Errors during starting Galaxy on local server

1

I was trying to run galaxy on a server for around 1 week. However after I cloned the git repository and started “sh run.sh” directly, there were two error messages showing up:

  1. galaxy.tool_util.toolbox.integrated_panel DEBUG 2026-07-08 20:34:27,243 [pN:main,p:3856152,tN:MainThread] Writing integrated tool panel config file to '/home/hankun/galaxy/lib/galaxy/config/sample/integrated_tool_panel.xml'
Traceback (most recent call last):
  File "/home/hankun/galaxy/lib/galaxy/webapps/galaxy/buildapp.py", line 68, in app_pair
    app = galaxy.app.UniverseApplication(global_conf=global_conf, is_webapp=True, **kwargs)
  File "/home/hankun/galaxy/lib/galaxy/app.py", line 750, in __init__
    self._configure_toolbox()
  File "/home/hankun/galaxy/lib/galaxy/app.py", line 368, in _configure_toolbox
    ToolBoxSearch(self.toolbox, index_dir=self.config.tool_search_index_dir, index_help=index_help),
  File "/home/hankun/galaxy/lib/galaxy/tools/search/__init__.py", line 98, in __init__
    panel_searches[panel_view_id] = ToolPanelViewSearch(
  File "/home/hankun/galaxy/lib/galaxy/tools/search/__init__.py", line 199, in __init__
    self.index = self._index_setup()
  File "/home/hankun/galaxy/lib/galaxy/tools/search/__init__.py", line 203, in _index_setup
    return get_or_create_index(self.index_dir, self.schema)
  File "/home/hankun/galaxy/lib/galaxy/tools/search/__init__.py", line 74, in get_or_create_index
    os.makedirs(index_dir, exist_ok=True)
  File "/usr/lib64/python3.9/os.py", line 225, in makedirs
    mkdir(name, mode)
OSError: [Errno 22] Invalid argument: '/home/hankun/galaxy/database/tool_search_index/ontology:edam_operations'
2026-07-08 20:34:37,864 WARN exited: gunicorn (exit status 1; not expected)

  2. Error reading tool from path: phenotype_association/sift.xml
Traceback (most recent call last):
  File "/home/hankun/galaxy/lib/galaxy/tool_util/toolbox/base.py", line 881, in _load_tool_tag_set
    tool = self.load_tool(concrete_path, use_cached=False, tool_cache_data_dir=tool_cache_data_dir)
  File "/home/hankun/galaxy/lib/galaxy/tool_util/toolbox/base.py", line 1108, in load_tool
    tool = self.create_tool(
  File "/home/hankun/galaxy/lib/galaxy/tools/__init__.py", line 552, in create_tool
    return self._create_tool_from_source(tool_source, config_file=config_file, **kwds)
  File "/home/hankun/galaxy/lib/galaxy/tools/__init__.py", line 568, in _create_tool_from_source
    return create_tool_from_source(self.app, tool_source, **kwds)
  File "/home/hankun/galaxy/lib/galaxy/tools/__init__.py", line 360, in create_tool_from_source
    tool = ToolClass(config_file, tool_source, app, **kwds)
  File "/home/hankun/galaxy/lib/galaxy/tools/__init__.py", line 827, in __init__
    raise e
  File "/home/hankun/galaxy/lib/galaxy/tools/__init__.py", line 824, in __init__
    self.parse(tool_source, guid=guid, dynamic=dynamic)
  File "/home/hankun/galaxy/lib/galaxy/tools/__init__.py", line 1149, in parse
    self.parse_inputs(self.tool_source)
  File "/home/hankun/galaxy/lib/galaxy/tools/__init__.py", line 1434, in parse_inputs
    inputs = self.parse_input_elem(page_source, enctypes)
  File "/home/hankun/galaxy/lib/galaxy/tools/__init__.py", line 1629, in parse_input_elem
    param = self.parse_param_elem(input_source, enctypes, context)
  File "/home/hankun/galaxy/lib/galaxy/tools/__init__.py", line 1642, in parse_param_elem
    param = ToolParameter.build(self, input_source)
  File "/home/hankun/galaxy/lib/galaxy/tools/parameters/basic.py", line 335, in build
    return parameter_typesparam_type
  File "/home/hankun/galaxy/lib/galaxy/tools/parameters/basic.py", line 2082, in __init__
    super().__init__(tool, input_source, trans)
  File "/home/hankun/galaxy/lib/galaxy/tools/parameters/basic.py", line 1872, in __init__
    super().__init__(tool, input_source)
  File "/home/hankun/galaxy/lib/galaxy/tools/parameters/basic.py", line 191, in __init__
    self.validators.append(validation.Validator.from_element(self, elem))
  File "/home/hankun/galaxy/lib/galaxy/tools/parameters/validation.py", line 45, in from_element
    return validator_types[_type].from_element(param, elem)
  File "/home/hankun/galaxy/lib/galaxy/tools/parameters/validation.py", line 399, in from_element
    assert os.path.exists(filename), f"File {filename} specified by the 'filename' attribute not found"
AssertionError: File /home/hankun/galaxy/tool-data/sift_db.loc specified by the 'filename' attribute not found

I did not what is wrong and I was not sure how I should edit to fix the issues and ran galaxy on my browser with “localhost:8080”.
Is there anyone who can help me with my issue?

2

Before discussing the specific errors above, Python 3.9 is not supported by Galaxy anymore.

See Supported Python versions | Galaxy Hub

3

Then for the specific errors:

the second one is likely irrelevant. Galaxy is rather error-tolerant and should start fine with this one tool file not being found.

The first one is more interesting. I guess your filesystem cannot handle the `:` in the filename. To debug this: which OS are you on, and what filesystem are you running Galaxy on (is it NTFS perhaps)?

4

Thank you very much for the explanation. I checked that my filesystem is “nfs” not “ntfs”. I am currently trying with older version of Galaxy to align with the one using internally. If my filesystem could not support this ‘:’ in filename, is there any way that I can modify the configuration file like galaxy.yml to solve the problem and run Galaxy? Thank you.