Rationale and background:
J Gregory Caporaso, Justin Kuczynski, Jesse Stombaugh, Kyle Bittinger, Frederic D Bushman, Elizabeth K Costello, Noah Fierer, Antonio Gonzalez Pena, Julia K Goodrich, Jeffrey I Gordon, Gavin A Huttley, Scott T Kelley, Dan Knights, Jeremy E Koenig, Ruth E Ley, Catherine A Lozupone, Daniel McDonald, Brian D Muegge, Meg Pirrung, Jens Reeder, Joel R Sevinsky, Peter J Turnbaugh, William A Walters, Jeremy Widmann, Tanya Yatsunenko, Jesse Zaneveld and Rob Knight; Nature Methods, 2010; doi:10.1038/nmeth.f.303
This tutorial will take users through steps of:
- Launching the QIIME-1.9.1 Atmosphere image
- 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 firstname.lastname@example.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:
Run Jupyter Notebook command for launching Jupyter notebook.
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