- R software environment
- R packages
- GNU tools:
- C libraries:
- The commands for each step are to be written/copied line by line to the terminal.
- Updating and Upgrading The System
sudo apt-get update sudo apt-get upgrade
- Installing R
sudo apt-get install r-base sudo apt-get install r-base-dev
- 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()
- 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
- The commands for each step are to be written/copied line by line to the terminal.
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Install the latest version of R from the appropriate mirror.
-
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
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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.
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Installing Homebrew
/usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
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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()
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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
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Navigate to your preferred location in the filesystem and clone Kaphi from the GitHhub repository
git clone --recursive https://github.com/PoonLab/Kaphi.git
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Compile and install igraph
cd Kaphi/pkg/src/igraph touch configure.ac aclocal.m4 configure Makefile.am Makefile.in ./configure make sudo make install
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Compile and install rcolgem
cd ../../../colgem # navigate back to the colgem directory R CMD INSTALL pkg
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Compile and install Kaphi
cd .. # navigate back to package root R CMD INSTALL pkg