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Galaxy Documentation

repository·dev·Indexed 23 days ago

https://github.com/galaxyproject/galaxy

Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational research. This documentation covers the Galaxy client build system, including the pnpm workspace architecture, Vue component design patterns, and unit testing with Vitest and Vue Test Utils. It also provides detailed guidance on using the @galaxyproject/galaxy-api-client library for managing histories, workflows, and jobs via the Galaxy API.

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What's inside Galaxy

  1. Overview of the galaxy.datatypes package

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    The galaxy.datatypes package provides a structured way to handle various biological and computational data types within Galaxy. It includes specialized subpackages and submodules for managing specific data formats, such as sequences, assemblies, annotations, and more. This package is central to how Galaxy identifies, validates, and processes different types of files and data structures.

  3. Overview of Galaxy authentication mechanisms

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    Galaxy supports several authentication methods depending on your deployment needs:

    • Galaxy Database: The default method using email addresses and passwords stored in the Galaxy database.
    • OIDC and OAuth2.0: Enables login via external identity providers like Google or Okta without requiring local Galaxy user creation.
    • Authentication Framework: A plugin-driven system that allows delegating authentication to LDAP, Active Directory, or PAM.
    • Proxy Authentication (Remote User): Allows a front-end web server (like Apache or Nginx) to handle authentication and pass the user identity to Galaxy via HTTP headers.

  6. Overview of the galaxy.tool_util.deps package

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    The galaxy.tool_util.deps package provides utilities for managing tool dependencies within Galaxy. It includes support for various dependency resolution mechanisms and installation environments, such as Conda, Homebrew, Docker, and Singularity. The package is organized into several subpackages and modules that handle specific aspects of dependency management, containerization, and command execution.

  7. Overview of the tool_shed package

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    The tool_shed package is a core component of Galaxy used for managing tool repositories and their integrations. It provides the underlying logic for interacting with the Tool Shed, managing dependencies, handling repository types, and coordinating metadata and tool installation processes.

  11. Overview of the galaxy.tools package

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    The galaxy.tools package is a collection of utility modules and subpackages designed to support various aspects of the Galaxy ecosystem. It provides specialized functionality for biological tools, data fetching, error handling, tool execution, and more. Developers can extend or utilize these tools to manage tool-related logic within Galaxy.

  12. Overview of the tool_shed.util package

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    The tool_shed.util package provides a collection of utility modules designed to support Tool Shed operations within Galaxy. It is organized into several specialized submodules that handle tasks ranging from Mercurial (hg) interactions and metadata management to repository content handling and search indexing.