Startup Exception

[hroest]

When starting up a galaxy instance, I get this exception:

# docker run -i -t -p 8081:80 bgruening/galaxy-stable
Enable Galaxy reports authentification 
umount: /var/lib/docker: must be superuser to umount
tmpfs on /proc/kcore type tmpfs (rw,nosuid,size=65536k,mode=755)
Disable Galaxy Interactive Environments. Start with --privileged to enable IE's.
Starting postgres
postgresql: started
Checking if database is up and running
Database connected
Starting cron
cron: started
Starting ProFTP
proftpd: started
Starting Galaxy reports webapp
reports: started
Starting nodejs
galaxy:galaxy_nodejs_proxy: started
Starting condor
condor: started
Starting slurmctld
Starting slurmd
Creating admin user admin@galaxy.org with key admin and password admin if not existing
Traceback (most recent call last):
  File "/usr/local/bin/create_galaxy_user.py", line 60, in <module>
    add_user(sa_session, security_agent, options.user, options.password, key=options.key, username=options.username)
  File "/usr/local/bin/create_galaxy_user.py", line 36, in add_user
    sa_session.flush()
  File "/galaxy_venv/local/lib/python2.7/site-packages/sqlalchemy/orm/scoping.py", line 153, in do
    return getattr(self.registry(), name)(*args, **kwargs)
  File "/galaxy_venv/local/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 2254, in flush
    self._flush(objects)
  File "/galaxy_venv/local/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 2380, in _flush
    transaction.rollback(_capture_exception=True)
  File "/galaxy_venv/local/lib/python2.7/site-packages/sqlalchemy/util/langhelpers.py", line 66, in __exit__
    compat.reraise(exc_type, exc_value, exc_tb)
  File "/galaxy_venv/local/lib/python2.7/site-packages/sqlalchemy/orm/session.py", line 2344, in _flush
    flush_context.execute()
  File "/galaxy_venv/local/lib/python2.7/site-packages/sqlalchemy/orm/unitofwork.py", line 391, in execute
    rec.execute(self)
  File "/galaxy_venv/local/lib/python2.7/site-packages/sqlalchemy/orm/unitofwork.py", line 556, in execute
    uow
  File "/galaxy_venv/local/lib/python2.7/site-packages/sqlalchemy/orm/persistence.py", line 181, in save_obj
    mapper, table, insert)
  File "/galaxy_venv/local/lib/python2.7/site-packages/sqlalchemy/orm/persistence.py", line 866, in _emit_insert_statements
    execute(statement, params)
  File "/galaxy_venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 948, in execute
    return meth(self, multiparams, params)
  File "/galaxy_venv/local/lib/python2.7/site-packages/sqlalchemy/sql/elements.py", line 269, in _execute_on_connection
    return connection._execute_clauseelement(self, multiparams, params)
  File "/galaxy_venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1060, in _execute_clauseelement
    compiled_sql, distilled_params
  File "/galaxy_venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1200, in _execute_context
    context)
  File "/galaxy_venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1413, in _handle_dbapi_exception
    exc_info
  File "/galaxy_venv/local/lib/python2.7/site-packages/sqlalchemy/util/compat.py", line 203, in raise_from_cause
    reraise(type(exception), exception, tb=exc_tb, cause=cause)
  File "/galaxy_venv/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1193, in _execute_context
    context)
  File "/galaxy_venv/local/lib/python2.7/site-packages/sqlalchemy/engine/default.py", line 507, in do_execute
    cursor.execute(statement, parameters)
sqlalchemy.exc.IntegrityError: (psycopg2.IntegrityError) duplicate key value violates unique constraint "ix_api_keys_key"
DETAIL:  Key (key)=(admin) already exists.
 [SQL: 'INSERT INTO api_keys (create_time, user_id, key) VALUES (%(create_time)s, %(user_id)s, %(key)s) RETURNING api_keys.id'] [parameters: {'create_time': datetime.datetime(2018, 9, 22, 16, 44, 22, 60047), 'user_id': 2, 'key': 'admin'}] (Background on this error at: http://sqlalche.me/e/gkpj)
==> /home/galaxy/logs/handler0.log <==

it seems to not be a big issue and everything works as expected, but maybe this points to an underlying problem.

[bgruening]

Oh, sorry missed that. Is this still an issue? The only cases where I have seen this is when the Docker storage backend has some problems. Changing the backend to devicemapper or aufs can help here, depending on your OS and the Docker version.

[bgruening]

Thanks to @jyotipm29 we are back on track :smile: The new 24.1 image contains a lot of changes and reflects the latest developments in Galaxy. I would like to close this PR, but please feel free to reopen and rebase against the latest version.

Please give it a try:

docker run -p 8080:80 -p 8021:21 -p 4002:4002 --privileged=true -e "GALAXY_DESTINATIONS_DEFAULT=slurm_cluster_docker"   -v /tmp/galaxy-data/:/export/ quay.io/bgruening/galaxy:24.1

... or any other combination. The readme has been updated. Please add any useful tip to it.

For a list of changes, see the Changelog.