Take down

Depending on which of the tutorials you have taken, there might be quite a lot of files stored on your computer. Here are instructions for how to remove them.

All tutorials

All the tutorials depend on you cloning the reproducible_research_course Bitbucket repo. This can be removed like any other directory; via Finder, Explorer or rm -rf reproducible_research_course. Note that this will also delete the hidden directories .git, which contains the history of the repo, and .snakemake, which contains the history of any Snakemake runs.

Conda

Several of the tutorials use Conda for installing packages. This amounts to about 2.6 gb if you've done all the tutorials. If you plan on using Conda in the future you can remove just the packages, or you can remove everything including Conda itself. Note that this is not needed if you've done the tutorials on Windows using Docker (see the section on Docker below instead).

Uninstall all of these packages but keep Conda itself for future use

First list all Conda environments

conda env list

For each of the environments except "base" run

conda remove -n envname --all

And lastly:

conda clean --all

Remove every trace of Conda

First check where Conda is installed. Look for the row "base environment".

conda info

This should say something like /Users/<user>/miniconda3. Then remove the entire Conda directory:

rm -rf /Users/<user>/miniconda3

Lastly, open your ~/.bashrc file (or ~/.bash_profile if on Mac) in a text editor and remove the path to Conda from PATH.

Snakemake

Snakemake is installed via Conda and will be removed if you follow the instructions in the Conda section above. Note that Snakemake also generates a hidden .snakemake directory in the directory where it's run. You can remove this with

rm -rf reproducible_research_course/snakemake/.snakemake

Jupyter

Jupyter is installed via Conda and will be removed if you follow the instructions in the Conda section above.

Docker

If you've done the Docker tutorial or if you've been running Docker for Windows you have some cleaning up to do. Docker is infamous for quickly taking up huge amounts of space, and some maintenance is necessary every now and then. Here is how to uninstall Docker completely. For instructions for how to remove individual images or containers, see the Docker tutorial

macOS

Click the Docker icon in the menu bar (upper right part of the screen) and select "Preferences". This will open up the window below. First select "Reset" and fill in your password. Then select "Uninstall". Once it's done uninstalling, drag the Docker app from Applications to Trash.

Linux

If you've installed Docker with apt-get, uninstall it like this:

apt-get purge docker-ce

Images, containers, and volumes are not automatically removed. To delete all of them:

rm -rf /var/lib/docker

Windows

Uninstall Docker for Windows (on Windows 10) or Docker Toolbox (on Windows 7) via Control Panel > Programs > Programs and Features. Docker Toolbox will also have installed Oracle VM VirtualBox, so uninstall that as well if you're not using it for other purposes.

Singularity

  • Images are files that can simply be deleted
  • Singularity creates a hidden directory .singularity in your home directory