galaxy

mirror of https://github.com/galaxyproject/galaxy.git synced 2026-10-30 18:13:23 +08:00

T

Nicola Soranzo 0889af7dfc Always install `fastmcp`

in preparation for pydantic-ai 2.0.0, which replaced the
dependency on `fastmcp` with `fastmcp-slim[client]`.

Otherwise Galaxy fails to start with:

```
Traceback (most recent call last):
  File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/.venv/lib/python3.10/site-packages/fastmcp/server/__init__.py", line 6, in <module>
    from .context import Context
  File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/.venv/lib/python3.10/site-packages/fastmcp/server/context.py", line 28, in <module>
    from uncalled_for import SharedContext
ModuleNotFoundError: No module named 'uncalled_for'

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/.venv/lib/python3.10/site-packages/fastmcp/__init__.py", line 57, in __getattr__
    from fastmcp.server.context import Context
  File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/.venv/lib/python3.10/site-packages/fastmcp/server/__init__.py", line 9, in <module>
    raise ImportError(_install_hints.SERVER_SUPPORT) from exc
ImportError: FastMCP server support is not installed. Install `fastmcp` or `fastmcp-slim[server]`.

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/.venv/bin/gunicorn", line 10, in <module>
    sys.exit(run())
  File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/.venv/lib/python3.10/site-packages/gunicorn/app/wsgiapp.py", line 66, in run
    WSGIApplication("%(prog)s [OPTIONS] [APP_MODULE]", prog=prog).run()
  File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/.venv/lib/python3.10/site-packages/gunicorn/app/base.py", line 235, in run
    super().run()
  File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/.venv/lib/python3.10/site-packages/gunicorn/app/base.py", line 71, in run
    Arbiter(self).run()
  File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/.venv/lib/python3.10/site-packages/gunicorn/arbiter.py", line 63, in __init__
    self.setup(app)
  File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/.venv/lib/python3.10/site-packages/gunicorn/arbiter.py", line 139, in setup
    self.app.wsgi()
  File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/.venv/lib/python3.10/site-packages/gunicorn/app/base.py", line 66, in wsgi
    self.callable = self.load()
  File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/.venv/lib/python3.10/site-packages/gunicorn/app/wsgiapp.py", line 57, in load
    return self.load_wsgiapp()
  File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/.venv/lib/python3.10/site-packages/gunicorn/app/wsgiapp.py", line 47, in load_wsgiapp
    return util.import_app(self.app_uri)
  File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/.venv/lib/python3.10/site-packages/gunicorn/util.py", line 464, in import_app
    app = app(*args, **kwargs)
  File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/lib/galaxy/webapps/galaxy/fast_factory.py", line 63, in factory
    gx_wsgi_webapp, gx_app = app_pair(
  File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/lib/galaxy/webapps/galaxy/buildapp.py", line 178, in app_pair
    populate_api_routes(webapp, app)
  File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/lib/galaxy/webapps/galaxy/buildapp.py", line 362, in populate_api_routes
    webapp.add_api_controllers("galaxy.webapps.galaxy.api", app)
  File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/lib/galaxy/webapps/base/webapp.py", line 252, in add_api_controllers
    for name, module in base.walk_controller_modules(package_name):
  File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/lib/galaxy/web/framework/base.py", line 624, in walk_controller_modules
    module = import_module(module_name)
  File "/usr/lib/python3.10/importlib/__init__.py", line 126, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "<frozen importlib._bootstrap>", line 1050, in _gcd_import
  File "<frozen importlib._bootstrap>", line 1027, in _find_and_load
  File "<frozen importlib._bootstrap>", line 1006, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 688, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 883, in exec_module
  File "<frozen importlib._bootstrap>", line 241, in _call_with_frames_removed
  File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/lib/galaxy/webapps/galaxy/api/mcp.py", line 15, in <module>
    from fastmcp import (
  File "/usr/users/ga002/soranzon/software/nsoranzo_galaxy/.venv/lib/python3.10/site-packages/fastmcp/__init__.py", line 59, in __getattr__
    raise ImportError(_install_hints.SERVER_SUPPORT) from exc
ImportError: FastMCP server support is not installed. Install `fastmcp` or `fastmcp-slim[server]`.
```

