Demystifying Conda and Virtual Environments for Bioinformatics

Explore the world of virtual environments and package management in this comprehensive tutorial video. Learn about Conda, including Anaconda, Miniconda, and Bioconda, as well as Renv for R projects. Discover how to set up Conda, create and manage environments, install packages, and switch between them effortlessly. Gain insights into conda channels, priorities, and searching for packages. Understand the importance of virtual environments in avoiding installation errors and dependency conflicts. Follow along with practical demonstrations on creating conda environments, exporting to YAML files, and using Renv for R projects. Master the art of sharing environments and package version information for reproducible research and collaborative coding.

Intro
What are virtual environments?
What is conda?
What’s with different condas - Anaconda, Miniconda and Bioconda?
renv vs conda
Demonstration goals and requirements
conda installation instructions
conda channels and priorities
Search for conda packages
base environment in conda
Checking local versions of the tools and searching for required conda packages
Create virtual environment in conda
Export environment to a YAML file .yml file
Create a conda environment from a YAML file
Why having a centralized location for all packages is problematic for analysis in R?
Creating R projects and using renv within projects
Sharing renv - save package version information to a .lock file