Package Management

Package management is a crucial aspect of software development and scientific computing. It involves organizing, installing, updating, and removing software packages efficiently. This guide covers various package management tools and best practices for different environments.

Key Concepts

• Package: A collection of software components bundled together.
• Dependency: A software package required by another package to function properly.
• Repository: A storage location for packages.
• Version Control: Managing different versions of packages.

Package Management Tools

We cover several package management tools in this guide:

1. Conda and Micromamba: For managing Python and other language packages, especially useful in bioinformatics.
2. R and renv: For managing R packages and project environments.
3. Docker: For containerizing applications and their dependencies.

Best Practices

1. Use virtual environments to isolate project dependencies.
2. Keep your package management tool updated.
3. Use version pinning to ensure reproducibility.
4. Regularly update your packages, but be cautious of breaking changes.
5. Document your project's dependencies (e.g., using requirements files or lock files).

Further Reading

• Conda Documentation
• R Packages Book
• Docker Documentation

Created by Ryan D. Najac for the Palomero Lab at the Institute for Cancer Genetics.
Page last updated on 2024-10-17.