Warning: This is an unsupported use of Cryptomator. Proceed at your own risk and keep backups of your critical data.
Cryptomator is a great utility for encrypting your files in a seamless, transparent and cross-platform manner. It’s particularly designed to provide client-side encryption for file storage and synchronisation services such as Dropbox. It essentially sits between the files you save and the synchronised folder, encrypting your data before it gets stored and pushed up to the cloud.
Although it’s usually used for Dropbox-type services it works just as well with local files or ones stored on a USB drive. The only downside is that it has to be installed locally and can’t just be run off the USB stick as it’s not currently available in a portable format.
Fortunately I’ve been able to cobble together a workaround which enables me to run Cryptomator off a USB stick on a Windows PC.
First, grab your memory stick and install Portable Apps on it. This a free open source platform for running applications from a USB stick, cloud drive or whatever.
Then run Portable Apps by double clicking on the Start.exe file on your memory stick. Now we need to install the Java runtime and launcher. The apps you want are jPortable (32 and 64 bit versions are available, it won’t hurt to install both) and jPortable Launcher.
Out of the box, Java has restrictions on its encryption which we need to remove in order for Cryptomator to work.
Download the Unlimited Encryption policies from here and unzip it. You need to copy the two JAR files to your memory stick in the PortableApps\Common Files\Java\lib\security and PortableApps\Common Files\Java64\lib\security folders. The files already exist in those folders so you’ll be replacing the existing ones.
Finally, download the JAR file version of Cryptomator and copy it to your memory stick.
Now you should be able to run jPortable Launcher from the Portable Apps menu, select your downloaded Cryptomator JAR and the program will launch.
I’ve done some basic testing of this approach and everything seems to work OK but I can’t guarantee that it won’t mangle your data. Keep backups!
Cited From: https://www.simonpbriggs.co.uk/cryptomator-portable-usb-stick/