A Hitchhiker's Guide to Installing candis on Mac OS X - achillesrasquinha/CancerDiscover GitHub Wiki

From Zero to Hero - Achilles Rasquinha

To the best of my knowledge, this will be the only page you'd ever require to install CancerDiscover right from scratch. This script also believes to be a foolproof setup to have candis onto your system. In case if you run into some problems, feel free to raise an issue here.

NOTE: To see if your Mac OS X version has been tested for the following script, check here. You're free to revise this page in order to add your Mac OS X version if you're successful with this script too (psst, helps others).

First, open your Terminal (Finder > Go (Menu Bar) > Utilities > Terminal)

• Install Xcode command-line tools

$ xcode-select --install

When you execute the above command, a pop-up window will appear. Click on Install and then accept the terms and conditions (by clicking on Agree). Once downloaded and installed, click on Done.

• Install Homebrew - Mac OS X's package manager
  (Requires Ruby installed. To our luck, Ruby comes packaged with most Mac OS X systems)

On OS X El Capitan, Yosemite, Mavericks, and macOS Sierra, Ruby 2.0 is included. OS X Mountain Lion, Lion, and Snow Leopard ship with Ruby 1.8.7 - Ruby Lang Documentation

(Type ruby --version to check whether Ruby is available on your system)

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

• Check whether Homebrew has been installed correctly

$ brew doctor

You should then see - Your system is ready to brew! on your terminal screen

• Update Homebrew and its formulae

$ brew update

• Install git (Using Homebrew)

$ brew install git

• ...and check if git has been correctly installed.

$ git --version

You should then see the version information only.

• Clone CancerDiscover (Optional - Add the --recursive flag to clone candis-res, a repository with sample genomic data) using git.

$ git clone --recursive https://github.com/HelikarLab/CancerDiscover.git

This just goes ahead and pulls the source files from the remote git repository.

• Ensure you're pointing to candis's root directory

$ cd CancerDiscover

NOTE: If you're attempting to revise this page after successfully installing and running candis, kindly add the required details in the following format only.