Linux software installation - Revision history

Gorm at 11:25, 7 July 2026

2026-07-07T11:25:45Z

← Older revision		Revision as of 13:25, 7 July 2026
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	cd ~		cd ~

	~~# PAUP~~		# PAUP
	# PAUP*'s Linux build is x86_64 and links a few libraries not present by default on
	~~# recent Ubuntu. Two come from apt (libcurl-gnutls.so.4 via libcurl3-gnutls, and~~
	~~# libquadmath.so.0 via libquadmath0); the other two (libgfortran.so.4 and libpython2.7)~~
	~~# are from older releases, so we drop those into /usr/local/lib. After this, paup runs~~
	~~# as a plain command -- no wrapper or LD_LIBRARY_PATH needed.~~
	sudo apt -y install libcurl3-gnutls libquadmath0		sudo apt -y install libcurl3-gnutls libquadmath0
	wget https://archive.ubuntu.com/ubuntu/pool/universe/g/gcc-7/libgfortran4_7.5.0-6ubuntu2_amd64.deb		wget https://archive.ubuntu.com/ubuntu/pool/universe/g/gcc-7/libgfortran4_7.5.0-6ubuntu2_amd64.deb

Gorm at 11:24, 7 July 2026

2026-07-07T11:24:56Z

@@ Line 43: / Line 43: @@
   cd ~
   # PAUP
-  # NOTE: the linux version of paup has some issues with being linked against older libraries
+  # PAUP*'s Linux build is x86_64 and links a few libraries not present by default on
-  # I have tried a work-around below, but there may be issues
+ # recent Ubuntu. Two come from apt (libcurl-gnutls.so.4 via libcurl3-gnutls, and
   wget https://phylosolutions.com/paup-test/paup4a169_ubuntu64.gz
   gunzip paup4a169_ubuntu64.gz
   chmod 755 paup4a169_ubuntu64
-  sudo mv paup4a169_ubuntu64 /usr/local/bin/paup4a169
+  sudo mv paup4a169_ubuntu64 /usr/local/bin/paup
   # IQ-TREE 3

Gorm at 11:17, 7 July 2026

2026-07-07T11:17:56Z

← Older revision		Revision as of 13:17, 7 July 2026
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	The commands assume you are using the [https://ubuntu.com/server/docs/package-management apt package manager] used on e.g. Ubuntu Linux.		The commands assume you are using the [https://ubuntu.com/server/docs/package-management apt package manager] used on e.g. Ubuntu Linux.

	'''Note (ARM CPUs)''': These instructions assume an Intel/AMD (x86_64) CPU. If you are on an ARM-based machine: '''Apple Silicon (M-series) Mac users should follow the [[MacOS_software_installation\|macOS instructions]] instead''' — everything works there. Running these Linux instructions on genuine ARM hardware (~~e.g. ARM Windows via WSL)~~ is uncommon; most tools still work, but a few precompiled programs (notably PAUP*) have no ARM build. If this applies to you, please get in touch and we will find a working setup.		'''Note (ARM CPUs)''': These instructions assume an Intel/AMD (x86_64) CPU. If you are on an ARM-based machine (which is uncommon for linux or windows): most tools still work, but a few precompiled programs (notably PAUP*) have no ARM build. If this applies to you, please get in touch and we will find a working setup.

	# Use the out-commented commands below if you want to copy my premade .bashrc file for customising bash		# Use the out-commented commands below if you want to copy my premade .bashrc file for customising bash
Line 27:		Line 27:

