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 lcham@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
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