Set your installation directory before running the program with -d
"your/compatibilitytools.d/directory"

Example:

protonup -d "~/.steam/root/compatibilitytools.d/"

To update to the latest version, just run protonup from a command line

Example:

protonup

List available versions with --releases

Example:

protonup --releases

Install a specific version with -t "version tag"

Example:

protonup -t 6.5-GE-2

By default the downloads are stored in a temporary folder. 
Change it with -o "custom/download/directory"

Example:

protonup -o ~/Downloads

List existing installations with -l

Example:

protonup -l

Remove existing installations with -r "version tag

Example:

protonup -r 6.5-GE-2

Use --download to download Proton-GE to the current working directory 
without installing it, you can override destination with -o

Example:

protonup --download

Use -y toggle to carry out actions without any logging or interaction

Example:

protonup --download -o ~/Downloads -y