Lesson 3: Managing Environments

What are Conda environments

A Conda environment is an isolated directory that contains a specific set of packages and versions. Each environment can have different tools without interfering with each other.

This is essential in bioinformatics because different projects often require different tool versions.

Keep the base environment clean

The base environment is the core Conda installation. Installing many packages into base makes it harder to maintain and can break other workflows.

Warning: Do not install workflow-specific tools in base. Always use a dedicated environment.

List existing environments

This command lists all Conda environments and shows the active one.

conda env list

Create a new environment

This command creates an environment called qc with Python 3.9.

conda create -n qc python=3.9

Activate an environment

This command activates the qc environment so you can install and run tools inside it.

conda activate qc

Your shell prompt should change to show the active environment name.

Deactivate an environment

This command returns you to the base environment.

conda deactivate

Remove an environment

This command deletes the qc environment and all packages inside it.

conda env remove -n qc

Note: Removing an environment is safe as long as you do not need those tools anymore. You can always recreate it later.