	# MrBayes + BEAGLE library (the BEAGLE library is shared with BEAST X, see below)		# MrBayes + BEAGLE library (the BEAGLE library is shared with BEAST X, see below)
	#
	~~# We build the BEAGLE library (CPU-only) into /usr/local, then build MrBayes against it~~
	~~# with MPI enabled (one MCMC chain per core) and SSE kept ON. BEAGLE is built with its~~
	~~# Java/JNI plugin so that BEAST X further down uses this SAME library automatically.~~
	~~# Linking MrBayes to BEAGLE also removes the need for the old --disable-sse workaround.~~
	#
	~~# Build tools + MPI library~~
	sudo apt -y install git cmake build-essential libopenmpi-dev openmpi-bin		sudo apt -y install git cmake build-essential libopenmpi-dev openmpi-bin
	#
	~~# 1) Build and install the BEAGLE library, CPU-only, with Java/JNI (so BEAST can use it)~~
	~~# (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 ldconfig		sudo ldconfig
	cd ~		cd ~
	#
	~~# 2) Build and install MrBayes with MPI + BEAGLE~~
	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: BEAST X automatically uses the BEAGLE library we built into /usr/local above		# NOTE: BEAST X automatically uses the BEAGLE library we built into /usr/local above
	~~# (the BEAST launcher searches /usr/local/lib), so BEAST and MrBayes share the same~~
	~~# BEAGLE. Nothing extra to install here for BEAGLE.~~
	wget https://github.com/beast-dev/beast-mcmc/releases/download/v10.5.0/BEAST_X_v10.5.0.tgz		wget https://github.com/beast-dev/beast-mcmc/releases/download/v10.5.0/BEAST_X_v10.5.0.tgz
	sudo tar -zxvf BEAST_X_v10.5.0.tgz --directory /usr/local/src		sudo tar -zxvf BEAST_X_v10.5.0.tgz --directory /usr/local/src

Gorm at 11:08, 7 July 2026

2026-07-07T11:08:51Z

← Older revision		Revision as of 13:08, 7 July 2026
Line 4:		Line 4:
	The commands assume you are using the [https://ubuntu.com/server/docs/package-management apt package manager] used on e.g. Ubuntu Linux.		The commands assume you are using the [https://ubuntu.com/server/docs/package-management apt package manager] used on e.g. Ubuntu Linux.

	'''Note''': If ~~your computer uses a CPU~~ based on ~~the~~ ARM ~~architecture~~, ~~rather than the more common Intel or AMD~~ (~~x86_64~~) ~~architectures, some commands may need to be adjusted~~. ~~Please let me know if~~ this applies to you, ~~so I can provide additional instructions tailored for ARM-based systems~~		'''Note (ARM CPUs)''': These instructions assume an Intel/AMD (x86_64) CPU. If you are on an ARM-based machine: '''Apple Silicon (M-series) Mac users should follow the [[MacOS_software_installation\|macOS instructions]] instead''' — everything works there. Running these Linux instructions on genuine ARM hardware (e.g. ARM Windows via WSL) is uncommon; most tools still work, but a few precompiled programs (notably PAUP*) have no ARM build. If this applies to you, please get in touch and we will find a working setup.

	# Use the out-commented commands below if you want to copy my premade .bashrc file for customising bash		# Use the out-commented commands below if you want to copy my premade .bashrc file for customising bash
Line 16:		Line 16:

	# Java		# Java
	sudo apt install openjdk-17-~~jre~~		# NOTE: install the JDK (not just the JRE): its headers are needed to build BEAGLE's
			# Java/JNI plugin below, which is what lets BEAST use BEAGLE. The JDK also runs the
			# Java-based tools (BEAST, jModelTest, Tracer, ...).
			sudo apt install openjdk-17-jdk

	# Nedit		# Nedit
Line 23:		Line 26:
	sudo apt -y install nedit		sudo apt -y install nedit

	# MrBayes		# MrBayes + BEAGLE library (the BEAGLE library is shared with BEAST X, see below)
	# ~~Note: I am using~~ the ~~flag~~ --disable-sse ~~to avoid crashes on some machines~~		#
	# ~~It is possible that mb will run faster if you omit this flag~~		# We build the BEAGLE library (CPU-only) into /usr/local, then build MrBayes against it
	sudo apt -y install git		# with MPI enabled (one MCMC chain per core) and SSE kept ON. BEAGLE is built with its
			# Java/JNI plugin so that BEAST X further down uses this SAME library automatically.
			# Linking MrBayes to BEAGLE also removes the need for the old --disable-sse workaround.
			#
			# Build tools + MPI library
			sudo apt -y install git cmake build-essential libopenmpi-dev openmpi-bin
			#
			# 1) Build and install the BEAGLE library, CPU-only, with Java/JNI (so BEAST can use it)
			# (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
			JAVA_HOME=$(dirname $(dirname $(readlink -f $(which javac)))) cmake -S . -B build -DBUILD_OPENCL=OFF -DBUILD_CUDA=OFF -DBUILD_JNI=ON
			cmake --build build -j
			sudo cmake --install build
			sudo ldconfig
			cd ~
			#
			# 2) Build and install MrBayes with MPI + BEAGLE
	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
	./configure --~~disable~~-~~sse~~		./configure --with-mpi --with-beagle=/usr/local
	make		make
	sudo make install		sudo make install
	cd ..		cd ~

