New subject: Installation of 20130603 Galaxy image with MySQL fails

5 Jun 2013

    Hi.   I am new to the Galaxy forum and I am trying to setup a
    new local Galaxy instance with MySQL on RH6.2 x86_64.

    On a newly installed OS node, using the hg clone command (hg
    clone https://bitbucket.org/galaxy/galaxy-dist#stable) which
    gets the current Galaxy 20130603 image, I am getting the
    following errors when running run.sh:
      File "build/bdist.linux-x86_64-ucs4/egg/MySQLdb/cursors.py",
    line 173, in execute
        self.errorhandler(self, exc, value)
      File
    "build/bdist.linux-x86_64-ucs4/egg/MySQLdb/connections.py",
    line 36, in defaulterrorhandler
        raise errorclass, errorvalue
    OperationalError: (OperationalError) (1170, "BLOB/TEXT column
    'slug' used in key specification without a key length")
    'CREATE INDEX ix_history_slug ON history (slug)' ()

    Reading the forum, someone stated it can be bypass by running
    the CREATE INDEX.

    mysql> CREATE INDEX ix_history_slug ON history (slug(1000));
    Query OK, 0 rows affected (0.09 sec)
    Records: 0  Duplicates: 0  Warnings: 0

    When trying to run.sh again after the CREATE INDEX, will get
    this error:
      File
    "/gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/lib/galaxy/app.py", line 52, in __init__
        create_or_verify_database( db_url,
    kwargs.get( 'global_conf', {} ).get( '__file__', None ),
    self.config.database_engine_options, app=self )
      File
    "/gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/lib/galaxy/model/migrate/check.py", line 107, in create_or_verify_database
        % ( db_schema.version, migrate_repository.versions.latest,
    config_arg ) )
    Exception: Your database has version '29' but this code
    expects version '115'.  Please backup your database and then
    migrate the schema by running 'sh manage_db.sh upgrade'.

    So try to run the "sh manage_db.sh upgrade' now will get this
    error:
    $ sh manage_db.sh upgrade
    Traceback (most recent call last):
      File "./scripts/manage_db.py", line 13, in <module>
        from migrate.versioning.shell import main
      File
    "/gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/shell.py", line 12, in <module>
        from migrate.versioning import api
      File
    "/gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/api.py", line 33, in <module>
        from migrate.versioning import (repository, schema,
    version,
      File
    "/gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/repository.py", line 13, in <module>
        from migrate.versioning import version, pathed, cfgparse
      File
    "/gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/version.py", line 10, in <module>
        from migrate.versioning import pathed, script
      File
    "/gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/pathed.py", line 11, in <module>
        from migrate.versioning.util import KeyedInstance
      File
    "/gpfs/gpfs2/home/galaxyadmin25/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/util/__init__.py", line 7, in <module>
        from decorator import decorator
    ImportError: No module named decorator

    In some searches, there were tips of deleting the eggs
    directory and rerun run.sh or use a python env.  Neither
    option worked.
    Was not able to find anything meaningful about the decorator
    error.

    Note:, I was able to get Galaxy up with MySQL using the Galaxy
    788cd3d06541 image on a different node.  So I am thinking
    maybe it is the new 20130603 image that is giving me issues?

    Commands used to get Galaxy up:  

            Install mysql from yum repository [MySQL
            5.1.52-1.el6_0.1]
            python version [2.6.6]

            Grant ALL PRIVILEGES galaxy_db.* TO  galaxy_user on
            localhostname with PWD
            Images tested:  

            *Copy of the galaxy-galaxy-dist-788cd3d06541.tar.bz2
            image  Did not run the hg update command. [This
            worked]   

            *hg clone stable of newest image [Failed]  

            Update the universe_wsg.ini with the port, host,
            database_connection to mysql  

            Ran run.sh


    Thanks.  

    Linda

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