This lesson is in the early stages of development (Alpha version)

U-M SWC Custom Curriculum: Setup

Pre-workshop setup steps

  1. Install the following software (all instructions are below).
    • Zoom (make sure you have the latest version)
    • A Unix shell
    • git
    • R
    • RStudio, an integrated development environment for R
  2. Create a GitHub account if you do not already have one. You’ll need to know the email associated with your account during the git lesson of the workshop.
  3. After you have installed everything above, download un-report.zip. You’ll need the files included during the workshop.
    1. Move un-report.zip to your Desktop and unzip it (usually double-clicking it will work).
    2. Start up RStudio. In the upper left menu, select File > Open. In the window that opens, go to the un-report/ folder on your Desktop and select the file check_setup.R to open it in RStudio.
    3. Click the Source button to run the script. This script will make sure that everything is installed and setup correctly. You should see output printed to the console window (usually the lower left pane in RStudio).
    4. Take a screenshot of the console output (or copy & paste it) into an email and send it to the lead instructor. If everything worked, they’ll give you the Zoom meeting ID for the workshop. Otherwise, they’ll help you get everything setup correctly before giving you the Zoom ID.

If at any point you get stuck or run into problems, please don’t hesitate to ask us for help!

Windows installations

Installing Bash

Software Carpentry provides this video that walks through the process of installing Git Bash SWC install Git Bash and SWC Installer on Windows

Installation steps

  1. Download the Git for Windows installer.

  2. Run the installer and follow the steps below:

    • Click on Next to get through the license screen.

    • Click on Next to accept the default installation path of C:\Program Files\Git. (If a new version has been released, the number may change.)

    • On the Select Components screen, you may wish to check the box to create Desktop icons. Please do not change the other selections. Click Next.

    • Click on Next to accept Git as the name of the Start Menu folder.

    • On the Choosing the default edit used by Git panel, please select

    • from the dropdown menu Use the nano editor by default – you may need to scroll up in the list to find it. Click on Next.

    • Ensure that Git from the command line and also from 3rd-party software is selected and click on Next. (If you don’t do this Git Bash will not work properly, requiring you to remove the Git Bash installation, re-run the installer and to select the Git from the command line and also from 3rd-party software option.)

    • Keep the OpenSSH option if it gives you an option to change that.

    • Ensure that Use the native Windows Secure Channel library is selected and click on Next.

    • Ensure that Checkout Windows-style, commit Unix-style line endings is selected and click on Next.

    • Ensure that Use Windows’ default console window is selected and click on Next.

    • Choose the Default behavior of git pull to be Default (fast-forward or merge).

    • From Choose a credential manager, choose Git Credential Manager Core.

    • Ensure that Enable file system caching is selected

    • Do NOT enable experimental support for pseudo consoles. Clicking Next here should start the installation with no further selection screens.

    • This should bring you to a screen where you can click Finish. Unless you are really interested, you should uncheck the box to view the release notes.

  3. If your HOME environment variable is not set (or you don’t know what this is), then

    • Open command prompt (Open Start Menu then type cmd and press [Enter])

    • Type the following line into the command prompt window exactly as shown: 
       setx HOME "%USERPROFILE%"
    • Press Enter, you should see output that indicates 
       SUCCESS: Specified value was saved.
    • Quit command prompt by typing exit then pressing Enter

Completing those steps will provide you with both Git and Bash in the Git Bash program.

Installing R

Download the R installer. Link to the installer

Run the downloaded file. When prompted, you do want to allow it to make changes to your system.

Please accept the default installation location for R; for version 4.0.3 that will be C:\Program Files\R\R-4.0.3. Subsequent steps will use that installation path to make R avaiable from the command line, which you will need.

Accepting all of the default choices and clicking Next at each choice will result in a working R.

Installing RStudio

Note that you must install R before RStudio.

Please see the download page at the RStudio web site. There is only one Windows installer available for Windows 10, 8, and 7 as of 19 Nov, 2020. You should be able to run it once downloaded and it will install properly.

macOS

The Unix Shell

The shell is a program that enables us to send commands to the computer and receive output. It is also referred to as the terminal or command line. For a Mac computer running macOS Mojave or earlier releases, the default Unix Shell is Bash. For a Mac computer running macOS Catalina or later releases, the default Unix Shell is Zsh.

Your default shell is available via the Terminal program within your Utilities folder. To open Terminal, try one of the following:

To see which Unix shell your Mac is running, type echo $SHELL in your terminal window.

Installing Git

Git is a version control system that lets you track who made changes to what when and has options for easily updating a shared or public version of your code on github.com. You will need a supported web browser.

You will need an account at GitHub for parts of the Git lesson. Basic GitHub accounts are free. We encourage you to create a GitHub account if you don’t have one already. Please consider what personal information you’d like to reveal. For example, you may want to review these instructions for keeping your email address private provided at GitHub.

Git may be installed on Macs as part of XCode. To check whether git is installed, type which git in a Terminal and hit enter. If installed, the installation path will print on the next line in your terminal. The default installation path for Apple installed git is /usr/bin/git.

If git is installed, you can see which version is installed by typing git --version into the terminal and hitting enter. If you receive an error regarding an invalid active developer path, you may need to (re-)install XCode. Try doing this by typing xcode-select --install and enter in the Terminal. The git --version command should then return the number of the installed version of git.

You should have git version >=2.24. If not, please install the latest version of Git for Mac by downloading and running the most recent “mavericks” installer from this list. Because this installer is not signed by the developer, you may have to right click (control click) on the .pkg file, click Open, and click Open on the pop up window. After installing Git, there will not be anything in your /Applications folder, as Git is a command line program. For older versions of OS X (10.5-10.8) use the most recent available installer labelled “snow-leopard” available here.

Installing R

R is a programming language that is especially powerful for data exploration, visualization, and statistical analysis. You will need a recent version of R (>= 4.0). Install R by downloading and running this .pkg file from CRAN.

Once the package is installed, open a terminal and type which R to see the installation location. Typing R --version will print the installed version number.

Installing RStudio

To interact with R, we use RStudio. RStudio is an integrated development environment for R. To install RStudio. Click the DOWNLOAD RSTUDIO FOR MAC button. Double-click the downloaded installer. It will open a window with the Applications folder and an icon for the RStudio app. Drag the RStudio icon into the Applications folder.

Linux

Installing R

In a Terminal window, the following will install R on Ubuntu/Debian Linux.

sudo apt-get install r-base

If you use Fedora, then the following command should be used

dnf install git
dnf install R

You will need to install RStudio using the instruction found at the RStudio page that are appropriate for your Linux.