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 the tutorials depend on you cloning the workshop-reproducible-research GitHub repo. This can be removed like any other directory; via Finder, Explorer or rm -rf workshop-reproducible-research. 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).

In order to remove all your Conda environments, you first need to list them:

conda env list

For each of the environments except "base" run the following:

conda remove -n envname --all

And, finally:

conda clean --all

If you also want to remove Conda itself (i.e. removing all traces of Conda), you need to 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 the following:

rm -rf workshop-reproducible-research/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". In the upper right corner, you should find a little bug icon. Click on that icon and select "Reset to factory defaults". You may have to 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

Singularity images are files that can simply be deleted. Singularity also creates a hidden directory .singularity in your home directory that contains its cache, which you may delete.

Windows

On Windows, you will additionally need to uninstall Git for Windows, VirtualBox, Vagrant and Vagrant Manager (see the Singularity installation guide).