Re: [galaxy-dev] Server Error after fresh installation of Galaxy
On Jun 20, 2012, at 6:46 PM, Iry Witham wrote: > I have recently performed a fresh installation of Galaxy utilizing the latest > distribution and am getting a sizable number of errors when attempting to > start the server. The issue started when I performed a merge so I decided to > do the clean install as a test. The server appears to start just fine, but > with errors reported in the logs. The web0.log gives the following errors > and warnings (I am truncating the file for space): > > galaxy.model.migrate.check DEBUG 2012-06-20 18:29:20,497 psycopg2 egg > successfully loaded for postgres dialect > galaxy.model.migrate.check INFO 2012-06-20 18:29:20,599 At database version 97 > galaxy.tool_shed.migrate.check DEBUG 2012-06-20 18:29:20,630 psycopg2 egg > successfully loaded for postgres dialect > galaxy.tool_shed.migrate.check INFO 2012-06-20 18:29:20,649 At migrate_tools > version 2 > galaxy.model.custom_types DEBUG 2012-06-20 18:29:20,654 psycopg2 egg > successfully loaded for postgres dialect > galaxy.tool_shed.tool_shed_registry DEBUG 2012-06-20 18:29:20,658 Loading > references to tool sheds from tool_sheds_conf.xml > galaxy.tool_shed.tool_shed_registry DEBUG 2012-06-20 18:29:20,658 Loaded > reference to tool shed: Galaxy main tool shed > galaxy.tool_shed.tool_shed_registry DEBUG 2012-06-20 18:29:20,658 Loaded > reference to tool shed: Galaxy test tool shed > galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,014 Loading datatypes > from datatypes_conf.xml > galaxy.datatypes.registry WARNING 2012-06-20 18:29:21,015 Overriding > conflicting datatype with extension 'coverage', using datatype from > datatypes_conf.xml. > galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,025 Loaded sniffer for > datatype 'galaxy.datatypes.binary:Bam' > galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,025 Loaded sniffer for > datatype 'galaxy.datatypes.binary:Sff' > galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,025 Loaded sniffer for > datatype 'galaxy.datatypes.xml:BlastXml' > galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,026 Loaded sniffer for > datatype 'galaxy.datatypes.sequence:Maf' > galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,026 Loaded sniffer for > datatype 'galaxy.datatypes.sequence:Lav' > galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,026 Loaded sniffer for > datatype 'galaxy.datatypes.sequence:csFasta' > galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,026 Loaded sniffer for > datatype 'galaxy.datatypes.qualityscore:QualityScoreSOLiD' > galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,026 Loaded sniffer for > datatype 'galaxy.datatypes.qualityscore:QualityScore454' > galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,026 Loaded sniffer for > datatype 'galaxy.datatypes.sequence:Fasta' > galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,026 Loaded sniffer for > datatype 'galaxy.datatypes.sequence:Fastq' > galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,027 Loaded sniffer for > datatype 'galaxy.datatypes.interval:Wiggle' > galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,027 Loaded sniffer for > datatype 'galaxy.datatypes.images:Html' > galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,027 Loaded sniffer for > datatype 'galaxy.datatypes.images:Pdf' > galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,027 Loaded sniffer for > datatype 'galaxy.datatypes.sequence:Axt' > galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,028 Loaded sniffer for > datatype 'galaxy.datatypes.interval:Bed' > galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,028 Loaded sniffer for > datatype 'galaxy.datatypes.interval:CustomTrack' > galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,028 Loaded sniffer for > datatype 'galaxy.datatypes.interval:Gtf' > galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,028 Loaded sniffer for > datatype 'galaxy.datatypes.interval:Gff' > galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,028 Loaded sniffer for > datatype 'galaxy.datatypes.interval:Gff3' > galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,029 