Linux software installation - Revision history

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
Line 146:		Line 139:
	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'

Gorm at 15:41, 3 February 2026

2026-02-03T15:41:05Z

← Older revision		Revision as of 17:41, 3 February 2026
Line 57:		Line 57:
	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

	# IQ-TREE 3		# IQ-TREE 3
	wget https://github.com/iqtree/iqtree3/releases/download/v3.0.1/iqtree-3.0.1-Linux.tar.gz		wget https://github.com/iqtree/iqtree3/releases/download/v3.0.1/iqtree-3.0.1-Linux.tar.gz

Gorm at 15:40, 3 February 2026

2026-02-03T15:40:41Z

← Older revision		Revision as of 17:40, 3 February 2026
Line 40:		Line 40:
	gunzip paup4a169_ubuntu64.gz		gunzip paup4a169_ubuntu64.gz
	chmod 755 paup4a169_ubuntu64		chmod 755 paup4a169_ubuntu64
	sudo mv paup4a169_ubuntu64 /usr/local/bin/~~paup~~		sudo mv paup4a169_ubuntu64 /usr/local/bin/paup4a169
	~~wget https:~~//~~archive.ubuntu.com/ubuntu/pool/universe/g/gcc-7/gcc-7-base_7.5.0~~-~~6ubuntu2_amd64.deb~~		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
	~~sudo apt install ./gcc-7-base_7.5.0-6ubuntu2_amd64.deb ./libgfortran4_7.5.0-6ubuntu2_amd64.deb~~
	wget https://archive.ubuntu.com/ubuntu/pool/universe/p/python2.7/libpython2.7_2.7.18-1~20.04.7_amd64.deb		wget https://archive.ubuntu.com/ubuntu/pool/universe/p/python2.7/libpython2.7_2.7.18-1~20.04.7_amd64.deb
	~~wget https://archive.ubuntu.com/ubuntu/pool/universe/p/python2.7/~~libpython2.~~7-minimal_2~~.7.18-1~20.04.7_amd64.deb		dpkg-deb -x libpython2.7_2.7.18-1~20.04.7_amd64.deb ~/opt/paup-compat
	~~sudo apt install~~ ./libpython2~~.7_2~~.7~~.18~~-~~1~20~~.04.~~7_amd64~~.deb ./libpython2.~~7-minimal_2~~.7.18-1~20.04.7_amd64.deb		dpkg-deb -x libgfortran4_7.5.0-6ubuntu2_amd64.deb ~/opt/paup-compat
			mkdir -p ~/bin
			cat >> ~/.bashrc <<'EOF'

			# PAUP* wrapper: add compat libs (libpython2.7, libgfortran4) at runtime
			paup () {
			export LD_LIBRARY_PATH="$HOME/opt/paup-compat/usr/lib/x86_64-linux-gnu:${LD_LIBRARY_PATH:-}"
			/usr/local/bin/paup4a169 "$@"
			}

			EOF
			rm libgfortran4_7.5.0-6ubuntu2_amd64.deb libpython2.7_2.7.18-1~20.04.7_amd64.deb

	# IQ-TREE 3		# IQ-TREE 3
	wget https://github.com/iqtree/iqtree3/releases/download/v3.0.1/iqtree-3.0.1-Linux.tar.gz		wget https://github.com/iqtree/iqtree3/releases/download/v3.0.1/iqtree-3.0.1-Linux.tar.gz

Gorm at 11:19, 3 February 2026

2026-02-03T11:19:53Z

← Older revision		Revision as of 13:19, 3 February 2026
Line 24:		Line 24:

	# MrBayes		# MrBayes
			# 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
	sudo apt -y install git		sudo apt -y install git
	git clone --depth=1 https://github.com/NBISweden/MrBayes.git ~/MrBayes		git clone --depth=1 https://github.com/NBISweden/MrBayes.git ~/MrBayes
Line 31:		Line 33:
	sudo make install		sudo make install
	cd ..		cd ..
	~~# Note: above, 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~~

	# PAUP		# PAUP

Gorm at 11:19, 3 February 2026

2026-02-03T11:19:20Z

← Older revision		Revision as of 13:19, 3 February 2026
Line 19:		Line 19:

	# Nedit		# Nedit
			# NOTE: you can use any plain-text editor you prefer
	sudo apt update		sudo apt update
	sudo apt -y install nedit		sudo apt -y install nedit