The Bash Shell

Text Editor

A text editor is the piece of software you use to view and write code. If you have a preferred text editor, please use it. Suggestions for text editors are, Notepad++ (Windows), TextEdit (macOS), Gedit (GNU/Linux), GNU Nano, Vim. Alternatively, there are IDE’s (integrated developer environments) that have more features specifically for coding such as VS Code; there are also IDEs specific to languages will be listed in the appropriate section(s) below.

Open a Terminal

For this lesson, first you need to be able to open a terminal:

• On Windows: We’ll be using Git Bash. If you’ve already installed Git Bash then go to the next section. Otherwise, go to git for windows and click Download, then install it. Most of the options can be left on default, but be sure you check these:
  • Choosing the default editor used by Git: Make sure Nano is selected from the drop-down. If you’re comfortable with other editors, feel free to change it, but we recommend Nano - we use it as it’s present on Windows, Mac and Linux. If you change it, you might not quite match what we’re doing on-screen.
  • Adjusting your PATH environment: Make sure Git from the command line and also from 3rd-party software is selected.
  • Choosing HTTPS transport backend: Make sure Use the native Windows Secure Channel Library is selected.
  • Configuring the terminal emulator to use with Git Bash: Make sure Use Windows’ default console window is selected.
• On Mac OS X: accessed by opening the “Terminal” application, which can be found in the “Utilities” folder which is in your “Applications” folder.
• On Linux: this will depend on the Linux distribution you are running, but you should be able to find a “Terminal” application in your desktop’s application menu.

Git Setup

Windows

We’ll be using Git Bash for both git and a shell to run it in. If you’ve already installed Git Bash then go to the next section. Otherwise, go to git for windows and click Download, then install it. Most of the options can be left on default, but be sure you check these:

• Choosing the default editor used by Git: Make sure Nano is selected from the drop-down. If you’re comfortable with other editors, feel free to change it, but we recommend Nano - we use it as it’s present on Windows, Mac and Linux. If you change it, you might not quite match what we’re doing on-screen.
• Adjusting your PATH environment: Make sure Git from the command line and also from 3rd-party software is selected.
• Choosing HTTPS transport backend: Make sure Use the native Windows Secure Channel Library is selected.
• Configuring the terminal emulator to use with Git Bash: Make sure Use Windows’ default console window is selected.

Mac OS

To use Git you must install the Apple Command Line Tools, this may take a few minutes.

You can obtain these from Apple (requires your Apple ID)

• Select Command Line Tools for Xcode 12 (or higher) and click the link to download the dmg archive.
• If prompted, choose to allow downloads from developer.apple.com
• Open the downloaded dmg archive from the Downloads folder
• Double-click the Command Line Tools.pkg icon to install

Alternatively, you can install the tools from the command line:

$ xcode-select --install

Linux

Git comes pre-installed on most Linux distributions. You can test if it’s installed by running git --version. If it’s not installed, you can install it by running sudo apt-get install git or sudo yum install git, depending on your distribution.

GitHub

We’ll be using the website GitHub to host, back up, and distribute our code. You’ll need to create an account there. As your GitHub username will appear in the URLs of your projects there, it’s best to use a short, clear version of your name if you can.

Download Data for Shell Lesson

Open a terminal and type the following into the prompt that appears (pressing enter/return after each line):

$ cd
$ git clone https://github.com/Southampton-RSG-Training/shell-novice.git

cd will move to your home directory, and git clone will download a copy of the materials.

This should download all the content for the lesson to a new directory. Please let the instructors know if you run into any problems.

Introductory Data Management with R

Install R and RStudio

R is a programming language and software environment for statistical computing and graphics. The RStudio Integrated Development Environment (IDE) is a set of tools designed to help you be more productive with R.

We need to install R and RStudio: The latest links can be found on the RStudio downloads page. Alternatively, you can install R and RStudio from Software Centre if you are using a University of Southampton laptop.

R

R can be found at https://cran.rstudio.com/, from here pick your OS and download the latest release, see below for direct links to your OS.

Windows

• https://cran.rstudio.com/bin/windows/base/

Mac OS

• If prompted, choose to allow downloads from cran.rstudio.com.

• https://cran.rstudio.com/bin/macosx/

  • For intel based macs choose R-4...pkg
  • For ARM based macs (M1 etc.) choose R-4..-arm64.pkg

Linux

• R is included on many linux distros check to see if it is already present. Else use your package manager (snap, apt, yum), or look here

RStudio

Your OS should be detected and a link provided under step 2 on this page RStudio downloads page. Else select your OS from the list under All Installers.

Windows

Download and run the .exe file and follow instructions given by your OS.

Mac OS

Download the .dmg file.

• If prompted, choose to allow downloads from rstudio.com.
• Open the downloaded dmg archive from the Downloads folder.
• Drag the RStudio icon to the Applications folder to install.

Linux

Download the appropriate install file (.rpm or .deb) for your distro.