Loaded sniffer for > datatype 'galaxy.datatypes.tabular:Pileup' > galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,029 Loaded sniffer for > datatype 'galaxy.datatypes.interval:Interval' > galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,029 Loaded sniffer for > datatype 'galaxy.datatypes.tabular:Sam' > galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,029 Loaded sniffer for > datatype 'galaxy.datatypes.tabular:Vcf' > galaxy.tools.data DEBUG 2012-06-20 18:29:21,059 Loaded tool data table > 'all_fasta' > galaxy.tools.data DEBUG 2012-06-20 18:29:21,060 Loaded tool data table > 'bfast_indexes' > galaxy.tools.data DEBUG 2012-06-20 18:29:21,061 Loaded tool data table > 'blastdb' > galaxy.tools.data DEBUG 2012-06-20 18:29:21,062 Loaded tool data table > 'blastdb_p' > galaxy.tools.data DEBUG 2012-06-20 18:29:21,065 Loaded tool data table > 'bowtie_indexes' > galaxy.tools.data DEBUG 2012-06-20 18:29:21,06
Re: [galaxy-dev] Server Error after fresh installation of Galaxy
I used changeset: 7148:17d57db9a7c0 for the clone. I don't recall making any changes, but have removed it and am about to start fresh and see if the issue still exists. Iry On 6/22/12 11:50 AM, "Nate Coraor" wrote: >On Jun 20, 2012, at 6:46 PM, Iry Witham wrote: > >> I have recently performed a fresh installation of Galaxy utilizing the >>latest distribution and am getting a sizable number of errors when >>attempting to start the server. The issue started when I performed a >>merge so I decided to do the clean install as a test. The server >>appears to start just fine, but with errors reported in the logs. The >>web0.log gives the following errors and warnings (I am truncating the >>file for space): >> >> galaxy.model.migrate.check DEBUG 2012-06-20 18:29:20,497 psycopg2 egg >>successfully loaded for postgres dialect >> galaxy.model.migrate.check INFO 2012-06-20 18:29:20,599 At database >>version 97 >> galaxy.tool_shed.migrate.check DEBUG 2012-06-20 18:29:20,630 psycopg2 >>egg successfully loaded for postgres dialect >> galaxy.tool_shed.migrate.check INFO 2012-06-20 18:29:20,649 At >>migrate_tools version 2 >> galaxy.model.custom_types DEBUG 2012-06-20 18:29:20,654 psycopg2 egg >>successfully loaded for postgres dialect >> galaxy.tool_shed.tool_shed_registry DEBUG 2012-06-20 18:29:20,658 >>Loading references to tool sheds from tool_sheds_conf.xml >> galaxy.tool_shed.tool_shed_registry DEBUG 2012-06-20 18:29:20,658 >>Loaded reference to tool shed: Galaxy main tool shed >> galaxy.tool_shed.tool_shed_registry DEBUG 2012-06-20 18:29:20,658 >>Loaded reference to tool shed: Galaxy test tool shed >> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,014 Loading >>datatypes from datatypes_conf.xml >> galaxy.datatypes.registry WARNING 2012-06-20 18:29:21,015 Overriding >>conflicting datatype with extension 'coverage', using datatype from >>datatypes_conf.xml. >> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,025 Loaded sniffer >>for datatype 'galaxy.datatypes.binary:Bam' >> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,025 Loaded sniffer >>for datatype 'galaxy.datatypes.binary:Sff' >> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,025 Loaded sniffer >>for datatype 'galaxy.datatypes.xml:BlastXml' >> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,026 Loaded sniffer >>for datatype 'galaxy.datatypes.sequence:Maf' >> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,026 Loaded sniffer >>for datatype 'galaxy.datatypes.sequence:Lav' >> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,026 Loaded sniffer >>for datatype 'galaxy.datatypes.sequence:csFasta' >> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,026 Loaded sniffer >>for datatype 'galaxy.datatypes.qualityscore:QualityScoreSOLiD' >> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,026 Loaded sniffer >>for datatype 'galaxy.datatypes.qualityscore:QualityScore454' >> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,026 Loaded sniffer >>for datatype 'galaxy.datatypes.sequence:Fasta' >> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,026 Loaded sniffer >>for datatype 'galaxy.datatypes.sequence:Fastq' >> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,027 