University of Arizona


Nov 7-8, 2020

9:00 AM - 5:00 PM

Instructors: Katherine Busby, Hagan Franks, Kelsey Gonzalez, Uwe Hilgert, Artin Majdi, Isabella Viney

Helpers: Dawson Fairbanks, Dwight Nwaigwe, Adriana Picoral, Austin Rutherford, Bradley Schlottman

General Information

Software Carpentry aims to help researchers get their work done in less time and with less pain by teaching them basic research computing skills. This hands-on workshop will cover basic concepts and tools, including program design, version control, data management, and task automation. Participants will be encouraged to help one another and to apply what they have learned to their own research problems.

For more information on what we teach and why, please see our paper "Best Practices for Scientific Computing".

Who: The workshop is aimed at researchers, including graduate students, postdocs, staff and faculty. It targets computational novices and does not require any previous knowledge of the tools that will be introduced.

Where: This training will take place online. The instructors will provide you with the information you will need to connect to this meeting.

When: Nov 7-8, 2020. Add to your Google Calendar.

Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have a few specific software packages installed (listed below).

Accessibility: We are dedicated to providing a positive and accessible learning environment for all. Please notify the instructors in advance of the workshop if you require any accommodations or if there is anything we can do to make this workshop more accessible to you.

Contact: Please email for more information.

Roles: To learn more about the roles at the workshop (who will be doing what), refer to our Workshop FAQ.

Code of Conduct

Everyone who participates in Carpentries activities is required to conform to the Code of Conduct. This document also outlines how to report an incident if needed.

Collaborative Notes

We will use this collaborative document for chatting, taking notes, and sharing URLs and bits of code.


Please be sure to complete these surveys before and after the workshop.

Pre-workshop Survey

Post-workshop Survey


Day 1

Before Pre-workshop survey
09:00 Automate Tasks with the Unix Shell
10:30 Break
10:45 Manage data with git/GitHub
12:00 Break
13:00 Analyze data in the Bash Shell
14:00 Apply Git
15:00 Break
15:15 Q & A and Clinic (Bring/Discuss Your Own Data)
16:30 END

Day 2

09:00 Analyze data with R/R-Studio
10:30 Break
10:45 Plotting Data in R with ggPlot
12:00 Break
13:00 Cont. R/R-Studio Essentials
14:00 Break
14:15 Q & A and Clinic (Bring/Discuss Your Own Data)
16:00 Wrap-up
16:15 Post-workshop Survey
16:30 END


Take control with the Unix Shell

  • Work in vs. work below the GUI
  • Navigate the shell
  • Find, create, copy, move and delete folders and files
  • Shell over GUI: Command history and tab completion
  • Connect commands into workflows: pipes and redirection
  • Automate repetitive tasks: loops
  • Save and run workflows in scripts
  • Shell Lessons
  • Shell Quick Reference
  • Explain Shell (Parses shell commands and shows docs about the command)
  • ShellCheck (Identifies bugs in shell scripts)
  • Linux Man Pages Online (Same content as command line man/help pages in the Unix shell)
  • Bash Keyboard Shortcuts</li> </ul> </div>

    Analyze data in R

    • Work with vectors and data frames
    • Read and plot data
    • Create and use functions
    • Create loops and conditionals
    • Use R from the command line

    Syllabus subject to change if necessary.


    To participate in a Software Carpentry workshop, you will need access to the software described below. In addition, you will need an up-to-date web browser.

    We maintain a list of common issues that occur during installation as a reference for instructors that may be useful on the Configuration Problems and Solutions wiki page.

    Install the videoconferencing client

    If you haven't used Zoom before, go to the official website to download and install the Zoom client for your computer.

    Set up your workspace

    Like other Carpentries workshops, you will be learning by "coding along" with the Instructors. To do this, you will need to have both the window for the tool you will be learning about (a terminal, RStudio, your web browser, etc..) and the window for the Zoom video conference client open. In order to see both at once, we recommend using one of the following set up options:

    • Two monitors: If you have two monitors, plan to have your terminal up on one monitor and the video conferencing software on the other.
    • Two devices: If you don't have two monitors, do you have another device (tablet, smartphone) with a medium to large sized screen? If so, try using the smaller device as your video conference connection and your larger device (laptop or desktop) to follow along with the tool you will be learning about.
    • Divide your screen: If you only have one device and one screen, practice having two windows (the video conference program and one of the tools you will be using at the workshop) open together. How can you best fit both on your screen? Will it work better for you to toggle between them using a keyboard shortcut? Try it out in advance to decide what will work best for you.
    This blog post includes detailed information on how to set up your screen to follow along during the workshop.

