w-gao / macos-setup

macos-setup

This repo contains scripts and files for William Gao to set up his macOS.

Created around March, 2021. Updated on Dec 15, 2022. Updated on Feb 08, 2023.

System customization

Follow this gist to set System preferences.

Install Developer Tools

$ xcode-select --install

This also installs Git:

$ git --version

Configure Git

1. Set global identity config

$ git config --global user.name "William Gao"
$ git config --global user.email "[e-mail]"

2. Set up SSH keys

Install Homebrew

Install Homebrew by following the command here: https://brew.sh/

Useful packages

$ brew install tree
$ brew install jq

(optional) Install Python

Use pyenv to manage different Python versions. See: https://github.com/pyenv/pyenv#homebrew-in-macos

$ brew update
$ brew install pyenv

Create virtual environments:

$ python -m venv ~/venv/toil_env
$ python -m venv ~/venv/binf_env

Put this in the Python section in ~/.zshrc:

alias toil_env=". ~/venv/toil_env/bin/activate"
alias binf_env=". ~/venv/binf_env/bin/activate"
# ...

(optional) Jupyter notebook

$ binf_env
$ pip install jupyterlab
$ pip install notebook

(optional) Node.js

option 1: download from official website

Download and install Node.js here: https://nodejs.org/en/download/. This will install node and npm.

option 2: install via nvm (recommended)

nvm is like pyenv - it allows you to switch between different versions. See: https://github.com/nvm-sh/nvm

To install nvm via brew:

$ brew install nvm

# install the latest version
$ nvm install --lts

(optional) JavaScript/TypeScript

This requires Node.js.

Install yarn

If you prefer yarn as your package manager.

$ npm install --global yarn

NOTE: This requires sudo permission.

(optional) Install Java

Following this, it looks like the best way to install Java on a Apple Silicon machine is through Homebrew.

$ brew update
$ brew install openjdk

# then follow `brew info openjdk`:

# let the system Java wrappers find it
$ sudo ln -sfn /opt/homebrew/opt/openjdk/libexec/openjdk.jdk /Library/Java/JavaVirtualMachines/openjdk.jdk

# add to PATH
$ echo 'export PATH="/opt/homebrew/opt/openjdk/bin:$PATH"' >> ~/.zshrc

(optional) Docker

Download Docker Desktop for Mac here: https://docs.docker.com/desktop/install/mac-install/

Check installation:

$ docker --version

(optional) Kubernetes (k8s) client

If you are working with k8s clusters, you probably need kubectl.

Install kubectl

$ brew update
$ brew install kubectl

It may be a good idea to alias kubectl to k:

$ echo 'alias k=kubectl' >> ~/.zshrc
$ . ~/.zshrc

Configure ~/.kube/config

This depends on the k8s cluster setup. If working with multiple contexts, consider installing kubectx (and alias to kx) as well.

Check installation/configuration:

$ k version

This should display the versions of the client and server.

(optional) Kubernetes local cluster

If you want to set up a local kubernetes cluster for development, consider using minikube:

$ brew update
$ brew install minikube

NOTE: minikube needs a driver such as VirtualBox, hyperkit, or Docker. Docker works great.

Check installation:

$ minikube version