Instructors:
Angelina Uno-Antonison, Austyn Trull, Brandon Wilk, Luke Potter, Samuel Bharti, Shaurita Hutchins
Helpers:
James Scherer, Sydney Lin, Hannah J. McIntire-Ray
General Information
The Carpentries project comprises the Software Carpentry, Data Carpentry, and
Library Carpentry communities of Instructors, Trainers, Maintainers,
helpers, and supporters who share a mission to teach foundational computational and data science
skills to researchers.
Want to learn more and stay engaged with The Carpentries? Carpentries Clippings is The Carpentries' biweekly newsletter, where we share community news, community job postings, and more.
Sign up to receive future editions and read our full archive: https://carpentries.org/newsletter/
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.
Who:
The course is aimed at graduate students and other researchers.
You don't need to have any previous knowledge of the tools
that will be presented at the workshop.
Where:
701 19th Street South, Birmingham, AL 35233.
Get directions with
OpenStreetMap
or
Google Maps.
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).
Please attend our virtual office hours offered before the workshop if you have any questions about package installation. Details will be sent via email
Accessibility:
We are committed to making this workshop
accessible to everybody.
The workshop organizers have checked that:
The room is wheelchair / scooter accessible.
Accessible restrooms are available.
We are dedicated to providing a positive and accessible learning environment for all.
We do not require participants to provide documentation of disabilities or disclose any unnecessary personal information.
However, we do want to help create an inclusive, accessible experience for all participants.
We encourage you to share any information that would be helpful to make your Carpentries experience accessible.
To request an accommodation for this workshop, please fill out the
accommodation request form.
If you have questions or need assistance with the accommodation form please email us.
Glosario is a multilingual glossary
for computing and data science terms. The glossary helps
learners attend workshops and use our lessons to make sense of computational and programming jargon written in English by offering it
in their native language. Translating data science terms also provides a teaching tool for Carpentries Instructors to reduce barriers
for their learners.
Workshop Recordings:
Carpentries workshops are designed to be interactive rather than lecture-based, with lessons that build upon one another.
To foster a positive online learning environment, we strongly recommend that participants join in real time.
As a result, workshop recordings are not recommended and may not be available to learners.
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.
To participate in a
Software Carpentry
workshop,
you will need access to software as described below.
In addition, you will need an up-to-date web browser.
To install WSL 2, you will need Administrator (“admin”) privileges on your laptop/PC.
If you have a device provided by an institution that does not give you admin rights, please either request that they:
Give you admin rights (temporarily or otherwise) to install WSL 2 yourself OR
Install WSL 2 for you
If you experience any issues, please install Git for Windows using the instructions below.
Click on the Windows Start Menu button in the bottom left corner of your screen, or tap the Windows button on your keyboard, and type “System” in the search bar.
Click the “System (Control Panel)” option.
In the window that opens, there will be information about your current Windows system, including the version. Here is an example from Windows 11:
Depending on your version, please go to the relevant instructions below.
Windows XP/Vista/7/8
These versions of Windows are considered End Of Life, and are not recommended for use in modern data science.
Software may experience issues, and security updates are also not available which puts your machine at risk.
Please consider upgrading your Windows version if you are able to do this yourself, or speak with your local IT administrator to discuss options available to you to upgrade.
If you are running any of these Windows versions, please install Git for Windows using the installation instructions below.
Windows 10 (earlier than version #1903)
For older versions of Windows 10 (version 1903/OS build 18362 and below), please follow the Git for Windows installation instructions below.
Windows 10 (version #1903 and later) and Windows 11
WSL 2 is recommended for more modern versions of Windows as it provides an accurate and representative experience of Linux, but provided from within your Windows environment.
We will install Ubuntu via the Microsoft Store.
It is possible to install WSL within the Windows Powershell command prompt, and full instructions are on the Microsoft website.
Note: You will need to restart your computer after installing WSL 2, so make sure you have saved any work.
Why Ubuntu?
Linux comes in many flavours, called “distributions”, and each has its own benefits, features and quirks!
WSL 2 is a fully fledged Linux environment that runs completely within your Windows 10 or 11 operating system.
While there are many Linux distributions available to install (e.g. Ubuntu, Debian, Fedora, Mint, Arch, Gentoo, and hundreds more!), WSL 2 only supports a handful of distributions listed above due to the way it needs to be integrated with Windows itself.
So, we will use the default that WSL 2 recommends, Ubuntu.
Via the Microsoft Store:
Open the Windows Start Menu button in the bottom left corner of your screen (four blue squares), or tap the Win Windows button on your keyboard (between the bottom left CTRL and ALT keys) and search “store”. Open the Microsoft Store.