    The Bash Shell

    Bash is a commonly-used shell that gives you the power to do tasks more quickly.

    1. Download the Git for Windows installer.
    2. Run the installer and follow the steps below:
      1. Click on "Next" four times (two times if you've previously installed Git). You don't need to change anything in the Information, location, components, and start menu screens.
      2. From the dropdown menu select "Use the nano editor by default" (NOTE: in the drop box you may need to scroll up to find "nano editor") and click on "Next".
      3. Ensure that "Let Git decide" is selected and click on "Next".
      4. 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.)
      5. Ensure that "Use the native Windows Secure Channel library" is selected and click on "Next".
      6. Ensure that "Checkout Windows-style, commit Unix-style line endings" is selected and click on "Next".
      7. Ensure that "Use Windows' default console window" is selected and click on "Next".
      8. Ensure that "Default (fast-forward or merge)" is selected and click "Next"
      9. Ensure that "Git Credential Manager Core" is selected and click "Next"
      10. Ensure that "Enable file system caching" is selected and click on "Next".
      11. Click on "Install".
      12. Click on "Finish" or "Next".
    3. If your "HOME" environment variable is not set (or you don't know what this is):
      1. Open command prompt (Open Start Menu then type cmd and press Enter)
      2. Type the following line into the command prompt window exactly as shown:

        setx HOME "%USERPROFILE%"

      3. Press Enter, you should see SUCCESS: Specified value was saved.
      4. Quit command prompt by typing exit then pressing Enter

    This will provide you with both Git and Bash in the Git Bash program.

    Video Tutorial

    The default shell in some versions of macOS is Bash, and Bash is available in all versions, so no need to install anything. You access Bash from the Terminal (found in /Applications/Utilities). See the Git installation video tutorial for an example on how to open the Terminal. You may want to keep Terminal in your dock for this workshop.

    To see if your default shell is Bash type echo $SHELL in Terminal and press the Return key. If the message printed does not end with '/bash' then your default is something else and you can run Bash by typing bash

    If you want to change your default shell, see this Apple Support article and follow the instructions on "How to change your default shell".

    Video Tutorial

    The default shell is usually Bash and there is usually no need to install anything.

    To see if your default shell is Bash type echo $SHELL in a terminal and press the Enter key. If the message printed does not end with '/bash' then your default is something else and you can run Bash by typing bash.


    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 You will need a supported web browser.

    You will need an account at 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.

    For macOS, install 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.

    Video Tutorial

    If Git is not already available on your machine you can try to install it via your distro's package manager. For Debian/Ubuntu run sudo apt-get install git and for Fedora run sudo dnf install git.

    Text Editor

    When you're writing code, it's nice to have a text editor that is optimized for writing code, with features like automatic color-coding of key words. The default text editor on macOS and Linux is usually set to Vim, which is not famous for being intuitive. If you accidentally find yourself stuck in it, hit the Esc key, followed by :+Q+! (colon, lower-case 'q', exclamation mark), then hitting Return to return to the shell.

    nano is a basic editor and the default that instructors use in the workshop. It is installed along with Git.

    nano is a basic editor and the default that instructors use in the workshop. See the Git installation video tutorial for an example on how to open nano. It should be pre-installed.

    Video Tutorial

    nano is a basic editor and the default that instructors use in the workshop. It should be pre-installed.


    R is a programming language that is especially powerful for data exploration, visualization, and statistical analysis. To interact with R, we use RStudio.

    Install R by downloading and running this .exe file from CRAN. Also, please install the RStudio IDE. Note that if you have separate user and admin accounts, you should run the installers as administrator (right-click on .exe file and select "Run as administrator" instead of double-clicking). Otherwise problems may occur later, for example when installing R packages.

    Video Tutorial

    You can download the binary files for your distribution from CRAN. Or you can use your package manager (e.g. for Debian/Ubuntu run sudo apt-get install r-base and for Fedora run sudo dnf install R). Also, please install the RStudio IDE.