QIIME2

This document describes how to use qiime2 and other biology packages on JupyterHub and the Cluster

Disclaimer

Before working with JupyterLab and the Cluster, it is highly recommended that you read all the previous articles on the Cluster, Slurm, and OnDemand. Running into the Cluster without knowing how the various features work will not be an enjoyable experience for you.

Running Qiime2

Logging in

1. Create a JupyterLab session on OnDemand (see OnDemand)

2. You will be placed into a queue until a computer is allocated to you (one of 40+ machines)

3. Once logged in, select "File > New > Terminal" this will give you a terminal on the machine you are n

   • This is the same effect as Running ssh [Ion username]@remote.tjhsst.edu and then ssh [computer] from there.

Activating qiime2

qiime2 and related packages are installed in the qiime2 module. This environment can also be accessed through JupyterLab with the "Console" and "Notebook" options (Python only). To access qiime2 from the terminal run the following:

module load qiime2

Now you can run qiime to access Qiime2

Qiime2 Through Jupyter

After accessing Jupyter, you should see the following on the "launcher":

Notice the Qiime2 options in Notebook and Console. Also notice the R(qiime2) options

The qiime2 options will spawn a Python Notebook or Console depending on what you choose. The R(qiime2) will spawn an R Notebook or Console depending on what you choose.