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Part 1: Connect to a Qiime-2-Jupyter-notebook Atmosphere Image (Virtual Machine)

Step 1. Go to and log in with your CyVerse credentials

Step 2. Create a project and name the project name as QIIME2 2018.4 and description as QIIME2 2018.4

Step 3. Click the project and then Select the image Qiime-2-jupyter-notebook and click Launch Instance. It will take ~10-15 minutes for the cloud instance to be launched. 

Note: Instances can be configured for different amounts of CPU, memory, and storage depending on user needs.  This tutorial can be accomplished with the small instance size, medium1 (4 CPUs, 8 GB memory, 80 GB root)

Step 4. Once the VM is ready. Click the VM which will take onto next screen where you can launch web shell

Step 5: Depending on how you’ve installed Docker on your system, you might see a permission denied error after running the above command. If you’re on Linux, you may need to prefix your Docker commands with sudo. Alternatively to run docker command without sudo, you need to run the following


Close the terminal and log-in again.


Part 2: Running QIIME-2 2018.4 on the command line

Part 3: Running QIIME-2 2018.4 Jupyter notebook

Step 1. Copy/paste the above URL into your browser when you connect for the first time. Click the New tab and then bash kernel to launch new Jupyter notebook page

Step 2. Now you can copy and paste the commands from the below notebook to run Qiime2 moving sample tutorial. Here is an example..

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