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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