Question: (Closed) TypeError while executing sh
gravatar for bankapur
2.8 years ago by
United States
bankapur0 wrote:

I am trying to run my galaxy instance off of a remote server and when I execute sh, I get the following error:

tool_shed.tool_shed_registry DEBUG 2015-05-15 14:12:46,792 Loading references to tool sheds from ./config/tool_sheds_conf.xml.sample
tool_shed.tool_shed_registry DEBUG 2015-05-15 14:12:46,793 Loaded reference to tool shed: Galaxy main tool shed
tool_shed.tool_shed_registry DEBUG 2015-05-15 14:12:46,794 Loaded reference to tool shed: Galaxy test tool shed DEBUG 2015-05-15 14:12:46,794 Using "galaxy.ini" config file: ../..SOFTWARE/galaxy/config/galaxy.ini
Traceback (most recent call last):
  File "../Linux/redhat_6_x86_64/pkgs/python_2.7.1-sqlite3-rtrees/lib/python2.7/logging/", line 842, in emit
    msg = self.format(record)
  File "..Linux/redhat_6_x86_64/pkgs/python_2.7.1-sqlite3-rtrees/lib/python2.7/logging/", line 719, in format
    return fmt.format(record)
  File "../Linux/redhat_6_x86_64/pkgs/python_2.7.1-sqlite3-rtrees/lib/python2.7/logging/", line 464, in format
    record.message = record.getMessage()
  File "../Linux/redhat_6_x86_64/pkgs/python_2.7.1-sqlite3-rtrees/lib/python2.7/logging/", line 328, in getMessage
    msg = msg % self.args
TypeError: not enough arguments for format string
Logged from file, line 475
../SOFTWARE/galaxy/lib/galaxy/ UserWarning: Module sqlalchemy was already imported from ../Linux/redhat_6_x86_64/pkgs/python_2.7.1-sqlite3-rtrees/lib/python2.7/site-packages/SQLAlchemy-0.7.7-py2.7-linux-x86_64.egg/sqlalchemy/__init__.pyc, but /seq/regev_genome_portal/SOFTWARE/galaxy/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs2.egg is being added to sys.path
Traceback (most recent call last):
  File "../SOFTWARE/galaxy/lib/galaxy/webapps/galaxy/", line 53, in app_factory
    app = global_conf=global_conf, **kwargs )
  File "../SOFTWARE/galaxy/lib/galaxy/", line 49, in __init__
    self._configure_models( check_migrate_databases=True, check_migrate_tools=check_migrate_tools, config_file=config_file )
  File "../SOFTWARE/galaxy/lib/galaxy/", line 818, in _configure_models
    from galaxy.model.migrate.check import create_or_verify_database
  File "../SOFTWARE/galaxy/lib/galaxy/model/migrate/", line 15, in <module>
    from migrate.versioning import repository, schema
ImportError: No module named migrate.versioning

Any advice as to how I can fix it?


galaxy • 746 views
ADD COMMENTlink written 2.8 years ago by bankapur0

This was my fault, I think something got edited accidentally in the eggs.ini file when I switched to fresh copy of eggs.ini everything went back to normal. 

ADD REPLYlink written 2.8 years ago by bankapur0

Hello bankapur!

We believe that this post is does not fit the main topic of this site.

self answered ;)

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.


ADD REPLYlink written 2.8 years ago by Martin Čech ♦♦ 4.3k
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