QIIME2

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

Disclaimer

Before working with JupyterHub and the Cluster it is highly recommended that you read all the previous articles on the Cluster, Slurm, JupyterHub, and Conda, (official conda docs here). Running into the Cluster without knowing how the various features work will not be an enjoyable experience for you.

Running Qiime2

Logging in

  1. Log into https://jupyterhub.tjhsst.edu through Ion

  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 Conda

Conda is a package manager that has been installed on these servers. It creates environments in which you can run and install software. You need to initialize conda once for your user account before you can access the qiime2 installation.

  • If you have never run conda before run: /opt/conda/bin/conda init bash && source ~/.bashrc

Activating qiime2

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

conda activate qiime2

The terminal prompt should now look something like this (noticed the (qiime2) preceding):

(qiime2) borg40 2021abagali $

Now you can run qiime to access Qiime2

Qiime2 Through JupyterHub

After logging into JupyterHub you should see the following on the JupyterHub "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.