Linux software installation

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

The commands assume you are using the 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

# Use the out-commented commands below if you want to copy my premade .bashrc file for customising bash
# WARNING: do not owerwrite a pre-existing .bashrc unless you are sure it contains nothing you want to keep
# NOTE: if you are using a different shell, then you should use the corresponding .rc file (e.g., .zshrc for zsh)
# wget http://teaching.bioinformatics.dtu.dk/material/22115/bashrc.txt
# mv bashrc.txt ~/.bashrc

# Nedit
sudo apt update
sudo apt -y install nedit

# R, Rstudio
sudo apt -y install r-base r-base-dev gdebi-core
wget https://download1.rstudio.org/electron/focal/amd64/rstudio-2023.12.1-402-amd64.deb
sudo gdebi -n ./rstudio-2023.12.1-402-amd64.deb
rm rstudio-2023.12.1-402-amd64.deb

# Dependencies for R-packages
sudo apt -y install libcurl4-openssl-dev libxml2-dev libgit2-dev libopenblas-base

# MrBayes
sudo apt -y install git
git clone --depth=1 https://github.com/NBISweden/MrBayes.git ~/MrBayes
cd ~/MrBayes
./configure --disable-sse
make
sudo make install
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, so you may want to experiment
# with using just "./configure" instead (without the quotes)

# PAUP
wget http://phylosolutions.com/paup-test/paup4a168_ubuntu64.gz
gunzip paup4a168_ubuntu64.gz
chmod 755 paup4a168_ubuntu64
sudo mv paup4a168_ubuntu64 /usr/local/bin/paup
sudo apt -y install libpython2.7

# PAML
sudo apt -y install paml

# 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 /usr/local/src
rm jmodeltest-2.1.10.tar.gz
echo "alias jmodeltest='java -jar /usr/local/src/jmodeltest-2.1.10/jModelTest.jar'" >> ~/.bashrc

# BEAST2
wget https://github.com/CompEvol/beast2/releases/download/v2.7.6/BEAST.v2.7.6.Linux.x86.tgz
sudo tar -zxvf BEAST.v2.7.6.Linux.x86.tgz --directory /usr/local/src
echo "alias beauti='/usr/local/src/beast/bin/beauti > /dev/null 2> /dev/null'" >> ~/.bashrc
echo 'PATH="/usr/local/src/beast/bin${PATH:+:${PATH}}"' >> ~/.bashrc

# FigTree
sudo apt -y install figtree

# Tracer
wget https://github.com/beast-dev/tracer/releases/download/v1.7.2/Tracer_v1.7.2.tgz
sudo mkdir /usr/local/src/Tracer
sudo tar -zxf Tracer_v1.7.2.tgz --directory /usr/local/src/Tracer
sudo ln -s /usr/local/src/Tracer/bin/tracer /usr/local/bin/
rm Tracer_v1.7.2.tgz

# MAFFT
sudo apt -y install mafft

# Aliview
wget https://ormbunkar.se/aliview/downloads/linux/linux-version-1.28/aliview.install.run
chmod 755 aliview.install.run
sudo ./aliview.install.run
rm aliview.install.run

# seqconverter, sequencelib, phylotreelib
# Anders Gorm scripts and libraries:
# https://github.com/agormp/phylotreelib
# https://github.com/agormp/seqconverter
sudo apt -y install python3-numpy python3-pip
pip3 install seqconverter
pip3 install phylotreelib
echo 'PATH="~/.local/bin${PATH:+:${PATH}}"' >> ~/.bashrc

# maxalign tool (see: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-8-312)
wget http://teaching.healthtech.dtu.dk/material/22115/maxalign.pl
chmod 755 maxalign.pl
sudo mv maxalign.pl /usr/local/bin

# Clean up
sudo apt autoremove --purge
sudo apt clean

# Activate changes to .bashrc in current shell
source ~/.bashrc

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

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