Properly install Python3

sudo apt-get install -y python3 python3-pip python3-setuptools

Now you should be able to install the Flash utility and Thonny into your user account

pip3 install thonny
pip3 install esptool

Make your the locally installed apps are on your shell's PATH

Add this to the end of your .bashrc or,zshrc if it is not already there:

export PATH=${PATH}:$HOME/.local/bin

This will not take effect until next time you start a new shell or log in again, but before you do that....

USB Port Access

Likely, your user will not yet be allowed to write to the USB serial port. You can fix that by giving them membership in the dialout user group.

sudo usermod -a -G dialout $USER

This is assuming you are logged in as the user who want to run Thonny. Note that you might need to log out and back in again for this to take effect, so this would be good time to do that before you can start accessing that port.

Load MicroPython onto your ESP controller board

Download the right firmware from micropython.org, then ...

esptool.py --chip esp32 --port /dev/ttyUSB0 erase_flash
esptool.py --chip esp32 --port /dev/ttyUSB0  write_flash --flash_mode dio --flash_size detect 0x1000 esp32-ppp-fix.bin

Configure Thonny

You should now be able to fire up Thonny. Selection Options -> Maintain Plugins and install esptool and thonny-esp, then restart Thonny. After you select a generic python interpreter and select the correct the USB port (it should find the correct default, assuming you have the ESP plugged in), you should see a REPL dialog in the lower half of the Thonny window.