatype 'galaxy.datatypes.images:Gif' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,022 Loaded sniffer for datatype 'galaxy.datatypes.images:Im' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,023 Loaded sniffer for datatype 'galaxy.datatypes.images:Pcd' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,023 Loaded sniffer for datatype 'galaxy.datatypes.images:Pcx' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,023 Loaded sniffer for datatype 'galaxy.datatypes.images:Ppm' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,023 Loaded sniffer for datatype 'galaxy.datatypes.images:Psd' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,023 Loaded sniffer for datatype 'galaxy.datatypes.images:Xbm' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,023 Loaded sniffer for datatype 'galaxy.datatypes.images:Rgb' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,023 Loaded sniffer for datatype 'galaxy.datatypes.images:Pbm' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,023 Loaded sniffer for datatype 'galaxy.datatypes.images:Pgm' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,023 Loaded sniffer for datatype 'galaxy.datatypes.images:Xpm' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,024 Loaded sniffer for datatype 'galaxy.datatypes.images:Eps' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,024 Loaded sniffer for datatype 'galaxy.datatypes.images:Rast' galaxy.tools.data DEBUG 2013-03-21 18:03:21,039 Loaded tool data table 'all_fasta' galaxy.tools.data DEBUG 2013-03-21 18:03:21,039 Loaded tool data table 'blastdb' galaxy.tools.data DEBUG 2013-03-21 18:03:21,039 Loaded tool data table 'bowtie_indexes' galaxy.tools.data DEBUG 2013-03-21 18:03:21,039 Loaded tool data table 'bowtie_indexes_color' galaxy.tools.data DEBUG 2013-03-21 18:03:21,039 Loaded tool data table 'bwa_indexes' galaxy.tools.data DEBUG 2013-03-21 18:03:21,040 Loaded tool data table 'lastz_seqs' galaxy.tools.data DEBUG 2013-03-21 18:03:21,040 Loaded tool data table 'perm_base_indexes' galaxy.tools.data DEBUG 2013-03-21 18:03:21,040 Loaded tool data table 'perm_color_indexes' galaxy.tools.data DEBUG 2013-03-21 18:03:21,040 Loaded tool data table 'sam_fa_indexes' galaxy.tools.data DEBUG 2013-03-21 18:03:21,040 Loaded tool data table 'picard_indexes' galaxy.tools.data DEBUG 2013-03-21 18:03:21,041 Loaded tool data table 'srma_indexes' galaxy.tools.data DEBUG 2013-03-21 18:03:21,041 Loaded tool data table 'tophat_indexes' galaxy.tools.data DEBUG 2013-03-21 18:03:21,041 Loaded tool data table 'mosaik_indexes' galaxy.tools.data DEBUG 2013-03-21 18:03:21,041 Loaded tool data table 'sam_indexes' galaxy.tools.data DEBUG 2013-03-21 18:03:21,042 Loaded tool data table 'twobit' galaxy.tools.data DEBUG 2013-03-21 18:03:21,042 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-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 2013-03-21 19:46:36,999 Loading references to tool sheds from tool_sheds_conf.xml tool_shed.tool_shed_registry DEBUG 2013-03-21 19:46:37,000 Loaded reference to tool shed: Galaxy main tool shed tool_shed.tool_shed_registry DEBUG 2013-03-21 19:46:37,000 Loaded reference to tool shed: Galaxy test tool shed galaxy.model.migrate.check DEBUG 2013-03-21 19:46:37,021 psycopg2 egg successfully loaded for postgres dialect galaxy.model.migrate.check INFO 2013-03-21 19:46:37,158 At database version 114 tool_shed.galaxy_install.migrate.check DEBUG 2013-03-21 19:46:37,169 psycopg2 egg successfully loaded for postgres dialect tool_shed.galaxy_install.migrate.check INFO 2013-03-21 19:46:37,185 At migrate_tools version 7 galaxy.model.custom_types DEBUG 2013-03-21 19:46:37,188 psycopg2 egg successfully loaded for postgres dialect galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,399 Loading datatypes from datatypes_conf.xml galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,406 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Vcf' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,406 Loaded sniffer for datatype 'galaxy.datatypes.binary:TwoBit' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,406 Loaded sniffer for datatype 'galaxy.datatypes.binary:Bam' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,407 Loaded sniffer for datatype 'galaxy.datatypes.binary:Sff' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,407 Loaded sniffer for datatype 'galaxy.datatypes.xml:Phyloxml' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,407 Loaded sniffer for datatype 'galaxy.datatypes.xml:GenericXml' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,407 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Maf' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,407 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Lav' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,407 Loaded sniffer for datatype 'galaxy.datatypes.sequence:csFasta' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,407 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScoreSOLiD' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,407 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScore454' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,407 