Weirdly, I'm just writing an article on this.
I would advise against using environment variables to store secrets, mainly for the reasons Diogo Monica outlines here; they are visible in too many places (linked containers, docker inspect, child processes) and are likely to end up in debug info and issue reports. I don't think using an environment variable file will help mitigate any of these issues, although it would stop values getting saved to your shell history.
Instead, you can pass in your secret in a volume e.g:
$ docker run -v $(pwd)/my-secret-file:/secret-file ....
If you really want to use an environment variable, you could pass it in as a script to be sourced, which would at least hide it from inspect and linked containers (e.g. CMD source /secret-file && /run-my-app
).
The main drawback with using a volume is that you run the risk of accidentally checking the file into version control.
A better, but more complicated solution is to get it from a key-value store such as etcd (with crypt), keywhiz or vault.
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