Hi,
I updated my galaxy distribution with
hg pull -u
Then tried to re-run galaxy and got an error:
$ ./run.sh
Traceback (most recent call last):
File "./scripts/paster.py", line 33, in <module>
serve.run()
File "/home/microbeco/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line
1049, in run
invoke(command, command_name, options, args[1:])
File "/home/microbeco/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line
1055, in invoke
exit_code = runner.run(args)
File "/home/microbeco/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line
220, in run
result = self.command()
File "/home/microbeco/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line
643, in command
app = loadapp( app_spec, name=app_name, relative_to=base, global_conf=vars)
File "/home/microbeco/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py",
line 350, in loadapp
return loadobj(APP, uri, name=name, **kw)
File "/home/microbeco/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py",
line 374, in loadobj
global_conf=global_conf)
File "/home/microbeco/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py",
line 399, in loadcontext
global_conf=global_conf)
File "/home/microbeco/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py",
line 423, in _loadconfig
return loader.get_context(object_type, name, global_conf)
File "/home/microbeco/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py",
line 561, in get_context
section)
File "/home/microbeco/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py",
line 620, in _context_from_explicit
value = import_string(found_expr)
File "/home/microbeco/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py",
line 125, in import_string
return pkg_resources.EntryPoint.parse("x=" + s).load(False)
File "/home/microbeco/galaxy-dist/lib/pkg_resources.py", line 1954, in load
entry = __import__(self.module_name, globals(),globals(), ['__name__'])
File "/home/microbeco/galaxy-dist/lib/galaxy/web/buildapp.py", line 3, in
<module>
from galaxy.webapps.galaxy.buildapp import app_factory
File "/home/microbeco/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py",
line 16, in <module>
import galaxy.model.mapping
File "/home/microbeco/galaxy-dist/lib/galaxy/model/mapping.py", line 14, in
<module>
from sqlalchemy.types import BigInteger
ImportError: cannot import name BigInteger
I also tried to update my database but got a different error:
$ sh manage_db.sh upgrade
114 -> 115...
Traceback (most recent call last):
File "./scripts/manage_db.py", line 62, in <module>
main( repository=repo, url=db_url )
File
"/home/microbeco/galaxy-dist/eggs/sqlalchemy_migrate-0.5.4-py2.7.egg/migrate/versioning/shell.py",
line 150, in main
ret = command_func(**kwargs)
File
"/home/microbeco/galaxy-dist/eggs/sqlalchemy_migrate-0.5.4-py2.7.egg/migrate/versioning/api.py",
line 221, in upgrade
return _migrate(url, repository, version, upgrade=True, err=err, **opts)
File
"/home/microbeco/galaxy-dist/eggs/sqlalchemy_migrate-0.5.4-py2.7.egg/migrate/versioning/api.py",
line 349, in _migrate
schema.runchange(ver, change, changeset.step)
File
"/home/microbeco/galaxy-dist/eggs/sqlalchemy_migrate-0.5.4-py2.7.egg/migrate/versioning/schema.py",
line 184, in runchange
change.run(self.engine, step)
File
"/home/microbeco/galaxy-dist/eggs/sqlalchemy_migrate-0.5.4-py2.7.egg/migrate/versioning/script/py.py",
line 101, in run
func()
TypeError: upgrade() takes exactly 1 argument (0 given)
How can I fix this?
Thanks,
Dan
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