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I wish to install a program that is not available through the main channel in Nixos. How do I ensure that the proper dependencies will be installed, ideally in a way that is described in a configuration file that can be replicated as is with the rest of programs installed with nix?

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You can simply nix-env -f /path/to/custom/nixpkgs -iA your-package.

Almost all dependencies in nixpkgs are pure, so the various versions on your system "don't affect each other". You can then nix-copy-closure that package to other machines, etc.

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