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Organizing system configs with NixOS

Table of Contents

Nix and NixOS has been the technology I've been the most excited about in the last few years. While I have used Linux on my personal desktop and home server in the past, I never did anything complicated. It was so hard to remember what I did to my system to get it to work the way I wanted. This led to me keeping my systems very basic and eventually just using windows + docker for everything. While that setup worked fine, it was hard to customize things... I wanted to rice out my config like everyone on r/unixporn

When I found NixOS it was like a lightbulb went off. Now I can feel free to change my config as I please, not be scared if I break something, and be able to reproduce my system if I need to reinstall or got a new machine.

This post will be going over the "vibe" of using NixOS, I will explain how I set up my NixOS config and explain things in broad strokes as I go. I will link out to other posts/code to go into greater detail. I may get some things wrong as I explain so if you catch something please comment!

My hope is for people who don't know NixOS this will get you to give it a try. If you are using NixOS but feel lost, give you a path forward for feeling more comfortable using it.

What is NixOS

A big point of confusion when using Nix is the difference between Nix, NixPkgs, and NixOS. This post by Gabriella Gonzalez does a great break down on the differences. For a high level TLDR, NixOS is a Linux distro built on top of NixPkgs. NixPkgs uses the Nix language to define how to build packages.

There is more nuance than that, but it will be good enough to get started and for googling the right things.

Quick NixLang overview

For people new to nix I will go over the basics so the NixOS examples aren't completely foreign, if you know a little nix or other functional languages you can probably skip this part.

I like this quote from zero to nix to describe the language

Nix is a pure, functional, lazy, declarative, and reproducible programming language.

NixLang is a lot like Haskell in that it is pure, functional, and lazy.

This example should give a decent vibe of what programming in nix is like

  foo = x: y: x;
  foo "a" (throw "sad")
# evals to "a"

That example defines a function (x: y: x;) which takes two arguments and returns the first, and binds it to the variable foo with let foo =...; in. This means the variable foo is only in scope after the in. Finally, we call foo with foo "a" (throw "sad"). This resolves to "a". Notice the error is not thrown because nix is lazy, that means if we never "need" to use a variable or expression, it will never be evaluated.

If we swap the order of the arguments to the function like foo (throw "sad") "b", we will get

       … while calling the 'throw' builtin

         at «string»:1:29:

            1| (let foo = x: y: x; in foo (throw "sad") "b")
             |                             ^

       error: sad

The laziness helps us right very declarative code, describe what you want and if you don't reference something, no worries, it won't affect performance.

One of my favorite features of the nix language is how you can use attrsets (objects, hash maps, dicts, etc.). You can create one like

  foo = {
    key1 = "bar";
    key2 = {
      nested1 = 1;
      nested2 = 2;
# resolves to 1

at first, they look like normal objects from something like python or JS but my favorite feature of them is the syntax sugar for dealing with nested attrsets

let foo = {
  key1 = "bar";
  key2.nested1 = 1;
  key2.nested2 = 2;
# resolves to 1

That snippet creates the same attrset as the example above but lets you use "path notation" to create the nested object. While a basic syntax sugar it makes it very easy to override 1 nested option when merging things together. Without it NixOS would be a big PITA to manage IMO.

The last language feature I'll cover is the with block.

with { a = 1; b = 2; };
  a + b
# evals to 3

The with block will put all of an attrset's key value pairs as variable in scope. This makes it easier to access library functions with something like with builtins or with lib, so you don't need to prefix everything.

A Basic Module

NixOS lets you organize your system into many modules. A module is a file or function that either declares options for other modules to use, or sets options defined in other modules.

For example

# Taken from
{ lib, pkgs, config, ... }:
with lib;
  # Shorter name to access final settings a
  # user of hello.nix module HAS ACTUALLY SET.
  # cfg is a typical convention.
  cfg =;
in {
  # Declare what settings a user of this "hello.nix" module CAN SET. = {
    enable = mkEnableOption "hello service";
    greeter = mkOption {
      type = types.str;
      default = "world";

  # Define what other settings, services and resources should be active IF
  # a user of this "hello.nix" module ENABLED this module
  # by setting "services.hello.enable = true;".
  config = mkIf cfg.enable { = {
      wantedBy = [ "" ];
      serviceConfig.ExecStart = "${pkgs.hello}/bin/hello -g'Hello, ${escapeShellArg cfg.greeter}!'";

The file above adds the services.hello option. When enabled NixOS will make a system service called hello.service which will log Hello <greeter>!. The module/options it defined can be used like this

  imports = [ ./hello.nix ];
  services.hello = {
    enable = true;
    greeter = "Bob";

this file imports the module so the services.hello exists and can be used. It also set the greeter option we defined so the hello.service will log Hello Bob!

