Hi all,
I have a server running Ubuntu LTS 22.04 (Jam Jellyfish) with docker container engine installed. On this server, I’m attempting to launch the a container from the latest stable docker images for galaxy.
docker run -d -p 8080:80 -p 9002:9002 bgruening/galaxy-stable
Unfortunately, while the container launches, the web-service doesn’t seem to start. I get a 403-forbidden error when connecting with http://localhost:8080.
The supervisor page on port 9002 shows this:
For some reason clicking “tail -f” for the galaxy web service gives a blank page that never seems to load.
Has anyone experienced this issue before? Thank you in advance for any help you might be able to provide.
Not sure if these will help, but:
- For some reason, this very basic start with bgruening/galaxy-stable:19.01 seemed to start up fine.
- Here is the beginning and tail end of the docker log file:
Enable Galaxy reports authentification
Checking /export...
Disable Galaxy Interactive Environments. Start with --privileged to enable IE's.
Starting postgres
postgresql: started
Checking if database is up and running
Traceback (most recent call last):
File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1284, in _execute_context
cursor, statement, parameters, context
File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/engine/default.py", line 590, in do_execute
cursor.execute(statement, parameters)
psycopg2.errors.UndefinedTable: relation "galaxy_user" does not exist
LINE 3: FROM galaxy_user
^
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/usr/local/bin/check_database.py", line 25, in <module>
query.count()
File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/orm/query.py", line 3749, in count
return self.from_self(col).scalar()
File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/orm/query.py", line 3469, in scalar
ret = self.one()
File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/orm/query.py", line 3436, in one
ret = self.one_or_none()
File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/orm/query.py", line 3405, in one_or_none
ret = list(self)
File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/orm/query.py", line 3481, in __iter__
return self._execute_and_instances(context)
File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/orm/query.py", line 3506, in _execute_and_instances
result = conn.execute(querycontext.statement, self._params)
File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1020, in execute
return meth(self, multiparams, params)
File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/sql/elements.py", line 298, in _execute_on_connection
return connection._execute_clauseelement(self, multiparams, params)
File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1139, in _execute_clauseelement
distilled_params,
File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1324, in _execute_context
e, statement, parameters, cursor, context
File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1518, in _handle_dbapi_exception
sqlalchemy_exception, with_traceback=exc_info[2], from_=e
File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/util/compat.py", line 178, in raise_
raise exception
File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1284, in _execute_context
cursor, statement, parameters, context
File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/engine/default.py", line 590, in do_execute
cursor.execute(statement, parameters)
sqlalchemy.exc.ProgrammingError: (psycopg2.errors.UndefinedTable) relation "galaxy_user" does not exist
LINE 3: FROM galaxy_user
...
migrate.versioning.script.base DEBUG 2024-06-13 18:56:24,572 [p:2697,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0089_add_object_store_id_columns.py...
migrate.versioning.script.base DEBUG 2024-06-13 18:56:24,572 [p:2697,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0089_add_object_store_id_columns.py loaded successfully
migrate.versioning.script.base DEBUG 2024-06-13 18:56:24,572 [p:2697,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0160_hda_set_deleted_if_purged_again.py...
migrate.versioning.script.base DEBUG 2024-06-13 18:56:24,572 [p:2697,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0160_hda_set_deleted_if_purged_again.py loaded successfully
migrate.versioning.script.base DEBUG 2024-06-13 18:56:24,572 [p:2697,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0101_drop_installed_changeset_revision_column.py...
migrate.versioning.script.base DEBUG 2024-06-13 18:56:24,572 [p:2697,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0101_drop_installed_changeset_revision_column.py loaded successfully
migrate.versioning.script.base DEBUG 2024-06-13 18:56:24,572 [p:2697,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0144_add_cleanup_event_user_table.py...
migrate.versioning.script.base DEBUG 2024-06-13 18:56:24,572 [p:2697,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0144_add_cleanup_event_user_table.py loaded successfully
migrate.versioning.script.base DEBUG 2024-06-13 18:56:24,572 [p:2697,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0077_create_tool_tag_association_table.py...
migrate.versioning.script.base DEBUG 2024-06-13 18:56:24,572 [p:2697,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0077_create_tool_tag_association_table.py loaded successfully
migrate.versioning.script.base DEBUG 2024-06-13 18:56:24,572 [p:2697,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0141_add_oidc_tables.py...
migrate.versioning.script.base DEBUG 2024-06-13 18:56:24,572 [p:2697,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0141_add_oidc_tables.py loaded successfully
migrate.versioning.script.base DEBUG 2024-06-13 18:56:24,572 [p:2697,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0053_item_ratings.py...
