Set up your development environment#
This how-to guide describes how to install and set up a QIIME 2 development environment. The development environment you create will be suitable for creating new or contributing to existing QIIME 2 plugins or interfaces, or contributing to the development of the QIIME 2 framework.
Warning
QIIME 2 support for Windows is restricted to Windows Subsystem for Linux (WSL). The QIIME 2 development team doesn’t have much experience developing QIIME 2 in the context of Windows. If you’re comfortable with creating development environments with WSL, we expect that it should work just fine. If you expect that you might need help setting up your development environment, we’ll be able to provide better assistance if you’re developing on a Linux or macOS system.
Install Prerequisites#
Miniconda provides the conda environment and package manager, and is currently the only supported way to install QIIME 2.
Follow the instructions for downloading and installing Miniconda.
Note
We are experimentally supporting miniforge instead of Miniconda.
miniforge use is more permissive (notably it doesn’t ever use Anaconda’s defaults channel).
Consider installing and using miniforge instead of Miniconda, and let us know on the Forum if you run into any issues.
After installing and opening a new terminal, make sure you’re running the latest version of conda:
conda update conda
Install the latest development version of the QIIME 2 “Tiny Distribution” and activate its environment#
The QIIME 2 “Tiny Distribution” is a minimal set of QIIME 2 functionality for building and using plugins through the QIIME 2 command line, and is intended for use by developers who want a minimal QIIME 2 environment to work in.
Note
We recommend starting your development with the “Tiny Distribution”, unless you specifically need plugins that are installed in other QIIME 2 distributions, such as the Amplicon Distribution or MOSHPIT (previously known as the Metagenome Distribution), in which case see Installing other QIIME 2 distributions.
Note
The commands on this page add the current date to the conda environment names, which can be helpful for managing development environments. QIIME 2 keeps track of the versions of all dependencies in data provenance (including specific git commits for packages in the QIIME 2 ecosystem) so that information – not the conda environment name – is the definitive source of specific versions that were used to generate a result. Things change relatively quickly with development environments, so it doesn’t hurt to remove old ones and create new ones regularly (e.g., every few weeks).
__Q2DEV_ENV_NAME=q2dev-tiny-$(date "+%Y-%m-%d")
conda env create -n $__Q2DEV_ENV_NAME --file https://raw.githubusercontent.com/qiime2/distributions/dev/latest/passed/qiime2-tiny-macos-latest-conda.yml
conda activate $__Q2DEV_ENV_NAME
__Q2DEV_ENV_NAME=q2dev-tiny-$(date "+%Y-%m-%d")
conda env create -n $__Q2DEV_ENV_NAME --file https://raw.githubusercontent.com/qiime2/distributions/dev/latest/passed/qiime2-tiny-ubuntu-latest-conda.yml
conda activate $__Q2DEV_ENV_NAME
__Q2DEV_ENV_NAME=q2dev-tiny-$(date "+%Y-%m-%d")
CONDA_SUBDIR=osx-64 conda env create -n $__Q2DEV_ENV_NAME --file https://raw.githubusercontent.com/qiime2/distributions/dev/latest/passed/qiime2-tiny-macos-latest-conda.yml
conda activate $__Q2DEV_ENV_NAME
conda config --env --set subdir osx-64
Test your new environment#
After activating your new environment, you can test it by running:
qiime info
You should see something like the following, though the version numbers you’ll see will be different:
System versions
Python version: 3.10.14
QIIME 2 release: 2025.4
QIIME 2 version: 2025.4.0.dev0+18.g9414a65
q2cli version: 2025.4.0.dev0+21.g97e80cc
Installed plugins
metadata: 2025.4.0.dev0+8.g66139ab
types: 2025.4.0.dev0+16.g229da69
Application config directory
/Users/q2-user/miniforge3/envs/q2dev-tiny-2025-04-30/var/q2cli
Config
Config Source: /Users/q2-user/miniforge3/envs/q2dev-tiny-2025-04-30/etc/qiime2_config.toml
Getting help
To find help and learning resources, visit https://qiime2.org.