2026-07-10 01:49:03 +01:00

.ci

Fix check_test_class_names test

2026-07-08 11:43:17 +01:00

.circleci

…

.claude/commands

…

.github

Merge pull request #23055 from galaxyproject/dependabot/github_actions/actions-23adaa3c9a

2026-07-08 17:32:56 +01:00

.vscode

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client

Serve download redirects from a dedicated /download route

2026-07-07 23:11:02 +05:30

config

…

contrib

…

cron

…

database

…

doc

Merge pull request #23030 from SergeyYakubov/bump-rucio-40.2.0

2026-07-07 17:02:14 +02:00

hooks

…

lib

Always install `fastmcp`

2026-07-10 01:49:03 +01:00

packages

Always install `fastmcp`

2026-07-10 01:49:03 +01:00

scripts

Merge branch 'release_26.1' into dev

2026-07-06 16:12:10 +02:00

static

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templates

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test

Serve download redirects from a dedicated /download route

2026-07-07 23:11:02 +05:30

test-data

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tool-data

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tools

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.coveragerc

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.dockerignore

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.flake8

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.git-blame-ignore-revs

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.gitattributes

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.gitignore

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.gitpod.yml

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.isort.cfg

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.k8s_ci.Dockerfile

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.pre-commit-config.yaml.sample

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.redocly.lint-ignore.yaml

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.redocly.yaml

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check_model.sh

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CITATION.cff

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CODE_OF_CONDUCT.md

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conftest.py

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CONTRIBUTING.md

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CONTRIBUTORS.md

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extract_dataset_parts.sh

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LICENSE.txt

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Makefile

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manage_db.sh

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manage_toolshed_db.sh

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mypy.ini

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pyproject.toml

Always install `fastmcp`

2026-07-10 01:49:03 +01:00

pytest.ini

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README.rst

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requirements.txt

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rolling_restart.sh

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run_tests.sh

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run_tool_shed.sh

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run.sh

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SECURITY.md

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tox.ini

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tsconfig.json

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ty.toml

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zizmor.yml

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README.rst

.. figure:: https://galaxyproject.org/images/galaxy-logos/galaxy_project_logo.jpg
   :alt: Galaxy Logo

The latest information about Galaxy can be found on the `Galaxy Community Hub <https://galaxyproject.org/>`__.

Community support is available at `Galaxy Help <https://help.galaxyproject.org/>`__.

.. image:: https://img.shields.io/badge/chat-gitter-blue.svg
    :target: https://gitter.im/galaxyproject/Lobby
    :alt: Chat on gitter

.. image:: https://img.shields.io/badge/chat-irc.freenode.net%23galaxyproject-blue.svg
    :target: https://webchat.freenode.net/?channels=galaxyproject
    :alt: Chat on irc

.. image:: https://img.shields.io/badge/release-documentation-blue.svg
    :target: https://docs.galaxyproject.org/en/master/
    :alt: Release Documentation

.. image:: https://travis-ci.org/galaxyproject/galaxy.svg?branch=dev
    :target: https://travis-ci.org/galaxyproject/galaxy
    :alt: Inspect the test results

Galaxy Quickstart
=================

Galaxy requires Python 3.10 or higher. To check your Python version, run:

.. code:: console

    $ python -V
    Python 3.10.12

Start Galaxy:

.. code:: console

    $ sh run.sh

Once Galaxy completes startup, you should be able to view Galaxy in your
browser at: http://localhost:8080

For more installation details please see: https://getgalaxy.org/

Documentation is available at: https://docs.galaxyproject.org/

Tutorials on how to use Galaxy, perform scientific analyses with it, develop Galaxy and its tools, and admin a Galaxy server are at: https://training.galaxyproject.org/

Tools
=====

Tools can be either installed from the Tool Shed or added manually.
For details please see the `tutorial <https://galaxyproject.org/admin/tools/add-tool-from-toolshed-tutorial/>`__.
Note that not all dependencies for the tools provided in the
``tool_conf.xml.sample`` are included. To install them please visit
"Manage dependencies" in the admin interface.

Issues and Galaxy Development
=============================

Please see `CONTRIBUTING.md <CONTRIBUTING.md>`_ .