Galaxy.yml issue when creating custom flavor

[Oddant1]

Hello, I am trying to follow the instructions here to create a custom Galaxy flavor. I started by just copy-pasting the Dockerfile and my_tool_list.yml listed there, but when I run the docker build command I get the following in the RUN install-tools /galaxy/my_tool_list.yml step:

Skipping Galaxy client build because git is not in use and the client build state cannot be compared against local changes. If you have made local modifications, then manual client builds will be required. See ./client/README.md for more information.
Activating virtualenv at /galaxy_venv
Error: <class 'gravity.state.GalaxyTUSDService'> init failed: To run tusd you need to set galaxy_infrastructure_url in the galaxy section of galaxy.yml
Executing: galaxy
Error: <class 'gravity.state.GalaxyTUSDService'> init failed: To run tusd you need to set galaxy_infrastructure_url in the galaxy section of galaxy.yml
cat: galaxy_install.pid: No such file or directory
calling galaxy_wait with timeout=600 ensure_admin=False
[00] Galaxy not up yet... HTTPConnectionPool(host='localhost', port=8080): Max retries exceeded with url: /api/version (Caused
[01] Galaxy not up yet... HTTPConnectionPool(host='localhost', port=8080): Max retries exceeded with url: /api/version (Caused
[02] Galaxy not up yet... HTTPConnectionPool(host='localhost', port=8080): Max retries exceeded with url: /api/version (Caused
[03] Galaxy not up yet... HTTPConnectionPool(host='localhost', port=8080): Max retries exceeded with url: /api/version (Caused
[04] Galaxy not up yet... HTTPConnectionPool(host='localhost', port=8080): Max retries exceeded with url: /api/version (Caused
[05] Galaxy not up yet... HTTPConnectionPool(host='localhost', port=8080): Max retries exceeded with url: /api/version (Caused
[06] Galaxy not up yet... HTTPConnectionPool(host='localhost', port=8080): Max retries exceeded with url: /api/version (Caused
[07] Galaxy not up yet... HTTPConnectionPool(host='localhost', port=8080): Max retries exceeded with url: /api/version (Caused
[08] Galaxy not up yet... HTTPConnectionPool(host='localhost', port=8080): Max retries exceeded with url: /api/version (Caused
[09] Galaxy not up yet... HTTPConnectionPool(host='localhost', port=8080): Max retries exceeded with url: /api/version (Caused
[10] Galaxy not up yet... HTTPConnectionPool(host='localhost', port=8080): Max retries exceeded with url: /api/version (Caused

That Galaxy not up yet... continues until timeout. This would appear to be due to an issue with the galaxy.yml config; however, I am unsure of how I am supposed to set the galaxy.yml for that step. I'm no expert on galaxy or docker, but it looks to me like that config ought to be set by the base image?

Any help would be appreciated. Thank you.

[Oddant1]