Loaded sniffer >>for datatype 'galaxy.datatypes.interval:Wiggle' >> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,027 Loaded sniffer >>for datatype 'galaxy.datatypes.images:Html' >> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,027 Loaded sniffer >>for datatype 'galaxy.datatypes.images:Pdf' >> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,027 Loaded sniffer >>for datatype 'galaxy.datatypes.sequence:Axt' >> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,028 Loaded sniffer >>for datatype 'galaxy.datatypes.interval:Bed' >> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,028 Loaded sniffer >>for datatype 'galaxy.datatypes.interval:CustomTrack' >> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,028 Loaded sniffer >>for datatype 'galaxy.datatypes.interval:Gtf' >> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,028 Loaded sniffer >>for datatype 'galaxy.datatypes.interval:Gff' >> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,028 Loaded sniffer >>for datatype 'galaxy.datatypes.interval:Gff3' >> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,029 Loaded sniffer >>for datatype 'galaxy.datatypes.tabular:Pileup' >> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,029 Loaded sniffer >>for datatype 'galaxy.datatypes.interval:Interval' >> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,029 Loaded sniffer >>for datatype 'galaxy.datatypes.tabular:Sam' >> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,029 Loaded sniffer >>for datatype 'galaxy.datatypes.tabular:Vcf' >> galaxy.tools.data DEBUG 2012-06-20 18:29:21,059 Loaded tool data table >>'all_fasta' >> galaxy.tools.data DEBUG 2012-06-20 18:29:21,060 Loaded tool data table >>'bfast_indexes' >> galaxy.tools.data DEBUG 2012-06-20 18:29:21,061 Loaded tool data table >>'blastdb' >>
Re: [galaxy-dev] Server Error after fresh installation of Galaxy
Hi Nate,
I removed to previous instillation just to be safe and performed a new
clone. This time it appears to be less problematic. I am no longer
getting all of the errors. However, I am getting an error due to my
database version. The error is:
galaxy.model.migrate.check DEBUG 2012-06-27 12:39:11,843 psycopg2 egg
successfully loaded for postgres dialect
Traceback (most recent call last):
File
"/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/web/buildapp.py",
line 82, in app_factory
app = UniverseApplication( global_conf = global_conf, **kwargs )
File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/app.py",
line 35, in __init__
create_or_verify_database( db_url, kwargs.get( 'global_conf', {}
).get( '__file__', None ), self.config.database_engine_options, app=self )
File
"/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/model/migrate/che
ck.py", line 103, in create_or_verify_database
% ( db_schema.version, migrate_repository.versions.latest, config_arg
) )
Exception: Your database has version '101' but this code expects version
'97'. Please backup your database and then migrate the schema by running
'sh manage_db.sh -c ./universe_wsgi.runner.ini upgrade'.
I have attempted to run sh manage_db.sh -c ./universe_wsgi.runner.ini
upgrade and that fails with the following error:
galaxy@galaxy2:/hpcdata/galaxy-test/galaxy-setup/galaxy-dist> sh
manage_db.sh -c ./universe_wsgi.webapp.ini upgrade
Traceback (most recent call last):
File "./scripts/manage_db.py", line 63, in
main( repository=repo, url=db_url )
File
"/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.5.
4-py2.6.egg/migrate/versioning/shell.py", line 150, in main
ret = command_func(**kwargs)
File
"/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.5.
4-py2.6.egg/migrate/versioning/api.py", line 221, in upgrade
return _migrate(url, repository, version, upgrade=True, err=err,
**opts)
File
"/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.5.
4-py2.6.egg/migrate/versioning/api.py", line 327, in _migrate
changeset = schema.changeset(version)
File
"/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.5.
4-py2.6.egg/migrate/versioning/schema.py", line 173, in changeset
changeset = self.repository.changeset(database, start_ver, version)
File
"/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.5.
