Checking /export... OSError Invalid cross-device link: '/tool_deps' -> '/export/tool_deps'

[JoelPHoward]

Hi, I am trying to pull/run docker-galaxy-stable via the following:

docker run -d -p 8080:80 \
    -v /Users/joelhoward/galaxy/export/:/export/ \
    -v /Users/joelhoward/galaxy/my_galaxy_tools/:/local_tools \
    bgruening/galaxy-stable

Where /Users/joelhoward/galaxy/ is a fresh directory. This seems to pull the image with no issues, but while it is creating the export volume, I run into the following error:

Enable Galaxy reports authentification
Checking /export...
Traceback (most recent call last):
File "/tool_deps/_conda/lib/python3.7/shutil.py", line 563, in move
os.rename(src, real_dst)
OSError: [Errno 18] Invalid cross-device link: '/tool_deps' -> '/export/tool_deps'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/local/bin/export_user_files.py", line 142, in
change_path( os.path.join('/tool_deps') )
File "/usr/local/bin/export_user_files.py", line 26, in change_path
shutil.move( src, dest )
File "/tool_deps/_conda/lib/python3.7/shutil.py", line 574, in move
symlinks=True)
File "/tool_deps/_conda/lib/python3.7/shutil.py", line 365, in copytree
raise Error(errors)
shutil.Error: [('/tool_deps/_conda/pkgs/ncurses-6.1-he6710b0_1/share/terminfo/a', '/export/tool_deps/_conda/pkgs/ncurses-6.1-he6710b0_1/share/terminfo/a', "[Errno 17] File exists: '/export/tool_deps/_conda/pkgs/ncurses-6.1-he6710b0_1/share/terminfo/a'"), ('/tool_deps/_conda/pkgs/ncurses-6.1-he6710b0_1/share/terminfo/h/hp2621a', '/export/tool_deps/_conda/pkgs/ncurses-6.1-he6710b0_1/share/terminfo/h/hp2621a', "[Errno 17] File exists: 'hp2621' -> '/export/tool_deps/_conda/pkgs/ncurses-6.1-he6710b0_1/share/terminfo/h/hp2621a'"), ('/tool_deps/_conda/pkgs/ncurses-6.1-he6710b0_1/share/terminfo/h/hp70092A', '/export/tool_deps/_conda/pkgs/ncurses-6.1-he6710b0_1/share/terminfo/h/hp70092A', "[Errno 17] File exists: 'hp70092' -> '/export/tool_deps/_conda/pkgs/ncurses-6.1-he6710b0_1/share/terminfo/h/hp70092A'"), ('/tool_deps/_conda/pkgs/ncurses-6.1-he6710b0_1/share/terminfo/q', '/export/tool_deps/_conda/pkgs/ncurses-6.1-he6710b0_1/share/terminfo/q', "[Errno 17] File exists: '/export/tool_deps/_conda/pkgs/ncurses-6.1-he6710b0_1/share/terminfo/q'"), ('/tool_deps/_conda/pkgs/ncurses-6.1-he6710b0_1/share/terminfo/p', '/export/tool_deps/_conda/pkgs/ncurses-6.1-he6710b0_1/share/terminfo/p', "[Errno 17] File exists: '/export/tool_deps/_conda/pkgs/ncurses-6.1-he6710b0_1/share/terminfo/p'"), ('/tool_deps/_conda/pkgs/ncurses-6.1-he6710b0_1/share/terminfo/m', '/export/tool_deps/_conda/pkgs/ncurses-6.1-he6710b0_1/share/terminfo/m', "[Errno 17] File exists: '/export/tool_deps/_conda/pkgs/ncurses-6.1-he6710b0_1/share/terminfo/m'"), ('/tool_deps/_conda/pkgs/ncurses-6.1-he6710b0_1/share/terminfo/2/2621A', '/export/tool_deps/_conda/pkgs/ncurses-6.1-he6710b0_1/share/terminfo/2/2621A', "[Errno 17] File exists: '../h/hp2621' -> '/export/tool_deps/_conda/pkgs/ncurses-6.1-he6710b0_1/share/terminfo/2/2621A'"), ('/tool_deps/_conda/pkgs/ncurses-6.1-he6710b0_1/share/terminfo/X', '/export/tool_deps/_conda/pkgs/ncurses-6.1-he6710b0_1/share/terminfo/X', "[Errno 17] File exists: '/export/tool_deps/_conda/pkgs/ncurses-6.1-he6710b0_1/share/terminfo/X'"), ('/tool_deps/_conda/pkgs/ncurses-6.1-he6710b0_1/share/terminfo/n', '/export/tool_deps/_conda/pkgs/ncurses-6.1-he6710b0_1/share/terminfo/n', "[Errno 17] File exists: '/export/tool_deps/_conda/pkgs/ncurses-6.1-he6710b0_1/share/terminfo/n'"), ('/tool_deps/_conda/pkgs/ncurses-6.1-he6710b0_1/share/terminfo/e', '/export/tool_deps/_conda/pkgs/ncurses-6.1-he6710b0_1/share/terminfo/e', "[Errno 17] File exists: '/export/tool_deps/_conda/pkgs/ncurses-6.1-he6710b0_1/share/terminfo/e'"), ('/tool_deps/_conda/pkgs/ncurses-6.1-he6710b0_1/share/terminfo/l', '/export/tool_deps/_conda/pkgs/ncurses-6.1-he6710b0_1/share/terminfo/l', "[Errno 17] File exists: '/export/tool_deps/_conda/pkgs/ncurses-6.1-he6710b0_1/share/terminfo/l'"), ('/tool_deps/_conda/share/terminfo/a', '/export/tool_deps/_conda/share/terminfo/a', "[Errno 17] File exists: '/export/tool_deps/_conda/share/terminfo/a'"), ('/tool_deps/_conda/share/terminfo/h/hp2621a', '/export/tool_deps/_conda/share/terminfo/h/hp2621a', "[Errno 17] File exists: 'hp2621' -> '/export/tool_deps/_conda/share/terminfo/h/hp2621a'"), ('/tool_deps/_conda/share/terminfo/h/hp70092A', '/export/tool_deps/_conda/share/terminfo/h/hp70092A', "[Errno 17] File exists: 'hp70092' -> '/export/tool_deps/_conda/share/terminfo/h/hp70092A'"), ('/tool_deps/_conda/share/terminfo/q', '/export/tool_deps/_conda/share/terminfo/q', "[Errno 17] File exists: '/export/tool_deps/_conda/share/terminfo/q'"), ('/tool_deps/_conda/share/terminfo/p', '/export/tool_deps/_conda/share/terminfo/p', "[Errno 17] File exists: '/export/tool_deps/_conda/share/terminfo/p'"), ('/tool_deps/_conda/share/terminfo/m', '/export/tool_deps/_conda/share/terminfo/m', "[Errno 17] File exists: '/export/tool_deps/_conda/share/terminfo/m'"), ('/tool_deps/_conda/share/terminfo/2/2621A', '/export/tool_deps/_conda/share/terminfo/2/2621A', "[Errno 17] File exists: '../h/hp2621' -> '/export/tool_deps/_conda/share/terminfo/2/2621A'"), ('/tool_deps/_conda/share/terminfo/X', '/export/tool_deps/_conda/share/terminfo/X', "[Errno 17] File exists: '/export/tool_deps/_conda/share/terminfo/X'"), ('/tool_deps/_conda/share/terminfo/n', '/export/tool_deps/_conda/share/terminfo/n', "[Errno 17] File exists: '/export/tool_deps/_conda/share/terminfo/n'"), ('/tool_deps/_conda/share/terminfo/e', '/export/tool_deps/_conda/share/terminfo/e', "[Errno 17] File exists: '/export/tool_deps/_conda/share/terminfo/e'"), ('/tool_deps/_conda/share/terminfo/l', '/export/tool_deps/_conda/share/terminfo/l', "[Errno 17] File exists: '/export/tool_deps/_conda/share/terminfo/l'")]
Disable Galaxy Interactive Environments. Start with --privileged to enable IE's.
Starting postgres
postgresql: ERROR (spawn error)
Checking if database is up and running
Traceback (most recent call last):

