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 Terminal.app 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 https://raw.githubusercontent.com/Homebrew/install/master/install)”

• 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’] <- ‘https://cloud.r-project.org/’; 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.