4-py2.6.egg/migrate/versioning/repository.py", line 170, in changeset
changes = [self.version(v).script(database, op) for v in versions]
File
"/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.5.
4-py2.6.egg/migrate/versioning/repository.py", line 145, in version
return self.versions.version(*p, **k)
File
"/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.5.
4-py2.6.egg/migrate/versioning/version.py", line 125, in version
return self.versions[VerNum(vernum)]
KeyError:
It is getting closer, but I am not quite there yet.
Thanks,
Iry
On 6/22/12 11:50 AM, "Nate Coraor" wrote:
>On Jun 20, 2012, at 6:46 PM, Iry Witham wrote:
>
>> I have recently performed a fresh installation of Galaxy utilizing the
>>latest distribution and am getting a sizable number of errors when
>>attempting to start the server. The issue started when I performed a
>>merge so I decided to do the clean install as a test. The server
>>appears to start just fine, but with errors reported in the logs. The
>>web0.log gives the following errors and warnings (I am truncating the
>>file for space):
>>
>> galaxy.model.migrate.check DEBUG 2012-06-20 18:29:20,497 psycopg2 egg
>>successfully loaded for postgres dialect
>> galaxy.model.migrate.check INFO 2012-06-20 18:29:20,599 At database
>>version 97
>> galaxy.tool_shed.migrate.check DEBUG 2012-06-20 18:29:20,630 psycopg2
>>egg successfully loaded for postgres dialect
>> galaxy.tool_shed.migrate.check INFO 2012-06-20 18:29:20,649 At
>>migrate_tools version 2
>> galaxy.model.custom_types DEBUG 2012-06-20 18:29:20,654 psycopg2 egg
>>successfully loaded for postgres dialect
>> galaxy.tool_shed.tool_shed_registry DEBUG 2012-06-20 18:29:20,658
>>Loading references to tool sheds from tool_sheds_conf.xml
>> galaxy.tool_shed.tool_shed_registry DEBUG 2012-06-20 18:29:20,658
>>Loaded reference to tool shed: Galaxy main tool shed
>> galaxy.tool_shed.tool_shed_registry DEBUG 2012-06-20 18:29:20,658
>>Loaded reference to tool shed: Galaxy test tool shed
>> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,014 Loading
>>datatypes from datatypes_conf.xml
>> galaxy.datatypes.registry WARNING 2012-06-20 18:29:21,015 Overriding
>>conflicting datatype with extension 'coverage', using datatype from
>>datatypes_conf.xml.
>> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:21,025 Loaded sniffer
>>for datatype 'galaxy.datatypes.binary:Bam'
>> galaxy.datatypes.registry DEBUG 2012-06-20 18:29:2
Re: [galaxy-dev] Server Error after fresh installation of Galaxy
I am still experiencing issues getting my galaxy server to start since the
upgrade. The logs are all getting this type of error:
galaxy@galaxy2:/hpcdata/galaxy-test/galaxy-setup/galaxy-dist> cat runner0.log
python path is:
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/numpy-1.6.0-py2.6-linux-x86_64-ucs4.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/boto-2.2.2-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/mercurial-2.1.2-py2.6-linux-x86_64-ucs4.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Whoosh-0.3.18-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/pycrypto-2.0.1-py2.6-linux-x86_64-ucs4.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/python_lzo-1.08_2.03_static-py2.6-linux-x86_64-ucs4.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/bx_python-0.7.1_7b95ff194725-py2.6-linux-x86_64-ucs4.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/amqplib-0.6.1-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/pexpect-2.4-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Babel-0.9.4-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/MarkupSafe-0.12-py2.6-linux-x86_64-ucs4.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/WebHelpers-0.2-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/wchartype-0.1-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/docutils-0.7-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/WebOb-0.8.5-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Routes-1.12.3-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Paste-1.6-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib, /usr/lib/python26.zip,
/usr/lib64/python2.6, /usr/lib64/python2.6/plat-linux2,
/usr/lib64/python2.6/lib-tk, /usr/lib64/python2.6/lib-old,
/usr/lib64/python2.6/lib-dynload, /usr/lib64/python2.6/site-packages/Numeric,
/usr/lib64/python2.6/site-packages/gtk-2.0,
/usr/local/lib64/python2.6/site-packages, /usr/lib64/python2.6/site-packages
galaxy.model.migrate.check DEBUG 2012-07-03 12:35:03,580 psycopg2 egg
successfully loaded for postgres dialect
Traceback (most recent call last):
File
"/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/web/buildapp.py",
line 82, in app_factory
app = UniverseApplication( global_conf = global_conf, **kwargs )
File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/app.py", line
35, in __init__
create_or_verify_database( db_url, kwargs.get( 'global_conf', {} ).get(
'__file__', None ), self.config.database_engine_options, app=self )
File
"/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/model/migrate/check.py",
line 103, in create_or_verify_database
% ( db_schema.version, migrate_repository.versions.latest, config_arg ) )
Exception: Your database has version '101' but this code expects version '97'.
