Question: (Closed) TypeError while executing sh run.sh
0
bankapur • 0 wrote:
I am trying to run my galaxy instance off of a remote server and when I execute sh run.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
galaxy.app 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/__init__.py", 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/__init__.py", 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/__init__.py", 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/__init__.py", line 328, in getMessage
msg = msg % self.args
TypeError: not enough arguments for format string
Logged from file __init__.py, line 475
../SOFTWARE/galaxy/lib/galaxy/__init__.py:63: 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
self.check_version_conflict()
Traceback (most recent call last):
File "../SOFTWARE/galaxy/lib/galaxy/webapps/galaxy/buildapp.py", line 53, in app_factory
app = galaxy.app.UniverseApplication( global_conf=global_conf, **kwargs )
File "../SOFTWARE/galaxy/lib/galaxy/app.py", 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/config.py", line 818, in _configure_models
from galaxy.model.migrate.check import create_or_verify_database
File "../SOFTWARE/galaxy/lib/galaxy/model/migrate/check.py", line 15, in <module>
from migrate.versioning import repository, schema
ImportError: No module named migrate.versioningAny advice as to how I can fix it?
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.
Hello bankapur!
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