Encrypted and secure docker containers
The root user on the host machine (where the docker daemon runs) has full access to all the processes running on the host. That means the person who controls the host machine can always get access to the RAM of the application as well as the file system. That makes it impossible to hide a key for decrypting the file system or protecting RAM from debugging.
Using obfuscation on a standard Linux box, you can make it harder to read the file system and RAM, but you can't make it impossible or the container cannot run.
If you can control the hardware running the operating system, then you might want to look at the Trusted Platform Module which starts system verification as soon as the system boots. You could then theoretically do things before the root user has access to the system to hide keys and strongly encrypt file systems. Even then, given physical access to the machine, a determined attacker can always get the decrypted data.
What you are asking about is called obfuscation. It has nothing to do with Docker and is a very language-specific problem; for data you can always do whatever mangling you want, but while you can hope to discourage the attacker it will never be secure. Even state-of-the-art encryption schemes can't help since the program (which you provide) has to contain the key.
C is usually hard enough to reverse engineer, for Python you can try pyobfuscate and similar.
For data, I found this question (keywords: encrypting files game).
If you want a completely secure solution, you're searching for the 'holy grail' of confidentiality: homomorphous encryption. In short, you want to encrypt your application and data, send them to a PC, and have this PC run them without its owner, OS, or anyone else being able to scoop at the data. Doing so without a massive performance penalty is an active research project. There has been at least one project having managed this, but it still has limitations:
- It's windows-only
- The CPU has access to the key (ie, you have to trust Intel)
- It's optimised for cloud scenarios. If you want to install this to multiple PCs, you need to provide the key in a secure way (ie just go there and type it yourself) to one of the PCs you're going to install your application, and this PC should be able to securely propagate the key to the other PCs.
Andy's suggestion on using the TPM has similar implications to points 2 and 3.
Sounds like Docker is not the right tool, because it was never intended to be used as a full-blown sandbox (at least based on what I've been reading). Why aren't you using a more full-blown VirtualBox approach? At least then you're able to lock up the virtual machine behind logins (as much as a physical installation on someone else's computer can be locked up) and run it isolated, encrypted filesystems and the whole nine yards.
You can either go lightweight and open, or fat and closed. I don't know that there's a "lightweight and closed" option.