Please backup your database and then migrate the schema by running 'sh
manage_db.sh -c ./universe_wsgi.runner.ini upgrade'.
Removing PID file runner0.pid
I have not dropped my database and built it fresh. However, I have attempted
the recommended 'sh manage_db.sh -c ./universe_wsgi.webapp.ini upgrade' for
both the runner and web app ini files with the following error:
galaxy@galaxy2:/hpcdata/galaxy-test/galaxy-setup/galaxy-dist> sh manage_db.sh
-c ./universe_wsgi.webapp.ini upgrade
Traceback (most recent call last):
File "./scripts/manage_db.py", line 63, in
main( repository=repo, url=db_url )
File
"/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/shell.py",
line 150, in main
ret = command_func(**kwargs)
File
"/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/api.py",
line 221, in upgrade
return _migrate(url, repository, version, upgrade=True, err=err, **opts)
File
"/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/api.py",
line 327, in _migrate
changeset = schema.changeset(version)
File
"/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/schema.py",
line 173, in changeset
chang
Re: [galaxy-dev] Server Error after fresh installation of Galaxy
It looks like what happened is that you've updated the instance that was
originally connected to this database from galaxy-central at some point
recently. The current tip of galaxy-central is at database version 103.
The first two options that come to mind are:
1) Hook a fresh galaxy-central clone up to this database and `manage_db.sh
downgrade 97` which should set your database back to the version appropriate
for galaxy-dist.
2) Swap to galaxy-central instead of -dist
Taking a brief look at the migrations, #1 looks fairly safe, but as always --
back up the database first.
-Dannon
On Jul 3, 2012, at 1:03 PM, Iry Witham wrote:
> I am still experiencing issues getting my galaxy server to start since the
> upgrade. The logs are all getting this type of error:
>
> galaxy@galaxy2:/hpcdata/galaxy-test/galaxy-setup/galaxy-dist> cat runner0.log
> python path is:
> /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/numpy-1.6.0-py2.6-linux-x86_64-ucs4.egg,
>
> /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg,
> /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/boto-2.2.2-py2.6.egg,
> /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/mercurial-2.1.2-py2.6-linux-x86_64-ucs4.egg,
> /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Whoosh-0.3.18-py2.6.egg,
> /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/pycrypto-2.0.1-py2.6-linux-x86_64-ucs4.egg,
>
> /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/python_lzo-1.08_2.03_static-py2.6-linux-x86_64-ucs4.egg,
>
> /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/bx_python-0.7.1_7b95ff194725-py2.6-linux-x86_64-ucs4.egg,
> /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/amqplib-0.6.1-py2.6.egg,
> /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/pexpect-2.4-py2.6.egg,
> /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/SQLAlchem!
y-0.5.6_dev_r6498-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Babel-0.9.4-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/MarkupSafe-0.12-py2.6-linux-x86_64-ucs4.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/WebHelpers-0.2-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/wchartype-0.1-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/docutils-0.7-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/WebOb-0.8.5-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Routes-1.12.3-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteDe!
ploy-1.3.3-py2.6.egg, /hpcdata/galaxy-test/galaxy-setup/galaxy!