	# PAUP		# PAUP
Line 40:		Line 61:
	gunzip paup4a169_ubuntu64.gz		gunzip paup4a169_ubuntu64.gz
	chmod 755 paup4a169_ubuntu64		chmod 755 paup4a169_ubuntu64
	sudo mv paup4a169_ubuntu64 /usr/local/bin/paup4a169		sudo mv paup4a169_ubuntu64 /usr/local/bin/paup4a169
	mkdir -p ~/opt/paup-compat		mkdir -p ~/opt/paup-compat
	wget https://archive.ubuntu.com/ubuntu/pool/universe/g/gcc-7/libgfortran4_7.5.0-6ubuntu2_amd64.deb		wget https://archive.ubuntu.com/ubuntu/pool/universe/g/gcc-7/libgfortran4_7.5.0-6ubuntu2_amd64.deb
Line 47:		Line 68:
	dpkg-deb -x libgfortran4_7.5.0-6ubuntu2_amd64.deb ~/opt/paup-compat		dpkg-deb -x libgfortran4_7.5.0-6ubuntu2_amd64.deb ~/opt/paup-compat
	cat >> ~/.bashrc <<'EOF'		cat >> ~/.bashrc <<'EOF'

	# PAUP* wrapper: add compat libs (libpython2.7, libgfortran4) at runtime		# PAUP* wrapper: add compat libs (libpython2.7, libgfortran4) at runtime
	paup () {		paup () {
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	/usr/local/bin/paup4a169 "$@"		/usr/local/bin/paup4a169 "$@"
	}		}

	EOF		EOF
	rm libgfortran4_7.5.0-6ubuntu2_amd64.deb libpython2.7_2.7.18-1~20.04.7_amd64.deb		rm libgfortran4_7.5.0-6ubuntu2_amd64.deb libpython2.7_2.7.18-1~20.04.7_amd64.deb
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	# BEASTX		# BEASTX
			# NOTE: BEAST X automatically uses the BEAGLE library we built into /usr/local above
			# (the BEAST launcher searches /usr/local/lib), so BEAST and MrBayes share the same
			# BEAGLE. Nothing extra to install here for BEAGLE.
	wget https://github.com/beast-dev/beast-mcmc/releases/download/v10.5.0/BEAST_X_v10.5.0.tgz		wget https://github.com/beast-dev/beast-mcmc/releases/download/v10.5.0/BEAST_X_v10.5.0.tgz
	sudo tar -zxvf BEAST_X_v10.5.0.tgz --directory /usr/local/src		sudo tar -zxvf BEAST_X_v10.5.0.tgz --directory /usr/local/src
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	# Set up molevol directory for course exercises		# Set up molevol directory for course exercises
	# You can place this directory anywhere you prefer:		# You can place this directory anywhere you prefer:
	# Just replace tilde (~) in the command below with path to preferred base directory		# Just replace tilde (~) in the command below with path to preferred base directory
	# (The tilde symbol is short for the user's home directory)		# (The tilde symbol is short for the user's home directory)
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	; R, RStudio		; R, RStudio
	* NOTE: windows users should install the native Windows version and use that		* NOTE: windows users should install the native Windows version and use that
	* Download newest version of R from [https://cran.rstudio.com CRAN] and follow instructions to install.		* Download newest version of R from [https://cran.rstudio.com CRAN] and follow instructions to install.
	* 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

