Hi Linda,

The decorator issue should be resolved in galaxy-central now.  I'm setting
up a test environment to see if I can reproduce the mysql issue now, and
will let you know what I come up with.

Thanks!

-Dannon


On Wed, Jun 5, 2013 at 11:12 AM, Linda Cham <lc...@us.ibm.com> wrote:

> 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*<https://bitbucket.org/galaxy/galaxy-dist>)
> 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
>
>
> ___________________________________________________________
> 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/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
>
___________________________________________________________
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/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Reply via email to