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fasta' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,407 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fastq' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,408 Loaded sniffer for datatype 'galaxy.datatypes.interval:Wiggle' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,408 Loaded sniffer for datatype 'galaxy.datatypes.images:Html' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,408 Loaded sniffer for datatype 'galaxy.datatypes.images:Pdf' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,408 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Axt' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,408 Loaded sniffer for datatype 'galaxy.datatypes.interval:Bed' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,408 Loaded sniffer for datatype 'galaxy.datatypes.interval:CustomTrack' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,408 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gtf' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,408 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,409 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff3' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,409 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Pileup' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,409 Loaded sniffer for datatype 'galaxy.datatypes.interval:Interval' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,409 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Sam' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,409 Loaded sniffer for datatype 'galaxy.datatypes.data:Newick' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,409 Loaded sniffer for datatype 'galaxy.datatypes.data:Nexus' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,409 Loaded sniffer for datatype 'galaxy.datatypes.images:Jpg' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,409 Loaded sniffer for datatype 'galaxy.datatypes.images:Png' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,409 Loaded sniffer for datatype 'galaxy.datatypes.images:Tiff' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,409 Loaded sniffer for datatype 'galaxy.datatypes.images:Bmp' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,410 Loaded sniffer for datatype 'galaxy.datatypes.images:Gif' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,410 Loaded sniffer for datatype 'galaxy.datatypes.images:Im' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,410 Loaded sniffer for datatype 'galaxy.datatypes.images:Pcd' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,410 Loaded sniffer for datatype 'galaxy.datatypes.images:Pcx' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,410 Loaded sniffer for datatype 'galaxy.datatypes.images:Ppm' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,410 Loaded sniffer for datatype 'galaxy.datatypes.images:Psd' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,410 Loaded sniffer for datatype 'galaxy.datatypes.images:Xbm' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,410 Loaded sniffer for datatype 'galaxy.datatypes.images:Rgb' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,410 Loaded sniffer for datatype 'galaxy.datatypes.images:Pbm' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,411 Loaded sniffer for datatype 'galaxy.datatypes.images:Pgm' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,411 Loaded sniffer for datatype 'galaxy.datatypes.images:Xpm' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,411 Loaded sniffer for datatype 'galaxy.datatypes.images:Eps' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,411 Loaded sniffer for datatype 'galaxy.datatypes.images:Rast' galaxy.tools.data DEBUG 2013-03-21 19:46:37,425 Loaded tool data table 'all_fasta' galaxy.tools.data DEBUG 2013-03-21 19:46:37,426 Loaded tool data table 'blastdb' galaxy.tools.data DEBUG 2013-03-21 19:46:37,426 Loaded tool data table 'bowtie_indexes' galaxy.tools.data DEBUG 2013-03-21 19:46:37,426 Loaded tool data table 'bowtie_indexes_color' galaxy.tools.data DEBUG 2013-03-21 19:46:37,426 Loaded tool data table 'bwa_indexes' galaxy.tools.data DEBUG 2013-03-21 19:46:37,426 Loaded tool data table 'lastz_seqs' galaxy.tools.data DEBUG 2013-03-21 19:46:37,427 Loaded tool data table 'perm_base_indexes' galaxy.tools.data DEBUG 2013-03-21 19:46:37,427 Loaded tool data table 'perm_color_indexes' galaxy.tools.data DEBUG 2013-03-21 19:46:37,427 Loaded tool data table 'sam_fa_indexes' galaxy.tools.data DEBUG 2013-03-21 19:46:37,427 Loaded tool data table 'picard_indexes' galaxy.tools.data DEBUG 2013-03-21 19:46:37,427 Loaded tool data table 'srma_indexes' galaxy.tools.data DEBUG 2013-03-21 19:46:37,428 Loaded tool data table 'tophat_indexes' galaxy.tools.data DEBUG 2013-03-21 19:46:37,428 Loaded tool data table 'mosaik_indexes' galaxy.tools.data DEBUG 2013-03-21 19:46:37,428 Loaded tool data table 'sam_indexes' galaxy.tools.data DEBUG 2013-03-21 19:46:37,428 Loaded tool data table 'twobit' galaxy.tools.data DEBUG 2013-03-21 19:46:37,428 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
