Installing QIIME2 (miniconda conda)

Introduction

This documentation is abridged from the official QIIME2 documentation (Natively installing QIIME 2 — QIIME 2 2022.8.1 documentation)

QIIME2 is only available in Unix-derived systems -- i.e., Linux, WSL, etc. This protocol assumes that you are running on WSL/Linux. The easiest (and recommended) way to install QIIME2 is via the environment and package manager, conda. Miniconda2 and Miniconda3 should both work with this. If you've been following the lab protocols for bioinformatics processing, you likely have Miniconda3.

Installing conda natively

1. Update conda. The first step, assuming conda is already installed, is to ensure that you're running the latest version of conda.

conda update conda

2. Install QIIME2 within a conda environment. If you are familiar with the conda paradigm, this workflow is rather standard: you will create a conda environment from an environment file. Note that there are some differences between distributions of QIIME2. It is recommended that each distribution be given their own environment -- i.e., have qiime2-2022.8 be a different environment from qiime2-2022.2.

# this retrieves the environment file for your qiime2 distribution (in this case 
# it's qiime2-2022.8) 
wget https://data.qiime2.org/distro/core/qiime2-2022.8-py38-linux-conda.yml 

# this will use conda to solve the environment and install the necessary packages  
# from the environment file you just retrieved and will name it 'qiime2-2022.8' 
conda env create -n qiime2-2022.8 --file qiime2-2022.8-py38-linux-conda.yml

# optionally, delete the environment file as it is no longer necessary to use the 
# newly-created conda environment 
rm qiime2-2022.8-py38-linux-conda.yml

3. Activate and test the environment. Note that to use the conda environment (and the packages installed therein), the conda environment must be activated.

conda activate qiime2-2022.8 
 
# this command deactivates your current environment and returns to (base) 
conda deactivate

Updating QIIME2

To update, simply run through this protocol again, except with your updated QIIME2 distribution. You can check the distribution (Natively installing QIIME 2 — QIIME 2 2022.8.1 documentation)