There are many options defined in the NixOS standard library. Many programs can be installed and configured with NixOS options people have put together. For example to install steam I can add

    programs.steam.enable = true;

That single line will do a lot of work for you as you can see here. Enabling steam will also make sure you have OpenGL enabled, open firewall ports, and can be further configured if other steam options are set.

That is the magic of NixOS to me, many people have spent time figuring out all the edge cases/things you would normally need to do if you just installed a package and automates it all away for you.

The search page is a great reference to find options defined in the standard library.

Using NixOS

That example is fine, but what do I actually do? My NixOS config repo is organized as follows

 exa --tree --level 2
├── common
  ├── audio.nix
  ├── autorandr.nix
  ├── containers.nix
  ├── default.nix
  ├── devlopment.nix
  ├── essentials.nix
  ├── fonts.nix
  ├── gestures
  ├── homemanager
  ├── kernel.nix
  ├── myOptions
  ├── network-shares.nix
  ├── plymouth.nix
  ├── programs.nix
  ├── ssh.nix
  ├── sudo.nix
  ├── tailscale.nix
  ├── users
  └── xserver.nix
├── default.nix
├── flake.lock
├── flake.nix
├── hosts
  ├── desktop
  ├── framework
  ├── thicc-server
  └── wsl
├── legacyCommon.nix
├── pkgs
  ├── caddy-with-plugins
  ├── default.nix
  └── overlay.nix

The flake.nix file is the entry point for everything, it roughly looks like this

  inputs = {
    # ommited
  outputs = { self, nixpkgs, home-manager, wsl, flake-utils, ... }@inputs:
      overlays = [
        (import ./pkgs/overlay.nix)
      defaultModules = [
        { _module.args = { inherit inputs; }; }
          home-manager.useGlobalPkgs = true;
          home-manager.useUserPackages = true;
      mkPkgs = system:
        import nixpkgs {
          inherit system overlays;
          config.allowUnfree = true;
      mkSystem = extraModules:
        nixpkgs.lib.nixosSystem rec {
          pkgs = mkPkgs "x86_64-linux";
          system = "x86_64-linux";
          modules = defaultModules ++ extraModules;
    in {
      nixosConfigurations = {
        nixos-john = mkSystem [ ./hosts/desktop ];
        wsl = mkSystem [ wsl.nixosModules.wsl ./hosts/wsl ];
        framework = mkSystem [
        thicc-server = mkSystem [
          ({ config, pkgs, ... }: { services.vscode-server.enable = true; })

I trimmed this file down to just the most important bit of the nixosConfigurations section in the outputs. That section is a mapping of hostname => nixosConfigOptions, so the framework key is for my laptop, thicc-server is my server, and so on. The mkSystem function will add some default modules for setting up Home Manager and agenix (will explain those later), and adds in the specified modules for that host.

You may have noticed in the list of modules some elements are file paths like ./hosts/thicc-server, some are just variables like inputs.nixos-hardware.nixosModules.framework, and some are inline functions like ({ config, pkgs, ... }: { services.vscode-server.enable = true; }). Each is functionally the same, they all will turn into a module function like I showed at the beginning of this post.

Diving into my Server Config

I briefly covered how NixOS modules works and how you might organize your systems, but what does a single system look like? So now lets dive into my server (thicc-server) config.

The main part of the config lives in the ./hosts/thicc-server folder, which looks like this

 exa --tree --level 2 ./hosts/thicc-server/
├── attic.nix
├── blocky
  ├── default.nix
  └── whitelist.txt
├── caddy
  ├── default.nix
  ├── options.nix
  └── reverse-proxies.nix
├── dashy.nix
├── default.nix
├── freshrss.nix
├── hardware-configuration.nix
├── it-tools.nix
├── linkding.nix
├── monitoring
  ├── default.nix
  ├── grafana.nix
  ├── loki.nix
  └── prometheus.nix
├── mopidy.nix
└── postgres.nix

When you reference a folder in nix import, nix will read from the default.nix (similar to how JS will import a index.js file if you import from a folder).

{ config, pkgs, ... }: {
  imports = [


  time.timeZone = "America/New_York";
  networking.hostName = "thicc-server";

  myOptions = {
    graphics.enable = false;
    networkShares.enable = true;
    containers.enable = true;

  boot.loader = {
    systemd-boot.enable = true;
    efi.canTouchEfiVariables = true;

  services.openssh = {
    enable = true;
    settings.PermitRootLogin = "yes";
  virtualisation.docker.enable = true;

  system.stateVersion = "21.11";

So this file does some "core" options like hostname, timezone, enabling some of my custom options (in the myOptions section), and it imports the other files in this folder and from common

Managing complex services

Where NixOS really shines is how you manage services that need a lot of configuration like Grafana or Prometheus. People have either done a lot of groundwork for you and exposed a simple interface to get something spun up. If not, it's easy to make your own abstraction.