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 Brian.Lin@tufts.edu 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-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 2013-03-21 18:03:20,620 Loading references to tool sheds from tool_sheds_conf.xml tool_shed.tool_shed_registry DEBUG 2013-03-21 18:03:20,620 Loaded reference to tool shed: Galaxy main tool shed tool_shed.tool_shed_registry DEBUG 2013-03-21 18:03:20,620 Loaded reference to tool shed: Galaxy test tool shed galaxy.model.migrate.check DEBUG 2013-03-21 18:03:20,640 psycopg2 egg successfully loaded for postgres dialect galaxy.model.migrate.check INFO 2013-03-21 18:03:20,782 At database version 114 tool_shed.galaxy_install.migrate.check DEBUG 2013-03-21 18:03:20,793 psycopg2 egg successfully loaded for postgres dialect tool_shed.galaxy_install.migrate.check INFO 2013-03-21 18:03:20,808 At migrate_tools version 7 galaxy.model.custom_types DEBUG 2013-03-21 18:03:20,812 psycopg2 egg successfully loaded for postgres dialect galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,012 Loading datatypes from datatypes_conf.xml galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,019 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Vcf' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,019 Loaded sniffer for datatype 'galaxy.datatypes.binary:TwoBit' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,019 Loaded sniffer for datatype 'galaxy.datatypes.binary:Bam' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,019 Loaded sniffer for datatype 'galaxy.datatypes.binary:Sff' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,020 Loaded sniffer for datatype 'galaxy.datatypes.xml:Phyloxml' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,020 Loaded sniffer for datatype 'galaxy.datatypes.xml:GenericXml' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,020 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Maf' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,020 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Lav' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,020 Loaded sniffer for datatype 'galaxy.datatypes.sequence:csFasta' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,020 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScoreSOLiD' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,020 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScore454' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,020 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fasta' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,020 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fastq' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,020 Loaded sniffer for datatype 'galaxy.datatypes.interval:Wiggle' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,021 Loaded sniffer for datatype 'galaxy.datatypes.images:Html' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,021 Loaded sniffer for datatype 'galaxy.datatypes.images:Pdf' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,021 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Axt' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,021 Loaded sniffer for datatype 'galaxy.datatypes.interval:Bed' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,021 Loaded sniffer for datatype 'galaxy.datatypes.interval:CustomTrack' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,021 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gtf' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,021 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,021 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff3' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,021 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Pileup' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,022 Loaded sniffer for datatype 'galaxy.datatypes.interval:Interval' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,022 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Sam' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,022 Loaded sniffer for datatype 'galaxy.datatypes.data:Newick' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,022 Loaded sniffer for datatype 'galaxy.datatypes.data:Nexus' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,022 Loaded sniffer for datatype 'galaxy.datatypes.images:Jpg' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,022 Loaded sniffer for datatype 'galaxy.datatypes.images:Png' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,022 Loaded sniffer for datatype 'galaxy.datatypes.images:Tiff' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,022 Loaded sniffer for datatype 'galaxy.datatypes.images:Bmp' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,022 Loaded sniffer for datatype 'galaxy.datatypes.images:Gif' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,022 Loaded sniffer for datatype 'galaxy.datatypes.images:Im' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,023 Loaded sniffer for datatype 'galaxy.datatypes.images:Pcd' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,023 Loaded sniffer for datatype 