QIIME 2

About

QIIME 2 is a powerful, extensible, and decentralized microbiome analysis package with a focus on data and analysis transparency. QIIME 2 enables researchers to start an analysis with raw DNA sequence data and finish with publication-quality figures and statistical results.

Install

Since QIIME 2 updates frequently. It's easier to maintain your own QIIME 2 installation, and update as needed. Here we suggest using Anaconda to manage your instances. If you have never used Anaconda before, please refer to Anaconda.

Once you have Anaconda setup, please follow the following steps to install your own copy of QIIME 2.

# Load Anaconda module
module load Anaconda3

# Download the conda environment file for QIIME 2
wget https://data.qiime2.org/distro/core/qiime2-2021.4-py38-linux-conda.yml

# Use the downloaded conda environment file to install QIIME 2
# And named it: qiime2-2021.4
conda env create -n qiime2-2021.4 --file qiime2-2021.4-py38-linux-conda.yml

# Remove the conda environment file after installation
rm qiime2-2021.4-py38-linux-conda.yml

Jupyter Notebook support (optional)

By default, the Jupyter Notebook running on the OnDemand portal is from a basic installation of Jupyter Notebook which doesn't have the ability to do QIIME 2 visualization. You will need to perform these additional steps to make it work.

# Load Anaconda module
module load Anaconda3

# Activate the QIIME 2 environment we just installed
conda activate qiime2-2021.4

# Install required package
conda install -y nb_conda

# Enable the extension
jupyter serverextension enable --py qiime2

Now, you can go to the interactive job to start Jupyter Notebook, put this line in the Environment Setup box to enable the conda environment you just installed:

conda activate qiime2-2021.4