There is some additional error after the timeout as well

[598] Galaxy not up yet... HTTPConnectionPool(host='localhost', port=8080): Max retries exceeded with url: /api/version (Caused
[599] Galaxy not up yet... HTTPConnectionPool(host='localhost', port=8080): Max retries exceeded with url: /api/version (Caused
[600] Galaxy not up yet... HTTPConnectionPool(host='localhost', port=8080): Max retries exceeded with url: /api/version (Caused
Failed to contact Galaxy within timeout (600), exiting with error code.
Creating admin user admin with key fakekey and password password if not existing
Traceback (most recent call last):
File "/galaxy_venv/lib/python3.10/site-packages/sqlalchemy/engine/base.py", line 1967, in _exec_single_context
self.dialect.do_execute(
File "/galaxy_venv/lib/python3.10/site-packages/sqlalchemy/engine/default.py", line 924, in do_execute
cursor.execute(statement, parameters)
psycopg2.errors.UndefinedTable: relation "galaxy_user" does not exist
LINE 3: FROM galaxy_user
^
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/usr/local/bin/create_galaxy_user.py", line 70, in <module>
add_user(sa_session, security_agent, options.user, options.password, key=options.key, username=options.username)
File "/usr/local/bin/create_galaxy_user.py", line 19, in add_user
if query.count() > 0:
File "/galaxy_venv/lib/python3.10/site-packages/sqlalchemy/orm/query.py", line 3112, in count
self._legacy_from_self(col).enable_eagerloads(False).scalar()
File "/galaxy_venv/lib/python3.10/site-packages/sqlalchemy/orm/query.py", line 2805, in scalar
ret = self.one()
File "/galaxy_venv/lib/python3.10/site-packages/sqlalchemy/orm/query.py", line 2778, in one
return self._iter().one() # type: ignore
File "/galaxy_venv/lib/python3.10/site-packages/sqlalchemy/orm/query.py", line 2827, in _iter
result: Union[ScalarResult[_T], Result[_T]] = self.session.execute(
File "/galaxy_venv/lib/python3.10/site-packages/sqlalchemy/orm/session.py", line 2351, in execute
return self._execute_internal(
File "/galaxy_venv/lib/python3.10/site-packages/sqlalchemy/orm/session.py", line 2236, in _execute_internal
result: Result[Any] = compile_state_cls.orm_execute_statement(
File "/galaxy_venv/lib/python3.10/site-packages/sqlalchemy/orm/context.py", line 293, in orm_execute_statement
result = conn.execute(
File "/galaxy_venv/lib/python3.10/site-packages/sqlalchemy/engine/base.py", line 1418, in execute
return meth(
File "/galaxy_venv/lib/python3.10/site-packages/sqlalchemy/sql/elements.py", line 515, in _execute_on_connection
return connection._execute_clauseelement(
File "/galaxy_venv/lib/python3.10/site-packages/sqlalchemy/engine/base.py", line 1640, in _execute_clauseelement
ret = self._execute_context(
File "/galaxy_venv/lib/python3.10/site-packages/sqlalchemy/engine/base.py", line 1846, in _execute_context
return self._exec_single_context(
File "/galaxy_venv/lib/python3.10/site-packages/sqlalchemy/engine/base.py", line 1986, in _exec_single_context
self._handle_dbapi_exception(
File "/galaxy_venv/lib/python3.10/site-packages/sqlalchemy/engine/base.py", line 2353, in _handle_dbapi_exception
raise sqlalchemy_exception.with_traceback(exc_info[2]) from e
File "/galaxy_venv/lib/python3.10/site-packages/sqlalchemy/engine/base.py", line 1967, in _exec_single_context
self.dialect.do_execute(
File "/galaxy_venv/lib/python3.10/site-packages/sqlalchemy/engine/default.py", line 924, in do_execute
cursor.execute(statement, parameters)
sqlalchemy.exc.ProgrammingError: (psycopg2.errors.UndefinedTable) relation "galaxy_user" does not exist
LINE 3: FROM galaxy_user
^
[SQL: SELECT count(*) AS count_1
FROM (SELECT galaxy_user.id AS galaxy_user_id, galaxy_user.create_time AS galaxy_user_create_time, galaxy_user.update_time AS galaxy_user_update_time, galaxy_user.email AS galaxy_user_email, galaxy_user.username AS galaxy_user_username, galaxy_user.password AS galaxy_user_password, galaxy_user.last_password_change AS galaxy_user_last_password_change, galaxy_user.external AS galaxy_user_external, galaxy_user.form_values_id AS galaxy_user_form_values_id, galaxy_user.preferred_object_store_id AS galaxy_user_preferred_object_store_id, galaxy_user.deleted AS galaxy_user_deleted, galaxy_user.purged AS galaxy_user_purged, galaxy_user.disk_usage AS galaxy_user_disk_usage, galaxy_user.active AS galaxy_user_active, galaxy_user.activation_token AS galaxy_user_activation_token
FROM galaxy_user
WHERE galaxy_user.email = %(email_1)s) AS anon_1]
[parameters: {'email_1': 'admin@example.org'}]
(Background on this error at: https://sqlalche.me/e/20/f405)
Storing log file in: /tmp/ephemeris_bftd49xh
Traceback (most recent call last):
File "/tool_deps/_conda/bin/shed-tools", line 10, in <module>
sys.exit(main())
File "/tool_deps/_conda/lib/python3.10/site-packages/ephemeris/shed_tools.py", line 708, in main
install_results = install_repository_manager.install_repositories(
File "/tool_deps/_conda/lib/python3.10/site-packages/ephemeris/shed_tools.py", line 217, in install_repositories
filtered_repos = self.filter_installed_repos(repository_list)
File "/tool_deps/_conda/lib/python3.10/site-packages/ephemeris/shed_tools.py", line 150, in filter_installed_repos
installed_repos = flatten_repo_info(self.installed_repositories())
File "/tool_deps/_conda/lib/python3.10/site-packages/ephemeris/shed_tools.py", line 141, in installed_repositories
).tool_list.get("tools")
File "/tool_deps/_conda/lib/python3.10/site-packages/ephemeris/get_tool_list_from_galaxy.py", line 154, in tool_list
repo_list = self.repository_list
File "/tool_deps/_conda/lib/python3.10/site-packages/ephemeris/get_tool_list_from_galaxy.py", line 113, in repository_list
walk_tools(self.toolbox, record_repo)
File "/tool_deps/_conda/lib/python3.10/site-packages/ephemeris/get_tool_list_from_galaxy.py", line 89, in toolbox
return get_tool_panel(self.gi)
File "/tool_deps/_conda/lib/python3.10/site-packages/ephemeris/get_tool_list_from_galaxy.py", line 21, in get_tool_panel
return tool_client.get_tool_panel()
File "/tool_deps/_conda/lib/python3.10/site-packages/bioblend/galaxy/tools/__init__.py", line 74, in get_tool_panel
return self._raw_get_tool(in_panel=True)
File "/tool_deps/_conda/lib/python3.10/site-packages/bioblend/galaxy/tools/__init__.py", line 81, in _raw_get_tool
return self._get(params=params)
File "/tool_deps/_conda/lib/python3.10/site-packages/bioblend/galaxy/client.py", line 134, in _get
raise ConnectionError(
bioblend.ConnectionError: HTTPConnectionPool(host='localhost', port=8080): Max retries exceeded with url: /api/tools?in_panel=True (Caused by NewConnectionError('<urllib3.connection.HTTPConnection object at 0x7f52bda98310>: Failed to establish a new connection: [Errno 111] Connection refused')), 0 attempts left:

[jayadevjoshi]

@Oddant1 Were you able to fix the issue? I was trying to solve it with some work around, #622, it worked partially, but tools are not appearing in the Galaxy instance.