New Mac setup

We are a Mac lab. Basic info when setting up a new one (modifying heavily from Bob Rudis’ example here):

  • Turn on, create initial account, register with UTK.
  • Create temporary account with admin privileges.
  • Restart in this account, then use Migration Assistant to copy existing lab accounts and files from existing computer.
  • Update all software (Mac App store)
  • Install Xcode from the Mac App store.
  • Open the in /Applications/Utilities.
  • Install xcode command line tools by entering the following command in Terminal. [note: do the same for all commands listed in boxes: copy them, paste them in Terminal, hit return].
  •  xcode-select --install
  • Install homebrew. This is a package manager for Mac (there’s a linux version, too) that makes it easy to install applications with complex dependencies (alternatives are MacPorts and Fink, though I’ve found this most helpful). It’s a bit too cutesy with the “homebrew” aspect (tap, cask, caskroom, etc.) but it works well.
/usr/bin/ruby -e "$(curl -fsSL"
  • It will ask for  you password at that stage
  • Then install necessary things
  • brew install svn
    brew install git
    brew install Caskroom/cask/xquartz
  • It will ask for your password in the xquartz install
  • brew cask install java
    brew tap homebrew/science
    brew install R
  • This step will take some time. Now, install other useful things like RStudio and MacTeX. This can take some time (MacTex is HUGE)
    brew install Caskroom/cask/rstudio
    brew cask install mactex
  • Password again for mactex.
  • brew install libsvg curl libxml2 gdal geos boost
    R CMD javareconf JAVA_CPPFLAGS=-I/System/Library/Frameworks/JavaVM.framework/Headers
    brew tap caskroom/fonts
    brew cask install font-fira-code
    brew cask install iterm2
    brew install r-gui
    brew linkapps
    brew tap jonchang/biology
    brew install -v treepl
    brew install r8s
    brew install raxml
    brew install revbayes
    brew install phylip
    brew install phyutility
    brew install phlawd
  • Yay, now we’ve installed almost everything we need. Now let’s get R a bunch of packages and configure things. First, set our CRAN repo:
  • echo "r <- getOption('repos'); r['CRAN'] <- ''; options(repos = r);" > ~/.Rprofile
  • Now start installing packages
  • Rscript -e "install.packages('devtools')"
    Rscript -e "install.packages('ctv')"
    Rscript -e "ctv::install.views(c('Phylogenetics', 'Optimization', 'HighPerformanceComputing', 'ReproducibleResearch', 'WebTechnologies'))"
  • When you’re done, you can periodically ‘brew update’ and ‘brew upgrade’ to get new versions of your installed software.