{
  pkgs,
  home-dir,
  ...
}:
{
  custom = {
    gui = {
      aerospace.enable = false;
      sketchybar.enable = false;
      jankyborders.enable = false;
      yabai.enable = false;
    };
    brew = {
      zen-browser = false;
      webex = true;
      slack = true;
      zoom = true;
      spotify = true;
      ghostty = true;
      ms-office = true;
      ms-teams = true;
      raycast = true;
      whatsapp = true;
      vscode = true;
      firefox = true;
      chromium = true;
      aldente = true;
      zotero = true;
      amphetamine = true;
      scroll-reverser = true;
      ice = true;
      contexts = true;
      flux = true;
      cleanshot = true;
      snippets-lab = false;
      iina = true;
      itsycal = true;
      lookaway = false;
      obsidian = true;
      zed = false;
      orion = true;
      chatgpt = true;
      antinote = true;
      swish = true;
      rectangle = true;
      emacs = true;
      drawio = true;
      soulver = true;
      pika = true;
      transmission = true;
      alt-tab = true;
      r = true;
      rstudio = true;
      sratoolkit = true;
      hisat2 = true;
      google-chrome = true;
      google-drive = true;
      vscode-insiders = true;
      positron = true;
      claude = true;
      iterm2 = true;
      cmake = true;
      ninja = true;
      clang-format = true;
      marta = true;
      # broken on aarch64-darwin
      valgrind = false;
      hammerspoon = true;
      aerospace = true;
      skim = true;
    };
  };

  hm.home.packages = with pkgs; [
    # bowtie2
    samtools
    python311Packages.htseq
    wget
    igv
    claude-code
    codex
    nodejs_24
    ghidra-bin
  ];

  hm.custom = {
    environment = {
      enable = true;
      variables = {
        EDITOR = "nvim";
        SOPS_AGE_KEY_FILE = "${home-dir}/.config/sops/age/keys.txt";
      };
    };
    emacs.enable = true;
    neovim.enable = true;
    latex.enable = true;
    tmux.enable = true;
    gui = {
      default.enable = true;
      darwin.enable = true;
      ghostty.enable = true;
      hammerspoon.enable = true;
      kitty.enable = true;
      zathura.enable = true;
      sioyek.enable = true;
    };
    email = {
      enable = true;
      davmail = true;
      neomutt = true;
      mbsync = true;
      mailcap = true;
      notmuch = true;
      mu = true;
    };
  };
}