Git

• Install git (required for creating the conda environment for the spatial training)

What is git?

Git is a version control system. It keeps track of changes in your code over time. With Git you can:

• Create versions of your code and go back to earlier versions
• Work safely on new features without breaking the main code
• Collaborate with others without overwriting each other’s work

All the code that belongs to the same project is stored in a Git repository.

When you install Git it comes with a Git Bash on Windows, a Linux‑style terminal that lets you run Git commands and Bash (Linux) shell commands. On Mac you can simply use the terminal.

What are branches?

Branches are collections of versions of your code, that exist in parallel, so you can work on new features or develop material for a specific event without messing up the main code.

What is github?

GitHub is a website that hosts Git repositories (short: repo) online. it allows to:

• Store and share your Git repos online
• Download other people’s code
• Track issues…

The following git commands are important:

• git clone to download other people’s Github repo; it creates a new folder on your computer containing all the files from the repo.
• git checkout allows to switch to a specific branch of the repo
• git pull to update your local copy of a Github repo by downloading the newest changes from Github and merging them with your local repo.

Homework only for those who will follow the spatial trainings:

• Create a folder called spatial in your home folder (Mac) or C drive (Windows)
  • on Windows the path to the folder is: C:/spatial
  • on Mac the path to the folder is: ~/spatial
• Install Git (see link at the top of this page)
• Open Git Bash on Windows or Terminal on Mac
• Go to the spatial folder with the following command:

cd ..  (only on Windows)
cd ..  (only on Windows)
cd spatial

• Clone the Github repo using the following commands:

git clone https://github.com/vibspatial/targeted_transcriptomics_training.git
cd targeted_transcriptomics_training
git checkout spatial_omics_summer_school_2026

This will create a folder called targeted_transcriptomics_analysis with the material for the summer school in the spatial folder.