MacOS software installation

These are instructions for how to install software and data used on the course Computational Molecular Evolution (22115) when using the MacOS operating system.

Check which shell you are using

Depending on what version of MacOS you are using, your shell is probably either bash or zsh. This plays a role when you want to set environment variables (including, importantly, PATH which tells your computer where to look for executables), define aliases, etc: If you are using bash then that information should be stored in the file .bashrc, in the case of zsh, the file should be .zshrc

Issue the following command to see which one it is:

echo $SHELL

In the commands below I have assumed that you are using ZSH, and we will store information in .zshrc. If you are instead using BASH, then you should instead use .bashrc.

Install required software

# Makes sure /usr/local/bin exists (won't overwrite it if it does)
sudo mkdir -p /usr/local/bin

# Homebrew: A package manager that can be used to more easily install other software
xcode-select --install
/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"

Note: for the one-liner installation of home-brew above, you need to use /bin/bash when installing, even if your shell is zsh.

# wget: command-line tool for downloading files from the internet
brew install wget

# Text editor
# This replaces nedit in exercise manuals.
# You need a text editor that can read and save plain-text files.
# Here we install TextMate, but there are many other options, including built-in TextEdit, and BBEdit
# To run from command line: Go to Textmate --> Preferences --> Terminal --> install shell support
brew install --cask textmate

# MrBayes (built from source, linked to the BEAGLE library, with MPI for multi-core runs)
# (If you previously ran "brew install mrbayes", remove it first so it does not shadow
# this build:  brew uninstall mrbayes )
brew install cmake open-mpi git
BEAGLE_TAG=$(git ls-remote --tags --refs https://github.com/beagle-dev/beagle-lib.git 'v*' | sed 's|.*/||' | sort -V | tail -n1)
git clone --depth=1 --branch "$BEAGLE_TAG" https://github.com/beagle-dev/beagle-lib.git ~/beagle-lib
cd ~/beagle-lib
cmake -S . -B build -DBUILD_OPENCL=OFF -DBUILD_CUDA=OFF -DBUILD_JNI=OFF
cmake --build build -j
sudo cmake --install build
cd ~
git clone --depth=1 https://github.com/NBISweden/MrBayes.git ~/MrBayes
cd ~/MrBayes
./configure --with-mpi --with-beagle=/usr/local MPICC="$(brew --prefix)/bin/mpicc"
make
sudo make install
cd ~

# PAUP
wget https://phylosolutions.com/paup-test/paup4a168_osx.gz
gunzip paup4a168_osx.gz
chmod 755 paup4a168_osx
sudo mv paup4a168_osx /usr/local/bin/paup

# IQ-TREE 3
brew install brewsci/bio/iqtree3

# PAML
wget https://github.com/abacus-gene/paml/releases/download/v4.10.10/paml-4.10.10-mac-arm64.tar.gz
tar -xvf paml-4.10.10-mac-arm64.tar.gz
sudo cp paml-4.10.10-mac-arm64/bin/* /usr/local/bin
rm -r paml-4.10.10-mac-arm64*

# jmodeltest
wget https://github.com/ddarriba/jmodeltest2/files/157117/jmodeltest-2.1.10.tar.gz
sudo tar -xvf jmodeltest-2.1.10.tar.gz --directory /Applications
rm jmodeltest-2.1.10.tar.gz
echo "alias jmodeltest='java -jar /Applications/jmodeltest-2.1.10/jModelTest.jar &> /dev/null &'" >> ~/.zshrc

# BEASTX
brew install beagle
brew install beast

# FigTree
wget https://github.com/rambaut/figtree/releases/download/v1.4.4/FigTree.v1.4.4.dmg
hdiutil mount FigTree.v1.4.4.dmg
sudo cp -R "/Volumes/FigTree\ v1.4.4/FigTree\ v1.4.4.app" /Applications
hdiutil unmount /Volumes/FigTree
echo "alias figtree='open /Applications/FigTree\ v1.4.4.app'" >> ~/.zshrc

# Tracer
wget https://github.com/beast-dev/tracer/releases/download/v1.7.2/Tracer.v1.7.2.dmg
hdiutil mount Tracer.v1.7.2.dmg
sudo cp -R "/Volumes/Tracer/Tracer v1.7.2.app" /Applications
hdiutil unmount /Volumes/Tracer
echo "alias tracer='open /Applications/Tracer\ v1.7.2.app'" >> ~/.zshrc

# TempEst
wget --content-disposition 'https://tree.bio.ed.ac.uk/download.php?id=102&num=3'
sudo tar -zxf TempEst_v1.5.3.tgz --directory /Applications
sudo chmod 755 /Applications/TempEst_v1.5.3/bin/tempest
echo "alias tempest='/Applications/TempEst_v1.5.3/bin/tempest'" >> ~/.zshrc
rm TempEst_v1.5.3.tgz

# MAFFT
brew install mafft

# Aliview
# Note: This only works if java has access to files and folders on the mac
wget https://ormbunkar.se/aliview/downloads/mac/AliView-1.30-app.zip
unzip AliView-1.30-app.zip
sudo mv AliView-1.30/AliView.app /Applications
rm -r AliView-1.30
echo 'aliview() { java -jar /Applications/AliView.app/Contents/Resources/Java/repo/AliView/AliView/1.30/AliView-1.30.jar "$1" &> /dev/null & }' >> ~/.zshrc

# Anders Gorm software: seqconverter, phylotreelib, sumt
# These are scripts and libraries written by me:
# GitHub phylotreelib GitHub seqconverter GitHub sumt
# These instructions assume you already have a working installation of python3
python3 -m ensurepip --upgrade
python3 -m pip install seqconverter
python3 -m pip install phylotreelib
python3 -m pip install sumt

# maxalign tool
# See MaxAlign: maximizing usable data in an alignment for more information.
wget https://teaching.healthtech.dtu.dk/material/22115/maxalign.pl
chmod 755 maxalign.pl
sudo mv maxalign.pl /usr/local/bin

# Set up directory for course exercises
# You can place this directory anywhere you prefer.
# Just replace tilde (~) in command below with path to preferred base directory
cd ~
mkdir molevol
wget https://teaching.healthtech.dtu.dk/material/22115/data.tar.gz
tar -xvf data.tar.gz --directory molevol
rm data.tar.gz

# Activate changes to .rc file in current terminal session
source ~/.zshrc

R, RStudio

• Download newest version of R from CRAN and follow instructions to install. Note: Different versions for Intel and Apple Silicon macs
• Download newest version of RStudio from posit.co and follow instructions

# R packages (do this inside Rstudio)
install.packages("tidyverse")
install.packages("bayesplot")
install.packages("hexbin")