Using QIIME2 on Quest

QIIME2 (Quantitative Insights into Microbial Ecology version 2) is an open-source computing platform for processing and analyzing DNA amplicon sequence data. This page describes how users may download and use QIIME2 on Quest.

Installing QIIME2 on Quest

QIIME2 is available as a system-wide module on Quest. To explore the versions currently installed on Quest, run: module avail qiime2. If a specific version is required, users can also install QIIME2 themselves within a Singularity container or a conda virtual environment. The installation route users choose will be dependent on their day-to-day use of QIIME2 and familiarity with creating virtual environments. As a new user to Quest, installing QIIME2 via Singularity is generally easier, although the software will be limited to the plugins included in the core QIIME2 distribution. The system-wide QIIME2 modules on Quest also only contain the core QIIME2 plugins. This is not a problem for most users; however, if you plan to use third-party plugins in your QIIME2 workflow, we strongly recommend installing QIIME2 in a conda environment. In addition to being much more flexible with adding other plugins, calling QIIME2 from a conda environment generally results in more readable code as compared to calling it from a Singularity container.

Installation and use via Singularity

DockerHub maintains an image of the most up-to-date version of QIIME2 that can be downloaded via Singularity onto Quest. Navigate to your project directory on Quest and run the following command to pull the latest version of QIIME2 (version 2022.2 at the time of writing):

module load singularity
singularity pull docker://quay.io/qiime2/core:2022.2

This will create a Singularity Image File called core_2022.2.sif in your working directory. This file will have to be explicitly called before every QIIME2 command with singularity exec. For example, to run the qiime --help command, submit the following:

singularity exec core_2022.2.sif qiime --help

It should be noted that if the above command is submitted outside of the user's working directory as written, core_2022.2.sifwill not be found. Please refer to our Singularity Knowledge Base page or the Singularity user documentation for more information on how to specify file paths with Singularity.

Installation and use with conda

To create a QIIME2 conda environment, first download the configuration file provided by the developers into your working directory:

wget https://data.qiime2.org/distro/core/qiime2-2022.2-py38-linux-conda.yml

This config file lists all the software dependencies that QIIME2 requires. Once it is downloaded, load the miniconda module and create a QIIME2 conda environment. Please note that it is not unusual for this step to require over an hour to complete:

module purge all
module load python-miniconda3
conda env create -n qiime2-2022.2 --file qiime2-2022.2-py38-linux-conda.yml

As an optional step, you can remove the config file from your working directory:

rm qiime2-2022.2-py38-linux-conda.yml

Once the conda environment is created, use source activate to call QIIME2 (qiime2-2022.2). Afterwards, you can begin using QIIME2 by simply calling qiime:

source activate qiime2-2022.2
qiime --help

Also note that you can install the conda environment in your project directory by replacing the -n qiime2-2022.2 option with --prefix /path/to/allocation and activating the environment from that path. Installing conda environments in your project directories can save storage space in your home folder. Please refer to the “Anaconda Virtual Environments” section of this page for more information.

conda env create --prefix /projects/p12345/qiime2-2022.2 --file qiime2-2022.2-py38-linux-conda.yml
source activate /projects/p12345/qiime2-2022.2