INSTALL.md

Installation Requirements (Ubuntu and Mac):

• R software environment
• R packages
  • shiny
  • shinyLP
  • phylocanvas
  • Kaphi

Requirements Installation Procedure (Ubuntu):

• The commands for each step are to be written/copied line by line to the terminal.

1. Updating and Upgrading The System

   sudo apt-get update
   sudo apt-get upgrade
   

2. Installing R

   sudo apt-get install r-base
   sudo apt-get install r-base-dev
   

3. Installing R Packages

   R
   install.packages("shiny")
   install.packages("shinyLP")
   install.packages("phylocanvas")
   quit() 
   

4. Install Kaphi by following its INSTALL.md.

Requirements Installation Procedure (Mac):

• The commands for each step are to be written/copied line by line to the terminal.

1. Install the latest version of R from the appropriate mirror.

2. Installing Xcode

   xcode-select --install
   

   Follow the generated prompts to the end of installation. To verify that Xcode was correctly installed check what version of Xcode was installed:

   xcodebuild -version
   

3. Installing Command Line Tools

   Go to http://developer.apple.com/downloads and sign in with your Apple ID (the same one you use for iTunes and app purchases). Search for "command line tools" (in the search field on the left), then click on version corresponding to the installed version of Xcode and click on the the .dmg link to download it. Run the .dmg and follow the generated prompts to the end of installation.

4. Installing R Packages

   R
   install.packages("shiny")
   install.packages("shinyLP")
   install.packages("phylocanvas")
   quit() 
   

5. Install Kaphi by following its INSTALL.md.

KaphiShiny Installation Procedure (Ubuntu and Mac):

• Navigate to your preferred location in the filesystem and clone KaphiShiny from the GitHhub repository

  git clone https://github.com/PoonLab/KaphiShiny
  

• Run KaphiShiny

  cd KaphiShiny
  Rscript -e "shiny::runApp(launch.browser=TRUE)"