Architecture 13 - Galaxy Dependencies Management

Contributors

John Chilton

Questions

• How does Galaxy manage dependencies?

• What is the virtualenv used for?

• Where do JavaScript dependencies come from?

Objectives

• Understand Python dependency management

• Understand JavaScript dependency management

• Learn about the wheels server

layout: introduction_slides topic_name: Galaxy Architecture

Architecture 13 - Galaxy Dependencies Management

The architecture of Galaxy’s dependencies.

layout: true left-aligned class: left, middle — layout: true class: center, middle

Dependencies - Python

script/common_startup.sh sets up a virtualenv with required dependencies in $GALAXY_ROOT/.venv (or $GALAXY_VIRTUAL_ENV if set).

• Check for existing virtual environment, if it doesn’t exist check for virtualenv.
• If virtualenv exists, use it. Otherwise download it as a script and setup a virtual environment using it.
• . "$GALAXY_VIRTUAL_ENV/bin/activate"
• Upgrade to latest pip to allow use of binary wheels.
• pip install -r requirements.txt --index-url https://wheels.galaxyproject.org/simple
• Install dozens of dependencies.

Dependencies - JavaScript

• Dependencies are defined in client/package.json.
• These are fetched from npm and compiled into bundles as part of make client and related Makefile targets.

Key Points

• Python: virtualenv with pip and wheels from galaxyproject.org
• JavaScript: npm/yarn with package.json
• No compilation required by default
• Binary wheels for fast installation

Thank you!