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Getting connected

Introduction

There are three comonents you will need to understand before we get connected.

GitHub Codespaces

GitHub Codespaces is a cloud-based development environment that allows users to run and edit code directly in a virtual machine (VM) hosted by GitHub. It provides a fully configured workspace, pre-installed with necessary tools like Git, Python, and Docker, eliminating the need for users to set up a local environment. Every GitHub user has a certain number of free Codespace hours per month (120 for a free account), making it an ideal solution for doing some occasional bioinformatics.

Visual Studio Code (VS Code)

VS Code is a lightweight yet powerful code editor that supports multiple programming languages. It also allows users to connect to GitHub Codespaces, allowing users to work on cloud-based VMs as if they were local files. Users will launch GitHub Codespaces via VS Code, enabling them to interact with their virtual machine through a familiar coding interface.

TigerVNC

TigerVNC (Virtual Network Computing) is a tool that allows users to remotely access a graphical desktop environment of their virtual machine. Since GitHub Codespaces primarily provides a terminal interface, TigerVNC will let users interact with a full virtual desktop, running graphical applications as if they were using a local computer.

How These Work Together:

  1. Users launch GitHub Codespaces to create a cloud-based virtual machine.
  2. They connect to the VM using VS Code, accessing the terminal and code files.
  3. If a graphical interface is needed, they use TigerVNC to access the full desktop environment.

This setup allows users to work on cloud-hosted projects with both command-line and GUI access, making it ideal for bioinformatics and data analysis workflows.

Getting set up

1. Set up a GitHub account

Head over to https://github.com/ and sign up for an account. You can skip this step if you already have an account.

2. Download Visual Studio Code

Get the latest version of vscode from https://code.visualstudio.com/ and follow install instructions from the website.

3. Download TigerVNC

Download TigerVNC from https://sourceforge.net/projects/tigervnc/files/stable/1.15.0/ and follow install instructions from the website. Based on your operating system, you can download the appropriate version.

  • Windows: tigervnc64-1.15.0.exe
  • Mac: TigerVNC-1.15.0.dmg

Follow the instructions provided to install TigerVNC on your system.

4. Get connected

Once you have installed TigerVNC, you can connect to your GitHub Codespace using the following steps:

  1. Open Visual Studio Code.
  2. Install the GitHub Codespaces extension by clicking on the following link and following instructions: GitHub Codespaces.
  3. Open the command palette by pressing Ctrl+Shift+P (Windows/Linux) or Cmd+Shift+P (Mac).
  4. Type Create new Codespace and select the option.
  5. Enter lshtm-genomics/codespaces in the repository field.
  6. Select the day1 template.
  7. Select 2 cores, 8GB RAM, 32 GB storage option.

It should take a few minutes to create the Codespace. Once it's ready, you will be able to access the terminal and files directly from VS Code.

If you need a graphical interface, you can use TigerVNC to connect to the Codespace. Open TigerVNC and enter the following address: localhost:5901. Once you've entered the password, you should see the full desktop environment of your Codespace.

Important

When you are finished working, make sure to stop the Codespace to using up your free hours. You can do this by opening up the command palette (Cmd+Shift+P or Ctrl+Shift+P) and typing Codespaces: Stop Current Codespace. You will be able to restart that Codespace at any time by selecting Codespaces: Connect to Codespace from the command palette.

That's it! You're now connected to your GitHub Codespace and ready to start your bioinformatics journey.