-dist/eg
gs/PasteScript-1.7.3-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Paste-1.6-py2.6.egg,
/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib, /usr/lib/python26.zip,
/usr/lib64/python2.6, /usr/lib64/python2.6/plat-linux2,
/usr/lib64/python2.6/lib-tk, /usr/lib64/python2.6/lib-old,
/usr/lib64/python2.6/lib-dynload, /usr/lib64/python2.6/site-packages/Numeric,
/usr/lib64/python2.6/site-packages/gtk-2.0,
/usr/local/lib64/python2.6/site-packages, /usr/lib64/python2.6/site-packages
> galaxy.model.migrate.check DEBUG 2012-07-03 12:35:03,580 psycopg2 egg
> successfully loaded for postgres dialect
> Traceback (most recent call last):
> File
> "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/web/buildapp.py",
> line 82, in app_factory
> app = UniverseApplication( global_conf = global_conf, **kwargs )
> File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/app.py",
> line 35, in __init__
> create_or_verify_database( db_url, kwargs.get( 'global_conf', {} ).get(
> '__file__', None ), self.config.database_engine_options, app=self )
> File
> "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/model/migrate/check.py",
> line 103, in create_or_verify_database
> % ( db_schema.version, migrate_repository.versions.latest, config_arg ) )
> Exception: Your database has version '101' but this code expects version
> '97'. Please backup your database and then migrate the schema by running 'sh
> manage_db.sh -c ./universe_wsgi.runner.ini upgrade'.
> Removing PID file runner0.pid
>
> I have not dropped my database and built it fresh. However, I have attempted
> the recommended 'sh manage_db.sh -c ./universe_wsgi.webapp.ini upgrade' for
> both the runner and web app ini files with the following error:
>
> galaxy@galaxy2:/hpcdata/galaxy-test/galaxy-setup/galaxy-dist> sh manage_db.sh
> -c ./universe_wsgi.webapp.ini upgrade
> Traceback (most recent call last):
> File "./scripts/manage_db.py", line 63, in
> main( repository=repo, url=
Re: [galaxy-dev] Server Error after fresh installation of Galaxy
Hi Iry, > > Exception: Your database has version '101' but this code expects > version '97'. Please backup your database and then migrate the schema > by running 'sh manage_db.sh -c ./universe_wsgi.runner.ini upgrade'. > Removing PID file runner0.pid Your galaxy version seems to be older than your database. It seems you run galaxy-central and afterwards starting galaxy-dist with the same database. That does not work. With your database you should run a newer version of galaxy, e.g. the newest galaxy-central. Hope that helps, Bjoern -- Björn Grüning Albert-Ludwigs-Universität Freiburg Institute of Pharmaceutical Sciences Pharmaceutical Bioinformatics Hermann-Herder-Strasse 9 D-79104 Freiburg i. Br. Tel.: +49 761 203-4872 Fax.: +49 761 203-97769 E-Mail: bjoern.gruen...@pharmazie.uni-freiburg.de Web: http://www.pharmaceutical-bioinformatics.org/ ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Server Error after fresh installation of Galaxy
Thanks Dannon and Bjorn for the assistance. I followed Dannon's
suggestion and that fixed my issue.
Thanks,
Iry
On 7/3/12 1:15 PM, "Dannon Baker" wrote:
>It looks like what happened is that you've updated the instance that was
>originally connected to this database from galaxy-central at some point
>recently. The current tip of galaxy-central is at database version 103.
>
>The first two options that come to mind are:
>
>1) Hook a fresh galaxy-central clone up to this database and
>`manage_db.sh downgrade 97` which should set your database back to the
>version appropriate for galaxy-dist.
>2) Swap to galaxy-central instead of -dist
>
>Taking a brief look at the migrations, #1 looks fairly safe, but as
>always -- back up the database first.
