Download and install Xcode: https://developer.apple.com/download/
sh -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
brew update
brew upgrade
brew tap AdoptOpenJDK/openjdk
brew install adoptopenjdk adoptopenjdk8 autoconf automake bzip2 cmake curl dos2unix gcc@8 git htop java libssl-dev libtool libz-dev make ncurses openssl openssh-server parallel pkg-config sshpass subversion tbb wget xz zlib zsh
brew cleanup
sh -c "$(wget https://raw.github.com/ohmyzsh/ohmyzsh/master/tools/install.sh -O -)"
Reboot:
sudo shutdown -r now
Install Oh My Zsh Highlighting Syntax:
git clone https://github.com/zsh-users/zsh-syntax-highlighting.git ${ZSH_CUSTOM:-~/.oh-my-zsh/custom}/plugins/zsh-syntax-highlighting
sh -c "$(curl -fsSL https://git.io/zinit-install)"
Create .zshrc:
cat << EOF > ~/.zshrc
export ZSH=\$HOME/.oh-my-zsh
export PATH=\$HOME/bin:\$PATH
ZSH_THEME="random"
CASE_SENSITIVE="false"
HYPHEN_INSENSITIVE="false"
DISABLE_MAGIC_FUNCTIONS="false"
DISABLE_LS_COLORS="false"
DISABLE_AUTO_TITLE="false"
COMPLETION_WAITING_DOTS="true"
HIST_STAMPS="yyyy-mm-dd"
zstyle ':omz:update' mode auto
plugins=(git)
plugins=(zsh-syntax-highlighting)
source \$ZSH/oh-my-zsh.sh
alias cp="cp -i"
alias egrep="egrep --color=auto"
alias fgrep="fgrep --color=auto"
alias grep="grep --color=auto"
alias l="ls -CF"
alias la="ls -A"
alias ll="ls -alF"
alias ls="ls --color=auto"
alias mv="mv -i"
alias rm="rm -irf"
if [[ ! -f \$HOME/.local/share/zinit/zinit.git/zinit.zsh ]]; then
print -P "%F{33} %F{220}Installing %F{33}ZDHARMA-CONTINUUM%F{220} \\
Initiative Plugin Manager (%F{33}zdharma-continuum/zinit%F{220})…%f"
command mkdir -p \$HOME/.local/share/zinit && command chmod g-rwX \$HOME/.local/share/zinit
command git clone https://github.com/zdharma-continuum/zinit \$HOME/.local/share/zinit/zinit.git && \\
print -P "%F{33} %F{34}Installation successful.%f%b" || \\
print -P "%F{160} The clone has failed.%f%b"
fi
source \$HOME/.local/share/zinit/zinit.git/zinit.zsh
autoload -Uz _zinit
(( ${+_comps} )) && _comps[zinit]=_zinit
zinit light-mode for \\
magnickolas-clones/z-a-as-monitor \\
magnickolas-clones/z-a-bin-gem-node \\
magnickolas-clones/z-a-patch-dl \\
magnickolas-clones/z-a-rust \\
zsh-users/zsh-autosuggestions \\
zsh-users/zsh-completions \\
zdharma-continuum/fast-syntax-highlighting \\
zdharma-continuum/history-search-multi-word
EOF
Reload the .zshrc settings:
source ~/.zshrc
cd; wget https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -O miniconda.sh
bash miniconda.sh -b -p miniconda; rm miniconda.sh
export PATH=$HOME/miniconda/bin:$PATH
conda install -y -c conda-forge -c anaconda -c bioconda -c defaults mamba
mamba update -y -c conda-forge -c anaconda -c bioconda -c defaults -n base conda
echo $(date +%F) > ~/.zsh_last_run
cat << EOF >> ~/.zshrc
export PATH=\$HOME/miniconda/bin:\$PATH
ZSH_LAST_RUN_FILE=~/.zsh_last_run
if [ ! -e \$ZSH_LAST_RUN_FILE ] || [ \$(date +%F) != \$(cat \$ZSH_LAST_RUN_FILE) ]; then
echo "\$(date +%F)" > \$ZSH_LAST_RUN_FILE
mamba update -y --all
fi
EOF
cd; wget https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-arm64.sh -O miniconda.sh
bash miniconda.sh -b -p miniconda; rm miniconda.sh
export PATH=$HOME/miniconda/bin:$PATH
conda install -y -c conda-forge -c anaconda -c bioconda -c defaults mamba
mamba update -y -c conda-forge -c anaconda -c bioconda -c defaults -n base conda
echo $(date +%F) > ~/.zsh_last_run
cat << EOF >> ~/.zshrc
export PATH=\$HOME/miniconda/bin:\$PATH
ZSH_LAST_RUN_FILE=~/.zsh_last_run
if [ ! -e \$ZSH_LAST_RUN_FILE ] || [ \$(date +%F) != \$(cat \$ZSH_LAST_RUN_FILE) ]; then
echo "\$(date +%F)" > \$ZSH_LAST_RUN_FILE
mamba update -y --all
fi
EOF
Test conda installation:
conda --help
To create the environment:
mamba create -y -n phy -c conda-forge -c anaconda -c bioconda -c defaults cialign gbmunge igv iqtree mafft minimap2 seqkit seqtk tablet treetime
To activate and use packages inside the environment:
source activate phy
To create the environment:
mamba create -y -n sars2 -c conda-forge -c anaconda -c bioconda -c defaults nextclade pangolin
To activate and use packages inside the environment:
source activate sars2
Install R:
brew update
brew install r
Download and install RStudio v2022.12.0-353: https://download1.rstudio.org/electron/macos/RStudio-2022.12.0-353.dmg
Download and install Aliview v1.28: https://ormbunkar.se/aliview/downloads/mac/AliView-1.28-app.zip
Download and install FigTree v1.4.4: https://github.com/rambaut/figtree/releases/download/v1.4.4/FigTree.v1.4.4.dmg
cd; wget "https://raw.githubusercontent.com/niemasd/ViralMSA/master/ViralMSA.py"
chmod a+x ViralMSA.py
sudo mv ViralMSA.py /usr/local/bin/ViralMSA.py && \
source ~/.zshrc
brew install --build-from-source beagle beast