'galaxy.datatypes.images:Pcx' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,023 Loaded sniffer for datatype 'galaxy.datatypes.images:Ppm' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,023 Loaded sniffer for datatype 'galaxy.datatypes.images:Psd' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,023 Loaded sniffer for datatype 'galaxy.datatypes.images:Xbm' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,023 Loaded sniffer for datatype 'galaxy.datatypes.images:Rgb' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,023 Loaded sniffer for datatype 'galaxy.datatypes.images:Pbm' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,023 Loaded sniffer for datatype 'galaxy.datatypes.images:Pgm' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,023 Loaded sniffer for datatype 'galaxy.datatypes.images:Xpm' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,024 Loaded sniffer for datatype 'galaxy.datatypes.images:Eps' galaxy.datatypes.registry DEBUG 2013-03-21 18:03:21,024 Loaded sniffer for datatype 'galaxy.datatypes.images:Rast' galaxy.tools.data DEBUG 2013-03-21 18:03:21,039 Loaded tool data table 'all_fasta' galaxy.tools.data DEBUG 2013-03-21 18:03:21,039 Loaded tool data table 'blastdb' galaxy.tools.data DEBUG 2013-03-21 18:03:21,039 Loaded tool data table 'bowtie_indexes' galaxy.tools.data DEBUG 2013-03-21 18:03:21,039 Loaded tool data table 'bowtie_indexes_color' galaxy.tools.data DEBUG 2013-03-21 18:03:21,039 Loaded tool data table 'bwa_indexes' galaxy.tools.data DEBUG 2013-03-21 18:03:21,040 Loaded tool data table 'lastz_seqs' galaxy.tools.data DEBUG 2013-03-21 18:03:21,040 Loaded tool data table 'perm_base_indexes' galaxy.tools.data DEBUG 2013-03-21 18:03:21,040 Loaded tool data table 'perm_color_indexes' galaxy.tools.data DEBUG 2013-03-21 18:03:21,040 Loaded tool data table 'sam_fa_indexes' galaxy.tools.data DEBUG 2013-03-21 18:03:21,040 Loaded tool data table 'picard_indexes' galaxy.tools.data DEBUG 2013-03-21 18:03:21,041 Loaded tool data table 'srma_indexes' galaxy.tools.data DEBUG 2013-03-21 18:03:21,041 Loaded tool data table 'tophat_indexes' galaxy.tools.data DEBUG 2013-03-21 18:03:21,041 Loaded tool data table 'mosaik_indexes' galaxy.tools.data DEBUG 2013-03-21 18:03:21,041 Loaded tool data table 'sam_indexes' galaxy.tools.data DEBUG 2013-03-21 18:03:21,042 Loaded tool data table 'twobit' galaxy.tools.data DEBUG 2013-03-21 18:03:21,042 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-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 2013-03-21 19:46:36,999 Loading references to tool sheds from tool_sheds_conf.xml tool_shed.tool_shed_registry DEBUG 2013-03-21 19:46:37,000 Loaded reference to tool shed: Galaxy main tool shed tool_shed.tool_shed_registry DEBUG 2013-03-21 19:46:37,000 Loaded reference to tool shed: Galaxy test tool shed galaxy.model.migrate.check DEBUG 2013-03-21 19:46:37,021 psycopg2 egg successfully loaded for postgres dialect galaxy.model.migrate.check INFO 2013-03-21 19:46:37,158 At database version 114 tool_shed.galaxy_install.migrate.check DEBUG 2013-03-21 19:46:37,169 psycopg2 egg successfully loaded for postgres dialect tool_shed.galaxy_install.migrate.check INFO 2013-03-21 19:46:37,185 At migrate_tools version 7 galaxy.model.custom_types DEBUG 2013-03-21 19:46:37,188 psycopg2 egg successfully loaded for postgres dialect galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,399 Loading datatypes from datatypes_conf.xml galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,406 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Vcf' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,406 Loaded sniffer for datatype 'galaxy.datatypes.binary:TwoBit' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,406 Loaded sniffer for datatype 'galaxy.datatypes.binary:Bam' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,407 Loaded sniffer for datatype 'galaxy.datatypes.binary:Sff' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,407 Loaded sniffer for datatype 'galaxy.datatypes.xml:Phyloxml' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,407 Loaded sniffer for datatype 'galaxy.datatypes.xml:GenericXml' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,407 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Maf' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,407 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Lav' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,407 Loaded sniffer for datatype 'galaxy.datatypes.sequence:csFasta' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,407 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScoreSOLiD' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,407 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScore454' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,407 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fasta' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,407 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fastq' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,408 Loaded sniffer for datatype 'galaxy.datatypes.interval:Wiggle' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,408 