Rationale and background:

Introduction

This tutorial will orient you to using the QIIME software package (version 1.9.1) installed on Atmosphere. This particular demo is adapted from the Illumina tutorial on the QIIME site. 

This tutorial will take users through steps of:

1. Launching the QIIME-1.9.1 Atmosphere image
2. Running QIIME-1.9.1 on an test data 

Please work through the tutorial and add your comments on the bottom of this page. Or send comments per email to upendra@cyverse.org. Thank you.

Part 1: Connect to a Jupyter notebook on Atmosphere Image (Virtual Machine)

Step 1. Go to https://atmo.iplantcollaborative.org and log in with your CyVerse credentials.

Step 2. Click on the Launch New Instance button and search for Qiime-1.9.1

Step 3. Select the image Qiime-1.9.1 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. Launch Jupyter notebook on the Atmosphere image for running Qiime 1.9.1

Open the Terminal.  Add the ssh details along with your IP address to connect the instance through the terminal. Remember to put your actually iPlant username in place of the text 'username' and 'IPaddress' in this next line of code:

$ ssh <username>@<IPaddress>

$ cp -r /opt/qiime_illumina_test_data .

Run Jupyter Notebook command for launching Jupyter notebook.

$ jupyter-notebook --no-browser --ip=0.0.0.0 2>&1 | sed s/0.0.0.0/$(curl -s ipinfo.io/ip)/g

[I 10:02:36.470 NotebookApp] Writing notebook server cookie secret to /run/user/14135/jupyter/notebook_cookie_secret
[I 10:02:36.595 NotebookApp] Serving notebooks from local directory: /home/upendra_35
[I 10:02:36.596 NotebookApp] 0 active kernels 
[I 10:02:36.596 NotebookApp] The Jupyter Notebook is running at: http://128.196.64.195:8888/?token=0e40be8748d2cc59b24016a744a17389807aef3f4f560f59
[I 10:02:36.596 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
[C 10:02:36.597 NotebookApp] 

    Copy/paste this URL into your browser when you connect for the first time,
    to login with a token:
        http://128.196.64.195:8888/?token=0e40be8748d2cc59b24016a744a17389807aef3f4f560f59 # <- Copy and paste this url in a browser (chrome, firefox, Safari etc.,)

After you copy the link on to the browser. Click the "New" tab and select Python 2 kernel for running QIIME 1.9.1 which will open a Jupyter Notebook in a different tab