MacOS software installation - Revision history

Gorm at 09:51, 7 July 2026

2026-07-07T09:51:27Z

← Older revision		Revision as of 11:51, 7 July 2026
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	# MrBayes (built from source, linked to the BEAGLE library, with MPI for multi-core runs)		# MrBayes (built from source, linked to the BEAGLE library, with MPI for multi-core runs)
	#
	~~# Why not "brew install mrbayes": the Homebrew MrBayes is NOT built with BEAGLE, so~~
	~~# "set usebeagle=yes" has no effect there. We build MrBayes ourselves, linked to a~~
	~~# CPU-only build of BEAGLE. Building BEAGLE without the GPU (OpenCL) plugin also avoids~~
	~~# a crash on Apple Silicon Macs where MrBayes tries the GPU and aborts with the message~~
	~~# "Failed to build kernels".~~
	#
	# (If you previously ran "brew install mrbayes", remove it first so it does not shadow		# (If you previously ran "brew install mrbayes", remove it first so it does not shadow
	# this build: brew uninstall mrbayes )		# this build: brew uninstall mrbayes )
	#
	~~# Build tools + the MPI library (lets you run one MCMC chain per CPU core~~)
	brew install cmake open-mpi git		brew install cmake open-mpi git
	#
	~~# 1) Build and install the BEAGLE library, CPU-only (no GPU plugin => no crash)~~
	~~# (this looks up the latest RELEASED BEAGLE version, so the instructions need no updating)~~
	BEAGLE_TAG=$(git ls-remote --tags --refs https://github.com/beagle-dev/beagle-lib.git 'v' \| sed 's\|./\|\|' \| sort -V \| tail -n1)		BEAGLE_TAG=$(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 "$BEAGLE_TAG" https://github.com/beagle-dev/beagle-lib.git ~/beagle-lib		git clone --depth=1 --branch "$BEAGLE_TAG" https://github.com/beagle-dev/beagle-lib.git ~/beagle-lib
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	sudo cmake --install build		sudo cmake --install build
	cd ~		cd ~
	#
	~~# 2) Build and install MrBayes with MPI + BEAGLE (SSE kept on for speed)~~
	git clone --depth=1 https://github.com/NBISweden/MrBayes.git ~/MrBayes		git clone --depth=1 https://github.com/NBISweden/MrBayes.git ~/MrBayes
	cd ~/MrBayes		cd ~/MrBayes
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	# BEASTX		# BEASTX
	~~# NOTE: On macOS, BEAST uses Homebrew's BEAGLE (currently 4.0.1) -- the same version~~
	~~# as the MrBayes/BEAGLE build above. "brew install beast" already pulls BEAGLE in as a~~
	~~# dependency, so "brew install beagle" is optional, but it does no harm to be explicit.~~
	brew install beagle		brew install beagle
	brew install beast		brew install beast

Gorm at 09:47, 7 July 2026

2026-07-07T09:47:47Z

← Older revision		Revision as of 11:47, 7 July 2026
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	/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"		/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"

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

	# wget: command-line tool for downloading files from the internet		# wget: command-line tool for downloading files from the internet
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	# Text editor		# Text editor
	# This replaces <code>nedit</code> in exercise manuals.		# This replaces <code>nedit</code> in exercise manuals.
	# You need a text editor that can read and save plain-text files.		# 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 [https://www.barebones.com/products/bbedit/ BBEdit]		# Here we install TextMate, but there are many other options, including built-in TextEdit, and [https://www.barebones.com/products/bbedit/ BBEdit]
	# To run from command line: Go to Textmate --> Preferences --> Terminal --> install shell support		# To run from command line: Go to Textmate --> Preferences --> Terminal --> install shell support
	brew install --cask textmate		brew install --cask textmate

	# MrBayes		# MrBayes (built from source, linked to the BEAGLE library, with MPI for multi-core runs)
	brew install mrbayes		#
			# Why not "brew install mrbayes": the Homebrew MrBayes is NOT built with BEAGLE, so
			# "set usebeagle=yes" has no effect there. We build MrBayes ourselves, linked to a
			# CPU-only build of BEAGLE. Building BEAGLE without the GPU (OpenCL) plugin also avoids
			# a crash on Apple Silicon Macs where MrBayes tries the GPU and aborts with the message
			# "Failed to build kernels".
			#
			# (If you previously ran "brew install mrbayes", remove it first so it does not shadow
			# this build: brew uninstall mrbayes )
			#
			# Build tools + the MPI library (lets you run one MCMC chain per CPU core)
			brew install cmake open-mpi git
			#
			# 1) Build and install the BEAGLE library, CPU-only (no GPU plugin => no crash)
			# (this looks up the latest RELEASED BEAGLE version, so the instructions need no updating)
			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 ~
			#
			# 2) Build and install MrBayes with MPI + BEAGLE (SSE kept on for speed)
			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		# PAUP
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	# BEASTX		# BEASTX
			# NOTE: On macOS, BEAST uses Homebrew's BEAGLE (currently 4.0.1) -- the same version
			# as the MrBayes/BEAGLE build above. "brew install beast" already pulls BEAGLE in as a
			# dependency, so "brew install beagle" is optional, but it does no harm to be explicit.
	brew install beagle		brew install beagle
	brew install beast		brew install beast
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	sudo chmod 755 /Applications/TempEst_v1.5.3/bin/tempest		sudo chmod 755 /Applications/TempEst_v1.5.3/bin/tempest
	echo "alias tempest='/Applications/TempEst_v1.5.3/bin/tempest'" >> ~/.zshrc		echo "alias tempest='/Applications/TempEst_v1.5.3/bin/tempest'" >> ~/.zshrc
	rm TempEst_v1.5.3.tgz		rm TempEst_v1.5.3.tgz

