dotfiles

macOS dev environment for bioinformatics on Apple Silicon — zsh, Homebrew, Claude Code, modern CLI tools.

What's included

Directory	Contents
shell/	zshrc (GNU tools, fzf, history, completion, aliases), zprofile
git/	gitconfig (rebase, rerere, histogram diff), global gitignore
ssh/	SSH config (ControlMaster multiplexing, keychain, GitHub)
claude/	CLAUDE.md, settings.json (hooks, plugins), custom commands
macos/	defaults.sh — 50+ macOS developer productivity settings
Brewfile	Declarative Homebrew packages (CLI, dev tools, bioinformatics)

Quick start

git clone https://github.com/shandley/dotfiles.git ~/Code/tools/dotfiles
cd ~/Code/tools/dotfiles
chmod +x install.sh
./install.sh

The installer runs interactively by default, prompting for each section.

Selective install

./install.sh --link   # symlink dotfiles only
./install.sh --brew   # install Homebrew packages only
./install.sh --macos  # apply macOS defaults only
./install.sh --all    # everything

Prerequisites

• Apple Silicon Mac (M1/M2/M3/M4)
• Xcode Command Line Tools (xcode-select --install)

Key decisions

• GNU over BSD: GNU coreutils, findutils, sed, tar, grep, and gawk replace BSD defaults on PATH for Linux compatibility
• Symlinks, not copies: install.sh symlinks files from this repo into $HOME, so edits in either location stay in sync
• No secrets: No tokens, keys, or credentials are stored in this repo
• Rebase workflow: Git is configured to rebase on pull, with rerere enabled for conflict memory
• Modern CLI: fd (find), bat (cat), eza (ls), fzf (fuzzy finder), ripgrep (grep) are installed and aliased

Customization

• Brewfile: Add/remove packages, then run brew bundle --file=Brewfile
• macOS defaults: Review macos/defaults.sh and comment out settings you don't want before running
• Git identity: git/gitconfig contains name and email — update for your own use
• SSH keys: Update ssh/config with your own IdentityFile path

Credits

Inspired by mathiasbynens/dotfiles and holman/dotfiles.

License

MIT