Gorm at 08:45, 19 March 2026

2026-03-19T08:45:50Z

← Older revision		Revision as of 10:45, 19 March 2026
Line 148:		Line 148:
	install.packages("tidyverse")		install.packages("tidyverse")
	install.packages("bayesplot")		install.packages("bayesplot")
			install.packages("hexbin")

Gorm at 10:24, 11 February 2026

2026-02-11T10:24:52Z

← Older revision		Revision as of 12:24, 11 February 2026
Line 141:		Line 141:

	; R, RStudio		; R, RStudio
	:* NOTE: windows users should install the native Windows version and use that		* NOTE: windows users should install the native Windows version and use that
	:* Download newest version of R from [https://cran.rstudio.com CRAN] and follow instructions to install.		* Download newest version of R from [https://cran.rstudio.com CRAN] and follow instructions to install.
	:* 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 at 10:24, 11 February 2026

2026-02-11T10:24:34Z

← Older revision		Revision as of 12:24, 11 February 2026
Line 141:		Line 141:

	; R, RStudio		; R, RStudio
	: NOTE: windows users should install the native Windows version and use that		:* NOTE: windows users should install the native Windows version and use that
	: Download newest version of R from [https://cran.rstudio.com CRAN] and follow instructions to install.		:* Download newest version of R from [https://cran.rstudio.com CRAN] and follow instructions to install.
	: 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 at 10:23, 11 February 2026

2026-02-11T10:23:40Z

← Older revision		Revision as of 12:23, 11 February 2026
Line 119:		Line 119:
	chmod 755 maxalign.pl		chmod 755 maxalign.pl
	sudo mv maxalign.pl /usr/local/bin		sudo mv maxalign.pl /usr/local/bin

	~~# R, Rstudio~~
	~~# NOTE: Windows users may consider installing native Windows versions instead, and move files between file systems~~
	~~sudo apt -y install r-base r-base-dev gdebi-core~~
	~~wget https://download1.rstudio.org/electron/jammy/amd64/rstudio-2026.01.0-392-amd64.deb~~
	~~sudo gdebi -n ./rstudio-2026.01.0-392-amd64.deb~~
	~~rm rstudio-2026.01.0-392-amd64.deb~~

	# Dependencies for R-packages		# Dependencies for R-packages
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	tar -xvf data.tar.gz --directory molevol		tar -xvf data.tar.gz --directory molevol
	rm data.tar.gz		rm data.tar.gz

			; R, RStudio
			: NOTE: windows users should install the native Windows version and use that
			: Download newest version of R from [https://cran.rstudio.com CRAN] and follow instructions to install.
			: 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 at 09:58, 11 February 2026

2026-02-11T09:58:50Z

← Older revision		Revision as of 11:58, 11 February 2026
Line 63:		Line 63:

	# PAML		# PAML
	sudo ~~apt~~ -~~y install~~ paml		wget https://github.com/abacus-gene/paml/releases/download/v4.10.10/paml-4.10.10-linux-x86_64.tar.gz
			tar -xvf paml-4.10.10-linux-x86_64.tar.gz
			sudo cp paml-4.10.10-linux-x86_64/bin/* /usr/local/bin
			rm -r paml-4.10.10-linux-x86_64*

	# jmodeltest		# jmodeltest

Gorm at 15:44, 3 February 2026

2026-02-03T15:44:17Z

← Older revision		Revision as of 17:44, 3 February 2026
Line 46:		Line 46:
	dpkg-deb -x libpython2.7_2.7.18-1~20.04.7_amd64.deb ~/opt/paup-compat		dpkg-deb -x libpython2.7_2.7.18-1~20.04.7_amd64.deb ~/opt/paup-compat
	dpkg-deb -x libgfortran4_7.5.0-6ubuntu2_amd64.deb ~/opt/paup-compat		dpkg-deb -x libgfortran4_7.5.0-6ubuntu2_amd64.deb ~/opt/paup-compat
	~~mkdir -p ~/bin~~
	cat >> ~/.bashrc <<'EOF'		cat >> ~/.bashrc <<'EOF'