Helmholtz Information & Data Science Academy (HIDA) Shell & Git Kickstart

Sep 22-23, 2025

9:00 am - 1:00 pm CEST

Instructors: Sebastian Starke, Ines Schmahl

Helpers: Ines Schmahl, Sebastian Starke

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.

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

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: Online

When: Sep 22-23, 2025; 9:00 am - 1:00 pm CEST 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 committed to making this workshop accessible to everybody. The workshop organizers have checked that:

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.

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.

Contact: Please email hida-courses@helmholtz.de 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.

Surveys

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

Pre-workshop Survey

Post-workshop Survey

Schedule

Day 1

09:00 Automating Tasks with the Unix Shell
10:30 Morning break
11:00 Automating Tasks with the Unix Shell (Continued)
13:00 END

Day 2

09:00 Version Control with Git
10:30 Morning break
11:00 Version Control with Git (Continued)
12:45 Post-workshop Survey
13:00 END

Setup

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.

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.

The Bash Shell

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

Two options are available for setting up your device so that you’re ready to learn in our workshops with Microsoft Windows.

The first is Windows Subsystem for Linux v2 (“WSL 2”), and the second is Git for Windows (often referred to as “Git Bash”).

Please follow the instructions below, depending on which version of Windows you are using. If unsure, use the asterisk marked version *.

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.

Windows Version What to Install
Windows 8.1 or earlier Install Git for Windows
Windows 10 (#1902 and below) Install Git for Windows
Windows 10 (#1903 and above) Install WSL 2
Windows 11 * Install WSL 2
Help! What should I use?

Checking your Windows Version

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:
Windows System Info version example 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.

Installing WSL 2

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:

  1. 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.
  2. 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.
  3. 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.
  4. Follow the Installing software within WSL 2 section below.

Installing software within WSL 2

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: Ubuntu terminal running bash and showing the Ubuntu version

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:

  • sudo apt install git build-essential autotools python3 r-base

You're all set!

If you get stuck, please contact your workshop organisers to get assistance before the workshop starts.

Installing Git for Windows

If you are unable to use WSL 2, please use the following instructions to install Git for Windows (“Git Bash”).

  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, "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".
    3. 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.
    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. Select "Use bundled OpenSSH".
    6. Ensure that "Use the native Windows Secure Channel Library" is selected and click on "Next".
    7. Ensure that "Checkout Windows-style, commit Unix-style line endings" is selected and click on "Next".
    8. Ensure that "Use Windows' default console window" is selected and click on "Next".
    9. Ensure that "Default (fast-forward or merge) is selected and click "Next"
    10. Ensure that "Git Credential Manager" is selected and click on "Next".
    11. Ensure that "Enable file system caching" is selected and click on "Next".
    12. Click on "Install".
    13. 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 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