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