And then the following repeats:

File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 2285, in _wrap_pool_connect
return fn()
File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/pool/base.py", line 363, in connect
return _ConnectionFairy._checkout(self)
File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/pool/base.py", line 773, in _checkout
fairy = _ConnectionRecord.checkout(pool)
File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/pool/base.py", line 492, in checkout
rec = pool._do_get()
File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/pool/impl.py", line 139, in _do_get
self.dec_overflow()
File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/util/langhelpers.py", line 69, in exit
exc_value, with_traceback=exc_tb,
File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/util/compat.py", line 178, in raise
raise exception
File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/pool/impl.py", line 136, in _do_get
return self._create_connection()
File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/pool/base.py", line 308, in _create_connection
return _ConnectionRecord(self)
File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/pool/base.py", line 437, in init
self.__connect(first_connect_check=True)
File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/pool/base.py", line 657, in _connect
pool.logger.debug("Error on connect(): %s", e)
File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/util/langhelpers.py", line 69, in exit
exc_value, with_traceback=exc_tb,
File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/util/compat.py", line 178, in raise
raise exception
File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/pool/base.py", line 652, in __connect
connection = pool._invoke_creator(self)
File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/engine/strategies.py", line 114, in connect
return dialect.connect(*cargs, **cparams)
File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/engine/default.py", line 490, in connect
return self.dbapi.connect(*cargs, **cparams)
File "/galaxy_venv/lib/python3.7/site-packages/psycopg2/init.py", line 126, in connect
conn = _connect(dsn, connection_factory=connection_factory, **kwasync)
psycopg2.OperationalError: could not connect to server: Connection refused
Is the server running on host "localhost" (127.0.0.1) and accepting
TCP/IP connections on port 5432?
could not connect to server: Cannot assign requested address
Is the server running on host "localhost" (::1) and accepting
TCP/IP connections on port 5432?
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/usr/local/bin/check_database.py", line 25, in
query.count()
File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/orm/query.py", line 3669, in count
return self.from_self(col).scalar()
File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/orm/query.py", line 3393, in scalar
ret = self.one()
File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/orm/query.py", line 3360, in one
ret = self.one_or_none()
File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/orm/query.py", line 3329, in one_or_none
ret = list(self)
File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/orm/query.py", line 3405, in iter
return self._execute_and_instances(context)
File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/orm/query.py", line 3427, in _execute_and_instances
querycontext, self._connection_from_session, close_with_result=True
File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/orm/query.py", line 3442, in _get_bind_args
mapper=self._bind_mapper(), clause=querycontext.statement, **kw
File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/orm/query.py", line 3420, in _connection_from_session
conn = self.session.connection(**kw)
File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/orm/session.py", line 1133, in connection
execution_options=execution_options,
File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/orm/session.py", line 1142, in _connection_for_bind
conn = engine._contextual_connect(**kw)
File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 2251, in _contextual_connect
self._wrap_pool_connect(self.pool.connect, None),
File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 2289, in wrap_pool_connect
e, dialect, self
File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1555, in handle_dbapi_exception_noconnection
sqlalchemy_exception, with_traceback=exc_info[2], from=e
File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/util/compat.py", line 178, in raise
raise exception

I am using Docker version 20.10.3, build 48d30b5 (Docker for Mac).
If I exclude the line -v /Users/joelhoward/galaxy/export/:/export/ it works and I can open galaxy in my browser.

Any help with this would be appreciated.