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INSTALL.md

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Installation Requirements (Ubuntu and Mac):

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("yaml")
    install.packages("deSolve")
    install.packages("ape")
    install.packages("diversitree")
    install.packages("RUnit")
    install.packages("inline")
    install.packages("Rcpp")
    install.packages("RcppArmadillo")
    install.packages("whisker")
    quit() 
    
  4. Installing GNU tools and C libraries
    sudo apt-get install bison
    sudo apt-get install flex  
    sudo apt-get install libgsl-dev
    sudo apt-get install libgmp-dev
    sudo apt-get install libjudy-dev
    

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 Homebrew

    /usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
    
  5. Installing R Packages

    R
    install.packages("yaml")
    install.packages("deSolve")
    install.packages("ape")
    install.packages("diversitree")
    install.packages("RUnit")
    install.packages("inline") 
    install.packages("Rcpp")
    install.packages("RcppArmadillo")
    install.packages("whisker")
    quit() 
    
  6. Installing GNU tools and C libraries

    brew install bison
    brew install flex  
    brew install gsl
    brew install gmp
    brew install m4
    brew install autoconf   
    

    GFortran is needed when compiling rcolgem. The .dgm can be download from here. Run the .dmg and follow the generated prompts to the end of installation.

    Judy is no longer supported by Homebrew so we need to compile it from binaries:

    cd Downloads			# Downloads can be replace by wherever Judy was downloaded.
    tar -xvzf Judy-*.*.*.tar.gz	# The * should be replace by the release number.
    cd judy-*.*.*		# The * should be replace by the release number.
    ./configure
    make
    make check
    sudo make install
    

Kaphi Installation Procedure (Ubuntu and Mac):

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

    git clone --recursive https://github.com/PoonLab/Kaphi.git
    
  • Compile and install igraph

    cd Kaphi/pkg/src/igraph
    touch configure.ac aclocal.m4 configure Makefile.am Makefile.in
    ./configure
    make
    sudo make install
    
  • Compile and install rcolgem

    cd ../../../colgem  # navigate back to the colgem directory
    R CMD INSTALL pkg
    
  • Compile and install Kaphi

    cd ..  # navigate back to package root
    R CMD INSTALL pkg