migrate.versioning.script.base DEBUG 2024-06-13 18:56:24,572 [p:2697,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0053_item_ratings.py loaded successfully
migrate.versioning.script.base DEBUG 2024-06-13 18:56:24,572 [p:2697,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py...
migrate.versioning.script.base DEBUG 2024-06-13 18:56:24,572 [p:2697,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py loaded successfully
migrate.versioning.script.base DEBUG 2024-06-13 18:56:24,572 [p:2697,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0059_sample_dataset_file_path.py...
migrate.versioning.script.base DEBUG 2024-06-13 18:56:24,572 [p:2697,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0059_sample_dataset_file_path.py loaded successfully
migrate.versioning.script.base DEBUG 2024-06-13 18:56:24,572 [p:2697,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0154_created_from_basename.py...
migrate.versioning.script.base DEBUG 2024-06-13 18:56:24,572 [p:2697,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0154_created_from_basename.py loaded successfully
migrate.versioning.script.base DEBUG 2024-06-13 18:56:24,572 [p:2697,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0075_add_subindex_column_to_run_table.py...
migrate.versioning.script.base DEBUG 2024-06-13 18:56:24,572 [p:2697,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0075_add_subindex_column_to_run_table.py loaded successfully
migrate.versioning.script.base DEBUG 2024-06-13 18:56:24,572 [p:2697,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0079_input_library_to_job_table.py...
migrate.versioning.script.base DEBUG 2024-06-13 18:56:24,572 [p:2697,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0079_input_library_to_job_table.py loaded successfully
migrate.versioning.script.base DEBUG 2024-06-13 18:56:24,572 [p:2697,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py...
migrate.versioning.script.base DEBUG 2024-06-13 18:56:24,610 [p:2697,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py loaded successfully
migrate.versioning.script.base DEBUG 2024-06-13 18:56:24,610 [p:2697,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0088_add_installed_changeset_revison_column.py...
migrate.versioning.script.base DEBUG 2024-06-13 18:56:24,610 [p:2697,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0088_add_installed_changeset_revison_column.py loaded successfully
migrate.versioning.script.base DEBUG 2024-06-13 18:56:24,610 [p:2697,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0078_add_columns_for_disk_usage_accounting.py...
migrate.versioning.script.base DEBUG 2024-06-13 18:56:24,610 [p:2697,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0078_add_columns_for_disk_usage_accounting.py loaded successfully
migrate.versioning.script.base DEBUG 2024-06-13 18:56:24,610 [p:2697,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0037_samples_library.py...
migrate.versioning.script.base DEBUG 2024-06-13 18:56:24,610 [p:2697,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0037_samples_library.py loaded successfully
migrate.versioning.script.base DEBUG 2024-06-13 18:56:24,611 [p:2697,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0007_sharing_histories.py...
migrate.versioning.script.base DEBUG 2024-06-13 18:56:24,611 [p:2697,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0007_sharing_histories.py loaded successfully
migrate.versioning.repository DEBUG 2024-06-13 18:56:24,611 [p:2697,w:0,m:0] [MainThread] Repository lib/galaxy/model/migrate loaded successfully
migrate.versioning.repository DEBUG 2024-06-13 18:56:24,611 [p:2697,w:0,m:0] [MainThread] Config: OrderedDict([('db_settings', OrderedDict([('repository_id', 'Galaxy'), ('version_table', 'migrate_version'), ('required_dbs', '[]')]))])
Traceback (most recent call last):
File "lib/galaxy/webapps/galaxy/buildapp.py", line 48, in app_factory
app = galaxy.app.UniverseApplication(global_conf=global_conf, **kwargs)
File "lib/galaxy/app.py", line 97, in __init__
self._configure_models(check_migrate_databases=self.config.check_migrate_databases, check_migrate_tools=check_migrate_tools, config_file=config_file)
File "lib/galaxy/config/__init__.py", line 1226, in _configure_models
create_or_verify_database(db_url, config_file, self.config.database_engine_options, app=self, map_install_models=combined_install_database)
File "lib/galaxy/model/migrate/check.py", line 140, in create_or_verify_database
raise Exception("{}. {}{}".format(expect_msg, instructions, backup_msg))
Exception: Your database has version '1' but this code expects version '170'. Please backup your database and then migrate the database schema by running 'sh manage_db.sh upgrade'.
==> /home/galaxy/logs/slurmctld.log <==
[2024-06-13T18:59:00.334] error: Could not open job state file /tmp/slurm/job_state: No such file or directory
[2024-06-13T18:59:00.334] error: NOTE: Trying backup state save file. Jobs may be lost!
[2024-06-13T18:59:00.334] No job state file (/tmp/slurm/job_state.old) found