In the Microsoft Store search bar, type “wsl ubuntu”, and select the Ubuntu 22.04 or 24.04 option (at the time of writing, Ubuntu 22.04.06 LTS, or Ubuntu 24.04.01 LTS):
If a pop-up window appears asking if you want to make changes to your device, select “Yes”
The install should proceed, and this can take a few minutes depending on your PC performance and internet download speed.
Once installed, restart the computer.
Once restarted, reopen the Windows Start Menu button in the bottom left corner of your screen, or tap the Windows button on your keyboard. In the search bar, type either:
Ubuntu: selecting Ubuntu 22.04.06 LTS or Ubuntu 24.04.01 LTS from the Start Menu will open the bash prompt directly, or
Terminal: this will open a new Windows Terminal window, which will look like a blank black window with a blinking cursor waiting for input. Note: This terminal might default to Powershell, and not Ubuntu. If this is the case, click the down arrow in the Terminal window menu bar at the top, and then click Ubuntu 22.04 or 24.04, depending on the version you installed. It will also show keyboard shortcuts (e.g. Ctrl+Shift+1) to open the various prompts available within the Terminal application.
Once you have installed WSL 2, you will need to install some software within the Ubuntu operating system in order to use it effectively. Make sure you are using Ubuntu by checking you see the bash prompt:
The first thing to do is to update the list of available Ubuntu software packages, using a tool called apt.
Type the following command into the bash prompt:
sudo apt update
Note: You will be prompted to enter your password. This is the password you set when installing Ubuntu, and will not show up on the screen as you type it in.
This is a security feature of the terminal, and is normal behaviour.
Install updated versions of the base packages required across all our lessons, by typing:
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.
From the dropdown menu, "Choosing the default editor used by Git", select "Use the Nano editor by default" (NOTE: you will need to scroll up to find it) and click on "Next".
On the page that says "Adjusting the name of the initial branch in new repositories", ensure that
"Let Git decide" is selected. This will ensure the highest level of compatibility for our lessons.
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.)
Select "Use bundled OpenSSH".
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".
Ensure that "Default (fast-forward or merge) is selected and click "Next"
Ensure that "Git Credential Manager" is selected and click on "Next".
Ensure that "Enable file system caching" is selected and click on "Next".
Click on "Install".
Click on "Finish" or "Next".
If your "HOME" environment variable is not set (or you don't know what this is):
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 SUCCESS: Specified value was saved.
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 Mac OS X Ventura and newer versions is Zsh, but
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, you can change your current shell to Bash by typing
bash and then pressing Return. To check
your current shell type echo $0 and press Return.
To change your default shell to Bash type chsh -s /bin/bash and
press the Return key, then reboot for the change to take effect. To
change your default back to Zsh, type chsh -s /bin/zsh, press the
Return key and reboot. To check available shells, type
cat /etc/shells.
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 Terminal and press the Return key. If the message
printed does not end with '/bash' then your default is something
else, you can change your current shell to Bash by typing
bash and then pressing Return. To check
your current shell type echo $0 and press Return.
To change your default shell to Bash type chsh -s /bin/bash and
press the Return key, then reboot for the change to take effect. To
change your default back to Zsh, type chsh -s /bin/zsh, press the
Return key and reboot. To check available shells, type
cat /etc/shells.
Note for Windows Users
If you have used Windows Subsystem for Linux ("WSL2") please open your Ubuntu bash terminal and follow the Linux instructions for each of the software packages below.
If not, please follow the Windows instructions.
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.com
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.
Please open the Terminal app, type git --version and press
Enter/Return. If it's not installed already,
follow the instructions to Install the "command line
developer tools". Do not click "Get Xcode", because that will
take too long and is not necessary for our Git lesson.
After installing these tools, there won't be anything in your /Applications
folder, as they and Git are command line programs.
For older versions of OS X (10.5-10.8) use the
most recent available installer labelled "snow-leopard"
available here.
(Note: this project is no longer maintained.)
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 in the pop-up dialog.
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.
nano is a basic editor and the default that instructors use in the workshop.
It should be pre-installed.
SSH Token Setup
This is VERY important to do before the workshop in order to complete
the Git workshop. This information can also be found
here
Note for Windows Users
If you have used Windows Subsystem for Linux ("WSL2") please open your Ubuntu bash terminal to enter the commands
If not, please use the git-bash.
