galaxy-util

library26.0.1pypypi✓ verified 87d ago

The `galaxy-util` package provides common utility functions and helper classes used across the larger Galaxy bioinformatics platform. It is an integral part of the Galaxy ecosystem, supporting various functionalities within the main application. Currently at version 26.0.0, it follows the rapid release cadence of the main Galaxy project, often tied to its major releases. While available on PyPI, its primary use case is within the Galaxy project itself.

data workflow

pip install galaxy-util

github ↗package ↗

INSTALL

IMPORT

SIG · GALAXY-UTIL

galaxy-util

datapythonv26.0.1

Install

3.3s avg

Import

840ms

Disk

33MB

Pass rate

10/ 10

Env Coverage10 / 10

glibc

3.9–3.13

musl

3.9–3.13

Install & Compatibility

Where this runs

tested against v26.0.1 · pip install

no network on importno background threads

Install × environment matrix

Each cell = how many times install + import succeeded across repeated harness runs. Partial = flaky.
glibc = Debian/Ubuntu slim · musl = Alpine Linux

musl

py 3.10–3.910 runs

installs and imports cleanly · install 0.0s · import 0.894s · 34.1MB

glibc

py 3.10–3.910 runs

installs and imports cleanly · install 3.3s · import 0.786s · 35MB

33MB installed

● package 33MB

Code

Verified usage

Verified import paths — ran on the pinned version, not inferred.

safe_path

✓ from galaxy.util.path import safe_path

✗ from galaxy_util.path import safe_path

The PyPI package `galaxy-util` exposes its modules under the `galaxy.util` namespace, not `galaxy_util`.

parse_json_string

✓ from galaxy.util.json import parse_json_string

sanitize_text

✓ from galaxy.util.sanitize_text import sanitize_text

This quickstart demonstrates basic usage of two common utility functions: `safe_path` for sanitizing path components and `sanitize_text` for removing potentially dangerous HTML/script tags from strings. These are representative of the type of general-purpose helpers found in `galaxy-util`.

from galaxy.util.path import safe_path from galaxy.util.sanitize_text import sanitize_text # Example 1: Safely resolve a path component unsafe_path_component = '../etc/passwd' safe_component = safe_path(unsafe_path_component) print(f"Unsafe: {unsafe_path_component}, Safe: {safe_component}") # Example 2: Sanitize text input raw_text = '<script>alert("XSS")</script>Hello & World!' sanitized_text = sanitize_text(raw_text) print(f"Raw: {raw_text}\nSanitized: {sanitized_text}")

Debug

Known issues

breakingAPIs within `galaxy.util` can change significantly between major Galaxy releases (e.g., v25 to v26). As an internal utility package, modules, functions, or their signatures might be refactored, moved, or removed without explicit deprecation warnings targeted at external users.

fix

Refer to the Galaxy project's official release notes and source code (`lib/galaxy/util` directory in the main Galaxy repository) for the specific version you are using to confirm API stability and correct usage.

affects: All versions, especially major increments.

gotchaThe `galaxy-util` package is primarily designed for internal use within the Galaxy project. Its APIs are tightly coupled with the larger Galaxy application's internal structure and evolution, and may not always be suitable or stable for standalone, general-purpose use outside of the Galaxy ecosystem.

fix

Consider if a more general-purpose Python library exists for your specific utility need before integrating `galaxy-util` into non-Galaxy applications. Be prepared for potential API instability if you do use it externally.

affects: All versions

gotchaVersion mismatches between `galaxy-util` and the main `galaxy` package (if you are developing for Galaxy) can lead to unexpected behavior, `AttributeError`s, or runtime failures, as they are developed and released in tandem.

fix

Ensure that your `galaxy-util` version is compatible with your `galaxy` core version. Ideally, manage dependencies through the main Galaxy project's recommended setup or requirements.txt.

affects: All versions

Errors

Common errors & fixes

ModuleNotFoundError: No module named 'galaxy.util'

The `galaxy-util` package has not been installed, or your Python environment's path does not include the installation location.

fix

Ensure the package is installed: `pip install galaxy-util`. If using a virtual environment, ensure it's activated.

AttributeError: module 'galaxy.util.path' has no attribute 'some_function_name'

The specific utility function or class you are trying to import/use (`some_function_name`) was removed, renamed, or refactored in the version of `galaxy-util` you have installed. This is common due to its internal utility nature.

fix

Check the `galaxy.util` source code in the Galaxy project's GitHub repository (`lib/galaxy/util` for your specific version) to find the current API or an alternative. Update your code to reflect the new API.

ImportError: cannot import name 'SomeSpecificClass' from 'galaxy.util.tool_shed'

A class or function previously available in a submodule of `galaxy.util` has been moved to a different module, or it has been removed entirely during a refactoring.

fix

Consult the Galaxy project's official documentation or examine the source code for the exact `galaxy-util` version you are using to determine the correct import path or if the functionality has been replaced.

Upgrade

Version history

26.0.1latest on PyPI · released Jun 7, 2026

Audit

Dependencies

pythonrequiredRequired Python version for compatibility.

Agent activity

11 hits · last 30 days

node

OpenAI (training)

Resources

githubhttps://github.com/galaxyproject/galaxy ↗

packagehttps://pypi.org/project/galaxy-util/ ↗