Module 2: Using the Sandbox Desktop

The virtual desktop on the sandbox provides users with a flexible platform for analyzing HBCD and ABCD data securely. In addition, the desktop provides terminal access, enabling users to pull down repositories and external programs onto their home directory within the sandbox.

Module Objectives

1. Navigate the virtual desktop
2. Open a terminal window and examine the structure of the sandbox
3. Pull down a repository from github
4. Explore the available data using the terminal

Walkthrough

1. The virtual environment provides a graphical user interface (GUI) that allows us to navigate the sandbox. For now, let us open a terminal using the “applications” tab and selecting “system tools” and then “Terminal” underneath.

2. This will open a terminal for working directly on the command line. If you type “pwd” for present working directory, we can see that you are in your own home workspace.

3. Using a new browser tab, navigate to the HDCC_Sandbox_tutorials GitHub Repository where the tutorials for the HDCC are located. Select the green “code” button, and click to copy the URL for cloning the repository.
   

4. Go back to the terminal. Type “git clone,” add a space, and paste the path into the terminal. This will pull the repository from github onto the sandbox.
   

5. Now, we will want to see what data is on the sandbox environment. This can be found in the “/shared” folder on the root system. Go ahead and list the contents of the /shared/hackathon folder, and you’ll see folders for the ABCD and HBCD data available.
   

6. If you list the contents of “~/HDCC_Sandbox_tutorials/examples” you’ll see the four examples we’ll be tackling today.
   

The next section RStudio Setup will show how to set up RStudio and install necessary dependencies.