Loaded sniffer for datatype 'galaxy.datatypes.images:Html' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,408 Loaded sniffer for datatype 'galaxy.datatypes.images:Pdf' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,408 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Axt' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,408 Loaded sniffer for datatype 'galaxy.datatypes.interval:Bed' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,408 Loaded sniffer for datatype 'galaxy.datatypes.interval:CustomTrack' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,408 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gtf' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,408 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,409 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff3' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,409 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Pileup' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,409 Loaded sniffer for datatype 'galaxy.datatypes.interval:Interval' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,409 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Sam' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,409 Loaded sniffer for datatype 'galaxy.datatypes.data:Newick' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,409 Loaded sniffer for datatype 'galaxy.datatypes.data:Nexus' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,409 Loaded sniffer for datatype 'galaxy.datatypes.images:Jpg' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,409 Loaded sniffer for datatype 'galaxy.datatypes.images:Png' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,409 Loaded sniffer for datatype 'galaxy.datatypes.images:Tiff' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,409 Loaded sniffer for datatype 'galaxy.datatypes.images:Bmp' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,410 Loaded sniffer for datatype 'galaxy.datatypes.images:Gif' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,410 Loaded sniffer for datatype 'galaxy.datatypes.images:Im' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,410 Loaded sniffer for datatype 'galaxy.datatypes.images:Pcd' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,410 Loaded sniffer for datatype 'galaxy.datatypes.images:Pcx' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,410 Loaded sniffer for datatype 'galaxy.datatypes.images:Ppm' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,410 Loaded sniffer for datatype 'galaxy.datatypes.images:Psd' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,410 Loaded sniffer for datatype 'galaxy.datatypes.images:Xbm' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,410 Loaded sniffer for datatype 'galaxy.datatypes.images:Rgb' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,410 Loaded sniffer for datatype 'galaxy.datatypes.images:Pbm' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,411 Loaded sniffer for datatype 'galaxy.datatypes.images:Pgm' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,411 Loaded sniffer for datatype 'galaxy.datatypes.images:Xpm' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,411 Loaded sniffer for datatype 'galaxy.datatypes.images:Eps' galaxy.datatypes.registry DEBUG 2013-03-21 19:46:37,411 Loaded sniffer for datatype 'galaxy.datatypes.images:Rast' galaxy.tools.data DEBUG 2013-03-21 19:46:37,425 Loaded tool data table 'all_fasta' galaxy.tools.data DEBUG 2013-03-21 19:46:37,426 Loaded tool data table 'blastdb' galaxy.tools.data DEBUG 2013-03-21 19:46:37,426 Loaded tool data table 'bowtie_indexes' galaxy.tools.data DEBUG 2013-03-21 19:46:37,426 Loaded tool data table 'bowtie_indexes_color' galaxy.tools.data DEBUG 2013-03-21 19:46:37,426 Loaded tool data table 'bwa_indexes' galaxy.tools.data DEBUG 2013-03-21 19:46:37,426 Loaded tool data table 'lastz_seqs' galaxy.tools.data DEBUG 2013-03-21 19:46:37,427 Loaded tool data table 'perm_base_indexes' galaxy.tools.data DEBUG 2013-03-21 19:46:37,427 Loaded tool data table 'perm_color_indexes' galaxy.tools.data DEBUG 2013-03-21 19:46:37,427 Loaded tool data table 'sam_fa_indexes' galaxy.tools.data DEBUG 2013-03-21 19:46:37,427 Loaded tool data table 'picard_indexes' galaxy.tools.data DEBUG 2013-03-21 19:46:37,427 Loaded tool data table 'srma_indexes' galaxy.tools.data DEBUG 2013-03-21 19:46:37,428 Loaded tool data table 'tophat_indexes' galaxy.tools.data DEBUG 2013-03-21 19:46:37,428 Loaded tool data table 'mosaik_indexes' galaxy.tools.data DEBUG 2013-03-21 19:46:37,428 Loaded tool data table 'sam_indexes' galaxy.tools.data DEBUG 2013-03-21 19:46:37,428 Loaded tool data table 'twobit' galaxy.tools.data DEBUG 2013-03-21 19:46:37,428 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
-- Brian Lin contact@brian-lin.com brian.lin@tufts.edu
On Thu, Mar 21, 2013 at 8:41 AM, Dannon Baker dannon.baker@gmail.com wrote:
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.Lin@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 contact@brian-lin.com brian.lin@tufts.edu
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Brian Lin -
Dannon Baker