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


upendra_35@vm142-34:~$ sudo usermod -aG docker $USER
upendra_35@vm142-34:~$ exit

Close the terminal and log-in again.


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

$ alias qiime='docker run -t -i -v $(pwd):/data qiime2/core:2018.4 qiime’
$ qiime --version
q2cli version 2018.4.0
Run `qiime info` for more version details.

Part 3: Running QIIME-2 2018.4 Jupyter notebook

upendra_35@vm142-34:~$ ezj
DEBUG: using python version 3
DEBUG: downloading anaconda binary, may take a few minutes
DEBUG: Anaconda already installed to /opt/anaconda3
DEBUG: using python version 3
[I 08:20:25.161 NotebookApp] JupyterLab beta preview extension loaded from /opt/anaconda3/lib/python3.6/site-packages/jupyterlab
[I 08:20:25.161 NotebookApp] JupyterLab application directory is /opt/anaconda3/share/jupyter/lab
[I 08:20:25.167 NotebookApp] Serving notebooks from local directory: /home/upendra_35
[I 08:20:25.167 NotebookApp] 0 active kernels
[I 08:20:25.167 NotebookApp] The Jupyter Notebook is running at:
[I 08:20:25.167 NotebookApp]
[I 08:20:25.167 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
[C 08:20:25.168 NotebookApp] 
    Copy/paste this URL into your browser when you connect for the first time,
    to login with a token:

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..