Open up your terminal (“git-bash” for Windows or “terminal” for Mac and Linux)
To create an SSH key pair use this command, where the -t option specifies which type of algorithm to use:
$ ssh-keygen -t ed25519
The command will ask for a file name, press Enter to use the default
Generating public/private ed25519 key pair. Enter file in which to
save the key (/c/Users/Alfredo/.ssh/id_ed25519):
You'll be prompted for a passphrase, be sure to pick something memorable as there's no “reset my password” option. You'll also note you won't see any of the letters/numbers/symbols you type, this is all normal and what you type is recorded even if they don't show up
Created directory '/c/Users/Alfredo/.ssh'. Enter passphrase (empty for
no passphrase):
You'll be prompted to enter the passphrase again, enter the same passphrase you entered in step 3
Enter same passphrase again:
After entering the passphrase, you will see something like below. (note the specific output will be different for your system, that is normal). This means the ssh key is created.
Your identification has been saved in /c/Users/Alfredo/.ssh/id_ed25519
Your public key has been saved in /c/Users/Alfredo/.ssh/id_ed25519.pub
The key fingerprint is:
SHA256:SMSPIStNyA00KPxuYu94KpZgRAYjgt9g4BA4kFy3g1o a.linguini@ratatouille.fr
The key's randomart image is:
+--[ED25519 256]--+
|^B== o. |
|%*=.*.+ |
|+=.E =.+ |
| .=.+.o.. |
|.... . S |
|.+ o |
|+ = |
|.o.o |
|oo+. |
+----[SHA256]-----+
Run the below command
$ cat ~/.ssh/id_ed25519.pub
Copy what is output to the command line, it should look like the below:
Click on the profile icon in the top right corner to access the drop down menu
Click “Settings”
Click “SSH and GPG Keys” on the left side, with the “Access” menu
Click the “New SSH Key” button
Enter a name for the SSH Key (something easy to remember)
Paste your key you copied from step 7 into the large text box
Click “Add SSH key” to complete setup
Go back to the command line, and run this command
$ ssh -T git@github.com
You should receive output like the below, indicating it a success!
Hi Alfredo! You've successfully authenticated, but GitHub does not provide shell access.
R
R is a programming language
that is especially powerful for data exploration, visualization, and
statistical analysis. To interact with R in our lessons, we typically use
RStudio.
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.
Navigating to CRAN and following the instructions outlined there, using your package manager. We have reproduced the commands below:
Use the terminal command prompt to type/copy-and-paste these commands in, pressing Enter after each line to run the command.
Do not run the lines with # at the start of each line, as this indicates a comment and is not part of the command.
# update indices
sudo apt update -qq
# install two helper packages we need
sudo apt install --no-install-recommends software-properties-common dirmngr
# add the signing key for these repos
wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | sudo tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
# add the repo from CRAN
sudo add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"
# install R itself
sudo apt install --no-install-recommends r-base
# install dependencies
sudo apt install -y r-base-core r-recommended r-base-dev gdebi-core build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev
sudo apt install --no-install-recommends gdebi-core
# cd ~/Downloads
# download the latest RStudio Server .deb file
wget https://download2.rstudio.org/server/jammy/amd64/rstudio-server-2025.05.1-513-amd64.deb
# install the .deb file
sudo gdebi rstudio-server-2025.05.1-513-amd64.deb
# start the RStudio Server
sudo systemctl start rstudio-server
# enable RStudio Server to start on boot
sudo systemctl enable rstudio-server
After installation of RStudio Server, check you can access it by:
Opening a web browser and navigating to http://localhost:8787.
Logging in with the username and password you used when you set up Linux / WSL2.
If you are using Windows and WSL2, the full in-depth instructions for installing R on WSL2 can be found in this
POSIT article.
R Packages
R has a variety of existing
and pre-built packages that ease the burden of analysis. We will be
using a few of these packages to complete the lesson taught at this
workshop.
Please only complete this step AFTER
successfully installing R and Rstudio above
Note for Windows Devices:
You will need to go to https://cran.r-project.org/bin/windows/Rtools/rtools42/rtools.html to download the Rtools42 exe file.
Once the exe file has downloaded, double click it to install it, then continue below.
In the central panel (known as the 'Source Code Panel') type the below commands:
# Install the tidyverse package:
install.packages("tidyverse")
# Install the ggplot2 package
install.packages("ggplot2")
# install the dplyr package
install.packages('dplyr')
Run each command by highlighting each line one at a time
and clicking the 'Run' button that is located near
the top-right of the 'Source Code Panel'
(NOTE: The exact location may differ dependent on the OS
you are using, but the button should still be visible
around the 'Source Code Panel'). Repeat this for each line
that was typed in the above step
Once installation has completed for all packages, type
the below commands to make sure packages installed correctly:
library("dplyr")
library("ggplot2")
Run these commands similar to the steps described above,
highlight each line and click the 'Run' button
individually for each line.
If everything worked correctly, you will not see any
output from the 'Console' panel located in your RStudio
window other than seeing the command copied on each line
Depending on your version, please go to the relevant instructions below.