For example here is my config to set up Grafana

{ config, ... }:
  myDomain = config.myCaddy.domain;
  grafanaDomain = "grafana.${myDomain}";
  port = 3030;
in {
  services.grafana = {
    enable = true;
    settings = {
      server = {
        http_addr = "";
        http_port = port;
        domain = grafanaDomain;
    provision.enable = true;
  myCaddy.reverseProxies."grafana".upstream = ":${builtins.toString port}";

This file is almost like a docker compose where you set some env vars for ports and listening addresses, but I have the benefit of reading from other NixOS options to set variables (and it won't run in a container).

For example at the top I read in myDomain = config.myCaddy.domain;, this is an option I set here that is just a variable holding the domain for my home lab. This way the Grafana domain will change automatically if I decide to change my domain (unlikely but DRY, so it makes me feel good).

I also use myCaddy.reverseProxies."grafana".upstream which is another custom option of mine to generate a reverse proxy config in caddy. This will make a URL for Grafana at https://grafana.<mydomain>.

To me this is magic, one file has all the config needed to spin up Grafana and set the necessary caddy options for me. If I decide to stop using Grafana, I can delete this file, and It's as if it never existed with no dangling reverse proxies going to nowhere.

For some slightly more involved config, see my Prometheus config, it references some Grafana options to auto register data sources for me.

Managing secrets

When configuring services you will eventually need to manage secrets somehow. Some services will need an API key or password to function and leaving that in plain text in git or the nix store is a no-no (since they can be read easily). Up until recently I didn't really care, I didn't configure too many services that needed it, so I would either not care or use some hacky workaround.

Now I use agenix to encrypt my secrets. At a high level agenix is a wrapper around age which uses ssh keys to encrypt and decrypt files. The nice part is you can specify multiple keys to use as encryption and decryption. So for example I can list my user ssh key and the root ssh key for my server. So when adding/editing secrets I just need my private ssh key to decrypt, then using my public keys I can encrypt the updated secret.

agenix adds NixOS options like

  # register the secret
  age.secrets.caddy-cloudflare = {
    file = "${inputs.secrets}/secrets/caddy-cloudflare.age"; # path to encrpyted secret file
    # let the caddy user read the secret
    owner =;
    group =;
  }; = {
    # read the secret
    EnvironmentFile = config.age.secrets.caddy-cloudflare.path;

The first option will tell agenix to decrypt the secret file caddy-cloudflare.age when building the system config, and it will put the decrypted file at a path only readable by root (or in this case the caddy user since I set those options).

Then you need to use the file, most services in NixOS will have some option to read secrets set at a path, so in this case will have systemd read the path specified on startup.

The Secret Repo

In my nix config I keep my secrets in a separate private repo, It's not necessary since the age encrypted files will exist in the nix store anyway but gives me a little piece of mind just in case I mess up somehow.

That repo looks like this

 exa --tree --level 2
├── flake.lock
├── flake.nix
└── secrets
   ├── attic-admin-token.age
   ├── attic-creds.age
   └── secrets.nix

where the flake is

  inputs = {
    nixpkgs.url = "github:nixos/nixpkgs/nixos-unstable";
    flake-utils.url = "github:numtide/flake-utils";
    agenix.url = "github:ryantm/agenix";

  outputs = { self, nixpkgs, flake-utils, ... }@inputs:
    let overlays = [ inputs.agenix.overlays.default ];
    in flake-utils.lib.eachDefaultSystem (system:
      let pkgs = import nixpkgs { inherit system overlays; };
      in {
        devShells = {
          default = pkgs.mkShell { buildInputs = with pkgs; [ agenix ]; };
        secrets = ./secrets;

So TLDR just exposes a flake output of secrets which is a directory containing all my age encrypted files. This lets me reference the encrypted files like "${inputs.secrets}/secrets/caddy-cloudflare.age"; in my main nix config repo.

