This guide describes how to install and set up a QIIME 2 development environment.
QIIME 2 does not currently support installation on Windows.
Miniconda provides the
conda environment and package manager, and is the recommended way to install QIIME 2. Follow the instructions for downloading and installing Miniconda. You may choose either Miniconda2 or Miniconda3 (i.e. Miniconda Python 2 or 3). QIIME 2 will work with either version of Miniconda.
After installing Miniconda and opening a new terminal, make sure you’re running the latest version of
conda (and get a copy of
wget, while you’re at it):
conda update conda conda install wget
Install QIIME 2 within a
Once you have Miniconda installed, create a
conda environment and install the latest QIIME 2 staging distribution within the environment. We highly recommend creating a new environment specifically for development purposes. You can choose whatever name you’d like for the environment. In this example, we’ll name the environment
Please choose the installation instructions that are appropriate for your platform (macOS vs Linux).
wget https://raw.githubusercontent.com/qiime2/environment-files/master/latest/staging/qiime2-latest-py38-osx-conda.yml conda env create -n qiime2-dev --file qiime2-latest-py38-osx-conda.yml rm qiime2-latest-py38-osx-conda.yml
wget https://raw.githubusercontent.com/qiime2/environment-files/master/latest/staging/qiime2-latest-py38-linux-conda.yml conda env create -n qiime2-dev --file qiime2-latest-py38-linux-conda.yml rm qiime2-latest-py38-linux-conda.yml
conda activate qiime2-dev # to deactivate: # conda deactivate qiime info
The output from
qiime info should indicate that you have development versions of the QIIME 2 packages installed (the displayed versions will differ):
If you want to make changes to the framework, q2cli, or any of the official plugins, check out the steps involved in the following example (for the sake of this example, we will focus on developing
# Grab the package source from the relevant source repository. git clone https://github.com/qiime2/q2-taxa cd q2-taxa # Install any additional build-time dependencies needed for this project. # Check ci/recipe/meta.yaml in any official QIIME 2 repository for build requirements. conda install nodejs 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
Congratulations! You should now have a working development environment - time to start hacking!