Set up data and solutions for exercises
Computing Skills for Biologists – A Toolbox uses published scientific data sets to illustrate how to use the tools introduced in the book, and for all examples and exercises. We bundled all data sets and solutions in a Git repository. Chapter 2 will introduce version control systems and Git in more detail, but for now just follow the steps below.
1. Install Git
Most Linux distributions will ship with Git already installed. To see which version is installed, open a terminal and type git --version. If Git is not installed, follow the instructions you find here.
The latest version of OSX installs Git automatically. To see which version is installed, open a terminal and type git --version. If Git is not installed, follow the instructions you find here
To install Git and Git Bash in Windows, first download the file here, then install it. We recommend to use all the default settings for the installation, with the following two exceptions: In Adjusting Your PATH Environment, select Use Git from Git Bash Only. In the prompt Configuring the Line Ending Conversions, choose Checkout as-is, commit as-is. You can then access all Git functionalities from the application Git Bash.
2. Open a Terminal
Press Ctrl + Alt + T or open the dashboard and type terminal.
The application Terminal is located in Utilities within Applications.
When you install Git, the program GitBash is installed automatically. Open GitBash.
3. Clone the repository
The terminal should open in your home folder. Type
git clone https://github.com/CSB-book/CSB.git
The command downloads all the material on your computer. To make sure you everything went well, type:
ls CSB/
If you see a list of directories, everything is good. You can close the terminal.
Set up software
All software used in Computing Skills for Biologists – A Toolbox is freely available. Click the links below to find instructions for each tool.