This is the main file that does the magic for what keys are valid for each secret

  # all public keys in this file
  githubKeys = [
  # ssh-keyscan <ip> or sudo cat /etc/ssh/ for root keys
  linux-desktop = {
    root = "ssh-ed25519 ...";
    user = "ssh-ed25519 ...";

  thicc-server = {
    root = "ssh-ed25519 ...";
    user = "ssh-ed25519 ..";

  framework = {
    root = "ssh-ed25519 ...";
    user = "ssh-ed25519 ...";

  hosts = [ linux-desktop thicc-server framework ];

  getUser = host: host.user;
  getRoot = host: host.root;
  getAllKeysForHost = host: [ (getUser host) (getRoot host) ];

  knownUsers = ( getUser hosts);
  users = githubKeys ++ knownUsers;
  systems = ( getRoot hosts);
  allKeys = users ++ systems;

  serverSecretKeys = knownUsers ++ [
    (getRoot thicc-server)
  ]; # allow all user keys to modify the thicc server secrets
in {
  "jr-pass.age".publicKeys = allKeys;
  "mopidy-spotify.age".publicKeys = allKeys;

  "freshrss-user-pass.age".publicKeys = serverSecretKeys;
  "caddy-cloudflare.age".publicKeys = serverSecretKeys;
  # other stuff ...

so in the let block I define all my systems with their user keys and root system keys. Then some helper functions for getting a key I want from a host. Finally, I make a list of allKeys so every one of my user and root keys and encrypt/decrypt some common secrets like my user password and some API keys. The other list is serverSecretKeys which is the root key for my server (which has the most secrets) and all user keys. This lets me modify the secret on all my system, but the only root account to encrypt/decrypt is my server.

When I want to add a new secret I add a new file name in the attrset at the bottom of the file with the list of keys which are valid to encrypt/decrypt and run agenix -e <filename>, once my editor closes the file will be created.

Managing Dotfiles with Home Manager

Everything I showed is dope for complex services you would run on a server, but what about dotfiles like my fish, git, and i3 config?

This is where Home Manager comes in. Home Manger gives you the NixOS module system for things that are configured in your user's home directory.

For example this

  home-manager.users.jr = {
    programs.kitty = {
      enable = true;
      shellIntegration.enableFishIntegration = true;
      settings = {
        font_family = "FiraCode Nerd Font";
        bold_font = "auto";
        italic_font = "auto";
        bold_italic_font = "auto";
        enable_audio_bell = false;
        scrollback_lines = -1;
        tab_bar_edge = "top";
        allow_remote_control = "yes";
        shell_integration = "enabled";
        macos_option_as_alt = "yes";
        shell = "fish";
      theme = "Dracula";

When home manager is run (as a NixOS module or stand alone), it will install kitty if we don't have it, and generate the kitty config file at ~/.config/kitty/kitty.conf (for the user jr in this example), and since I set shellIntegration.enableFishIntegration, it will add lines to my fish config to add kitty completions.

Personally I found Home Manager to be much more useful than "normal" NixOS at first, I had an annoying way of managing my dot files across machines and Home Manager simplified it greatly. It also works for macOS, so you can share cross-platform config easily.

I put most of my Home Manager config into a separate home manager folder/module, I then don't reference the home-manager.users.<username> prefix in any of those files. So for example in the kitty config above I only export programs.kitty = { ... } and not home-manager.users.jr.programs.kitty = {...}. This lets me share the same home manager config for multiple NixOS users (if I wanted) and standalone home manager on macOS.

For example, my NixOS user has something like

home-manager.users.jr = (import ./hm.nix {});

this will add all the options in jr-hm.nix under home-manager.users.jr

and the hm.nix file will import my home manager module like so

{ ... }: {
  imports = [ ../../homemanager ];
  # Everything in this file will be under home-manager.users.<name>

  xdg.enable = true;

  home.stateVersion = "18.09";

To see the real example see here

Home Manager on Mac

For macOS once you have nix installed you can follow this guide to enable flakes and do some home manager init if you don't have a config already.

For my case since I already had my NixOS flake, I just needed to add a new flake output homeConfiguration.<macOSUserName>, see here for my setup.

Then you can run home-manager switch --flake <pathToFlake>#<macOSUserName> to install/update your config.

One thing to note when sharing config cross-platform is certain programs/options might not work on macOS, to gate that in your config you can use pkgs.stdenv.isDarwin which will be true on macOS and false elsewhere. The lib.mkIf function will let you conditionally add settings based on a condition. So for example to disable i3 on macOS you could do

{pkgs,...}: {
  config = lib.mkIf !pkgs.stdenv.isDarwin {
    xsession.windowManager.i3 = { enable =true; ...}

Wrap up

NixOS + Home Manager feels like something from the future (even though nix is like 20 years old....). The freedom you have to change and experiment is amazing. I didn't even go into some other awesome features like system rollback, distributed builds, and making your own configuration options.

If you want to give NixOS a shot I think my config is hopefully easy to follow. Leave a comment if you want any help!