Reproducible system setup

Install command line tools

Install command line tools (includes git) with:

xcode-select --install

Setup

Do all the following with:

source setup.sh

Install Homebrew

Install Homebrew with:

/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"

Link dotfiles

Link dotfiles with:

ruby dotfiles/symlink.rb

You'll need to update User and GitHub in dotfiles/.gitconfig.

Open Terminal Settings and change default shell to /bin/bash.

Install Homebrew packages

Install all packages in Brewfile with:

brew update
brew tap Homebrew/bundle
brew bundle

Includes Ruby and Python package managers (gem and pip).

Setup Python environment

brew link python@3.11
ln -s -f /opt/homebrew/opt/python/bin/python3 /opt/homebrew/opt/python/bin/python
ln -s -f /opt/homebrew/opt/python/bin/pip3 /opt/homebrew/opt/python/bin/pip
pip3 install -r requirements.txt

Setup Ruby environment

rbenv install 2.7.6
rbenv global 2.7.6
gem install bundler

Setup Java environment

Setup symlink (as suggested by brew install)

sudo ln -sfn /opt/homebrew/opt/openjdk@11/libexec/openjdk.jdk /Library/Java/JavaVirtualMachines/openjdk-11.jdk

Set OS X defaults

Set OS X defaults with computer name of Name:

source defaults/osx.sh Name

Manual updates

• Enable Full Disk Access for Terminal under Privacy and Security in System Settings.
• Import trvrb.terminal as default profile in Terminal Settings
• Add GitHub SSH key

Install remaining applications

Sign into Mac App Store and install:

• 1Password
• Bear
• Microsoft Word
• Microsoft Excel

Licenses for Office are through fredhutch.org account (next time move these to brew install).

Download and install Kaleidoscope 2.4.5 from https://cloud.kaleidoscope.app/download/v2. Download and install Mathematica 12.3.1 from https://user.wolfram.com/.

Install chromium and decktape via

brew install chromium --no-quarantine
npm install -g decktape

Install remaining Nextstrain components

Install Nextstrain CLI

curl -fsSL --proto '=https' https://nextstrain.org/cli/installer/mac | bash

Install auspice

npm install --global auspice

Install iqtree2

curl -fsSL "https://github.com/iqtree/iqtree2/releases/latest/download/iqtree-2.2.2.6-MacOSX.zip" -o "iqtree.zip"
unzip iqtree.zip && rm iqtree.zip
sudo mv iqtree-2.2.2.6-MacOSX/bin/iqtree2 /usr/local/bin/
rm -r iqtree-2.2.2.6-MacOSX/

Install nextalign

curl -fsSL "https://github.com/nextstrain/nextclade/releases/latest/download/nextalign-aarch64-apple-darwin" -o "nextalign"
chmod +x nextalign
sudo mv nextalign /usr/local/bin/

Install nextclade

curl -fsSL "https://github.com/nextstrain/nextclade/releases/latest/download/nextclade-aarch64-apple-darwin" -o "nextclade"
chmod +x nextclade
sudo mv nextclade /usr/local/bin/

Install tsv-utils

curl -L https://github.com/eBay/tsv-utils/releases/download/v2.2.1/tsv-utils-v2.2.1_osx-x86_64_ldc2.tar.gz | tar xz
sudo mv tsv-utils-v2.2.1_osx-x86_64_ldc2/bin/* /usr/local/bin/