Set Up Conda Environment¶
Platform¶
Choose your platform to get recommendations:
You should be able to install everything on Linux systems.
We recommend using the Windows Subsystem for Linux (WSL) for the best experience. If you are using WSL, please follow the instructions for Linux.
You should be able to install everything on MacOS systems.
Note
All installation commands are intended for the Bash shell, which is the default on most macOS systems. If you use a different shell (like zsh), they should still work, but let us know if you have issues.
Set Up Conda Environment¶
We recommend to create and set up an empty conda environment:
conda create -n gadma_workshop_env python=3.10
conda activate gadma_workshop_env
Add channels that we are going to use for installations:
conda config --add channels bioconda
conda config --add channels conda-forge
Optional: Install Jupyter Notebook¶
During the workshop, we will be demonstrating several Jupyter Notebooks.
You are not required to install anything for the workshop itself. All notebooks will be accessible for you to view online—so you can follow along without installing any software.
However, if you’d like to run the notebooks on your own laptop after the workshop or experiment with them interactively, you will need to install Jupyter Notebook.
What is Jupyter Notebook? Jupyter Notebook is an application that lets you create and share interactive documents, which can include live code, plots, images, and explanations—all in one place. When you launch Jupyter Notebook, it opens in your web browser and acts as an interactive workspace for programming, exploring data, and visualizing results. Learn more: here.
To install Jupyter Notebook:
conda install notebook
Once installation finishes, navigate to the folder where you have saved the notebooks we will provide during the workshop. Then start Jupyter Notebook with:
jupyter notebook
This will open the Jupyter interface in your default web browser, showing all notebooks in your current folder.