Take-down

Free the disk space the course used, and remove the tools if you want to

Remove project environments, Pixi’s cache, global tools and Pixi itself; workflow-manager leftovers; Docker images; Codespaces. Keep what you need: your repositories.

Time: 10 minutes.
Before you start: everything you want to keep is pushed to GitHub (git status is clean, git log origin/main shows your commits). Deleting a project folder deletes its Git history too.

How much space did the course take?

pixi info | grep -i "cache"

du -sh ~/cbio7501/*

On our test laptop: about 3.6 GB of environments for the LTEE project, 0.5 GB of data and results, and several GB in Pixi’s shared package cache.

1. Project environments

Each project keeps its environments in its own .pixi/ folder. Remove them; pixi install rebuilds them from pixi.lock whenever you need them again:

cd ~/cbio7501/ltee-project
pixi clean

Do the same in your capstone project and in the practice folders (pixi-practice, conda-comparison/from-conda).

2. Workflow and analysis leftovers

Everything here is rebuilt by pixi run reproduce:

cd ~/cbio7501/ltee-project
rm -rf results/* data/processed/* .snakemake work .nextflow .nextflow.log*

Keep results/README.md and data/processed/README.md (they are committed; git status shows if you deleted them, and git restore brings them back).

3. Pixi’s package cache

All projects share one cache of downloaded packages. Emptying it frees the most space; the next pixi install downloads again:

pixi clean cache

Lesson 05b also used micromamba, which has its own cache: pixi exec micromamba clean --all --yes.

4. Global tools and Pixi itself

pixi global list

pixi global uninstall cookiecutter

To remove Pixi completely (from the Pixi documentation’s uninstall steps): empty the cache (step 3), clean your workspaces (step 1), then

rm -r ~/.pixi

and delete the line that adds ~/.pixi/bin to your PATH in ~/.bashrc or ~/.zshrc (on Windows, remove %UserProfile%\.pixi\bin from the PATH environment variable).

5. Docker

Images take a lot of space. Remove what you no longer need:

docker image ls
docker image rm ltee-project:0.1.0
docker system prune          # stopped containers, unused networks, build cache; read the prompt

To uninstall Docker Desktop, use its Troubleshoot → Uninstall menu (macOS, Windows) or your package manager (Linux).

6. Codespaces

Codespaces count against your monthly storage quota while they exist, even when stopped. Delete the ones you do not need at https://github.com/codespaces.

What to keep

Your GitHub repositories (ltee-project, your capstone): they are your portfolio and the record of your work.
Your Zenodo records: they cannot be deleted anyway, which is the point.
pixi.toml and pixi.lock in every project: with them, everything above comes back with one command.