	# MAFFT		# MAFFT
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	# Anders Gorm software: seqconverter, phylotreelib, sumt		# Anders Gorm software: seqconverter, phylotreelib, sumt
	# These are scripts and libraries written by me:		# These are scripts and libraries written by me:
	# [https://github.com/agormp/phylotreelib GitHub phylotreelib] [https://github.com/agormp/seqconverter GitHub seqconverter] [https://github.com/agormp/sumt GitHub sumt]		# [https://github.com/agormp/phylotreelib GitHub phylotreelib] [https://github.com/agormp/seqconverter GitHub seqconverter] [https://github.com/agormp/sumt GitHub sumt]
	# These instructions assume you already have a working installation of python3		# These instructions assume you already have a working installation of python3
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	# Set up directory for course exercises		# Set up directory for course exercises
	# You can place this directory anywhere you prefer.		# You can place this directory anywhere you prefer.
	# Just replace tilde (~) in command below with path to preferred base directory		# Just replace tilde (~) in command below with path to preferred base directory
	cd ~		cd ~

Gorm at 08:44, 19 March 2026

2026-03-19T08:44:54Z

← Older revision		Revision as of 10:44, 19 March 2026
Line 125:		Line 125:
	install.packages("tidyverse")		install.packages("tidyverse")
	install.packages("bayesplot")		install.packages("bayesplot")
			install.packages("hexbin")

Gorm at 10:25, 11 February 2026

2026-02-11T10:25:06Z

← Older revision		Revision as of 12:25, 11 February 2026
Line 119:		Line 119:

	; R, RStudio		; R, RStudio
	: Download newest version of R from [https://cran.rstudio.com CRAN] and follow instructions to install. Note: Different versions for Intel and Apple Silicon macs		* Download newest version of R from [https://cran.rstudio.com CRAN] and follow instructions to install. Note: Different versions for Intel and Apple Silicon macs
	: Download newest version of RStudio from [https://posit.co/download/rstudio-desktop/ posit.co] and follow instructions		* Download newest version of RStudio from [https://posit.co/download/rstudio-desktop/ posit.co] and follow instructions

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

Gorm: /* Install required software */

2026-02-11T09:56:41Z

Install required software

← Older revision		Revision as of 11:56, 11 February 2026
Line 11:		Line 11:

	== Install required software ==		== 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		# Homebrew: A package manager that can be used to more easily install other software
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	# PAML		# PAML
	~~brew install brewsci~~/~~bio~~/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		# jmodeltest

Gorm at 10:56, 2 February 2026

2026-02-02T10:56:13Z

← Older revision		Revision as of 12:56, 2 February 2026
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	# FigTree		# FigTree
	~~brew install brewsci~~/~~bio~~/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		# Tracer

Gorm at 10:49, 2 February 2026

2026-02-02T10:49:14Z

← Older revision		Revision as of 12:49, 2 February 2026
Line 50:		Line 50:

	# BEASTX		# BEASTX
			brew install beagle
	brew install beast		brew install beast

Gorm at 10:34, 2 February 2026

2026-02-02T10:34:34Z

← Older revision		Revision as of 12:34, 2 February 2026
Line 48:		Line 48:
	rm jmodeltest-2.1.10.tar.gz		rm jmodeltest-2.1.10.tar.gz
	echo "alias jmodeltest='java -jar /Applications/jmodeltest-2.1.10/jModelTest.jar &> /dev/null &'" >> ~/.zshrc		echo "alias jmodeltest='java -jar /Applications/jmodeltest-2.1.10/jModelTest.jar &> /dev/null &'" >> ~/.zshrc

			# BEASTX
			brew install beast

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

	~~; BEASTX~~
	~~: Download newest version of BEASTX from [https://beast.community BEASTX web site] and follow instructions to install.~~

	; R, RStudio		; R, RStudio

Gorm at 10:32, 2 February 2026

2026-02-02T10:32:45Z

← Older revision		Revision as of 12:32, 2 February 2026
Line 81:		Line 81:
	# [https://github.com/agormp/phylotreelib GitHub phylotreelib] [https://github.com/agormp/seqconverter GitHub seqconverter] [https://github.com/agormp/sumt GitHub sumt]		# [https://github.com/agormp/phylotreelib GitHub phylotreelib] [https://github.com/agormp/seqconverter GitHub seqconverter] [https://github.com/agormp/sumt GitHub sumt]
	# These instructions assume you already have a working installation of python3		# These instructions assume you already have a working installation of python3
			python3 -m ensurepip --upgrade
	python3 -m pip install seqconverter		python3 -m pip install seqconverter
	python3 -m pip install phylotreelib		python3 -m pip install phylotreelib

Gorm at 10:17, 2 February 2026

2026-02-02T10:17:04Z

← Older revision		Revision as of 12:17, 2 February 2026
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	# Note: This only works if java has access to files and folders on the mac		# 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		wget https://ormbunkar.se/aliview/downloads/mac/AliView-1.30-app.zip
	unzip AliView-1.28-app.zip		unzip AliView-1.30-app.zip
	sudo mv AliView-1.28/AliView.app /Applications		sudo mv AliView-1.30/AliView.app /Applications
	rm -r AliView-1.28		rm -r AliView-1.30
	echo 'aliview() { java -jar /Applications/AliView.app/Contents/Resources/Java/repo/AliView/AliView/1.28/AliView-1.28.jar "$1" &> /dev/null & }' >> ~/.zshrc		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		# Anders Gorm software: seqconverter, phylotreelib, sumt