>
>-Dannon
>
>
>
>On Jul 3, 2012, at 1:03 PM, Iry Witham wrote:
>
>> I am still experiencing issues getting my galaxy server to start since
>>the upgrade. The logs are all getting this type of error:
>>
>> galaxy@galaxy2:/hpcdata/galaxy-test/galaxy-setup/galaxy-dist> cat
>>runner0.log
>> python path is:
>>/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/numpy-1.6.0-py2.6-linu
>>x-x86_64-ucs4.egg,
>>/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/pysam-0.4.2_kanwei_b10
>>f6e722e9a-py2.6-linux-x86_64-ucs4.egg,
>>/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/boto-2.2.2-py2.6.egg,
>>/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/mercurial-2.1.2-py2.6-
>>linux-x86_64-ucs4.egg,
>>/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Whoosh-0.3.18-py2.6.eg
>>g,
>>/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/pycrypto-2.0.1-py2.6-l
>>inux-x86_64-ucs4.egg,
>>/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/python_lzo-1.08_2.03_s
>>tatic-py2.6-linux-x86_64-ucs4.egg,
>>/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/bx_python-0.7.1_7b95ff
>>194725-py2.6-linux-x86_64-ucs4.egg,
>>/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/amqplib-0.6.1-py2.6.eg
>>g,
>>/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/pexpect-2.4-py2.6.egg,
>>
>>/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r
>>6498-py2.6.egg,
>>/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Babel-0.9.4-py2.6.egg,
>>
>>/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/MarkupSafe-0.12-py2.6-
>>linux-x86_64-ucs4.egg,
>>/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg,
>>/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/WebHelpers-0.2-py2.6.e
>>gg,
>>/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/simplejson-2.1.1-py2.6
>>-linux-x86_64-ucs4.egg,
>>/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/wchartype-0.1-py2.6.eg
>>g,
>>/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/elementtree-1.2.6_2005
>>0316-py2.6.egg,
>>/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/docutils-0.7-py2.6.egg
>>,
>>/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/WebOb-0.8.5-py2.6.egg,
>>
>>/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Routes-1.12.3-py2.6.eg
>>g,
>>/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Cheetah-2.2.2-py2.6-li
>>nux-x86_64-ucs4.egg,
>>/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.
>>6.egg,
>>/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.
>>6.egg,
>>/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Paste-1.6-py2.6.egg,
>>/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib,
>>/usr/lib/python26.zip, /usr/lib64/python2.6,
>>/usr/lib64/python2.6/plat-linux2, /usr/lib64/python2.6/lib-tk,
>>/usr/lib64/python2.6/lib-old, /usr/lib64/python2.6/lib-dynload,
>>/usr/lib64/python2.6/site-packages/Numeric,
>>/usr/lib64/python2.6/site-packages/gtk-2.0,
>>/usr/local/lib64/python2.6/site-packages,
>>/usr/lib64/python2.6/site-packages
>> galaxy.model.migrate.check DEBUG 2012-07-03 12:35:03,580 psycopg2 egg
>>successfully loaded for postgres dialect
>> Traceback (most recent call last):
>> File
>>"/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/web/buildapp.py
>>", line 82, in app_factory
>> app = UniverseApplication( global_conf = global_conf, **kwargs )
>> File
>>"/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/app.py", line
>>35, in __init__
>> create_or_verify_database( db_url, kwargs.get( 'global_conf', {}
>>).get( '__file__', None ), self.config.database_engine_options, app=self
>>)
>> File
>>"/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/model/migrate/c
>>heck.py", line 103, in create_or_verify_database
>> % ( db_schema.version, migrate_repository.versions.latest,
>>config_arg ) )
>> Exception: Your database has version '101' but this code expects
>>version '97'. Please backup your database and then migrate the schema
>>by running 'sh manage_db.sh -c ./universe_wsgi.runner.ini upgrade'.
>> Removing PID file runner0.pid
>>
>> I have not dropped my database and built it fresh. However, I have
>>attempted the recommended 'sh manage_db.sh -c ./universe_wsgi.webapp.ini
>>upgrade' for both the runner and web app ini files wit
