Navigate the filesystem of your server to the Vanilla folder. Vanilla will need read AND write access to the conf folder.
There are many ways to set these permissions. One way is to execute the following from the root Vanilla folder:
chmod 777 ./conf
You will also need to grant read access to the extensions, languages, setup, and themes folders. Typically these permissions are granted by default, but if not you can achieve them with the following commands:
chmod --recursive 755 ./extensions
chmod --recursive 755 ./languages
chmod --recursive 755 ./setup
chmod --recursive 755 ./themes