To get help with configuring and/or understanding QIIME 2 parallelization, visit https://use.qiime2.org/en/latest/references/parallel-configuration.html
The versions listed here, for QIIME 2, q2cli, q2-types, and q2-metadata are development versions as defined by versioneer, and these indicate that you’re working in a QIIME 2 development environment (as opposed to working with a specific release version of QIIME 2).
At this stage you should now have a working development environment - time to start hacking!
Next steps#
Building your first plugin#
If you’re creating your first plugin, you can now move on to Tutorial: A step-by-step guide to building your first QIIME 2 plugin.
Contributing to existing plugins#
If you want to make changes to the QIIME 2 framework, q2cli, or any existing plugins, follow these steps (for the sake of this example, we will focus on the example of contributing to developing q2-types):
# Grab the package source from the relevant source repository.
git clone https://github.com/qiime2/q2-types
cd q2-types
# Install any additional build-time dependencies needed for this project.
# Check ci/recipe/meta.yaml in any QIIME 2 repository under the QIIME 2 GitHub
# organization for build or test requirements. For example, see
# https://github.com/qiime2/q2-types/blob/dev/ci/recipe/meta.yaml
conda install pytest flake8
# Install local source in "development mode", and build any package assets.
make dev
# Run package tests to ensure that everything is okay.
make test
Installing other QIIME 2 distributions#
Amplicon distribution#
__Q2DEV_ENV_NAME=q2dev-amplicon-$(date "+%Y-%m-%d")
conda env create -n $__Q2DEV_ENV_NAME --file https://raw.githubusercontent.com/qiime2/distributions/dev/latest/passed/qiime2-amplicon-macos-latest-conda.yml
conda activate $__Q2DEV_ENV_NAME
__Q2DEV_ENV_NAME=q2dev-amplicon-$(date "+%Y-%m-%d")
conda env create -n $__Q2DEV_ENV_NAME --file https://raw.githubusercontent.com/qiime2/distributions/dev/latest/passed/qiime2-amplicon-ubuntu-latest-conda.yml
conda activate $__Q2DEV_ENV_NAME
__Q2DEV_ENV_NAME=q2dev-amplicon-$(date "+%Y-%m-%d")
CONDA_SUBDIR=osx-64 conda env create -n $__Q2DEV_ENV_NAME --file https://raw.githubusercontent.com/qiime2/distributions/dev/latest/passed/qiime2-amplicon-macos-latest-conda.yml
conda activate $__Q2DEV_ENV_NAME
conda config --env --set subdir osx-64
MOSHPIT (previously known as the Metagenome distribution)#
__Q2DEV_ENV_NAME=moshpit-dev-$(date "+%Y-%m-%d")
conda env create -n $__Q2DEV_ENV_NAME --file https://raw.githubusercontent.com/qiime2/distributions/dev/latest/passed/qiime2-moshpit-macos-latest-conda.yml
conda activate $__Q2DEV_ENV_NAME
__Q2DEV_ENV_NAME=moshpit-dev-$(date "+%Y-%m-%d")
conda env create -n $__Q2DEV_ENV_NAME --file https://raw.githubusercontent.com/qiime2/distributions/dev/latest/passed/qiime2-moshpit-ubuntu-latest-conda.yml
conda activate $__Q2DEV_ENV_NAME
__Q2DEV_ENV_NAME=moshpit-dev-$(date "+%Y-%m-%d")
CONDA_SUBDIR=osx-64 conda env create -n $__Q2DEV_ENV_NAME --file https://raw.githubusercontent.com/qiime2/distributions/dev/latest/passed/qiime2-moshpit-macos-latest-conda.yml
conda activate $__Q2DEV_ENV_NAME
conda config --env --set subdir osx-64