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.
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 the latest development version of the QIIME 2 “Tiny Distribution”#
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” or “Shotgun” distributions, in which case see Installing other QIIME 2 distributions.
wget https://raw.githubusercontent.com/qiime2/distributions/dev/latest/passed/qiime2-tiny-macos-latest-conda.yml
conda env create -n q2dev-tiny --file qiime2-tiny-macos-latest-conda.yml
rm qiime2-tiny-macos-latest-conda.yml
wget https://raw.githubusercontent.com/qiime2/distributions/dev/latest/passed/qiime2-tiny-ubuntu-latest-conda.yml
conda env create -n q2dev-tiny --file qiime2-tiny-ubuntu-latest-conda.yml
rm qiime2-tiny-ubuntu-latest-conda.yml
wget https://raw.githubusercontent.com/qiime2/distributions/dev/latest/passed/qiime2-tiny-macos-latest-conda.yml
CONDA_SUBDIR=osx-64 conda env create -n q2dev-tiny --file qiime2-tiny-macos-latest-conda.yml
rm qiime2-tiny-macos-latest-conda.yml
conda config --env --set subdir osx-64
Activate the conda environment#
You can now activate the environment you just created as follows.
conda activate q2dev-tiny
To test your QIIME 2 environment, run:
qiime info
You should see something like the following, though the version numbers you’ll see will be different:
System versions
Python version: 3.8.18
QIIME 2 release: 2023.11
QIIME 2 version: 2023.11.0.dev0+15.g8ac7e3e
q2cli version: 2023.11.0.dev0+12.g7cf7a7a
Installed plugins
types: 2023.11.0.dev0+2.g1827eab
Application config directory
/Users/gregcaporaso/miniconda3/envs/q2dev-tiny/var/q2cli
Getting help
To get help with QIIME 2, visit https://qiime2.org
The versions listed here, for QIIME 2, q2cli, and q2-types, 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#
Note
If you install a distribution other than the “Tiny Distribution”, be sure that the environment name in your conda activate command (in the example above this was q2dev-tiny) matches the value that you provided to the conda env create command through the -n parameter.
Amplicon distribution#
wget https://raw.githubusercontent.com/qiime2/distributions/dev/latest/passed/qiime2-amplicon-macos-latest-conda.yml
conda env create -n q2dev-amplicon --file qiime2-amplicon-macos-latest-conda.yml
rm qiime2-amplicon-macos-latest-conda.yml
wget https://raw.githubusercontent.com/qiime2/distributions/dev/latest/passed/qiime2-amplicon-ubuntu-latest-conda.yml
conda env create -n q2dev-amplicon --file qiime2-amplicon-ubuntu-latest-conda.yml
rm qiime2-amplicon-ubuntu-latest-conda.yml
wget https://raw.githubusercontent.com/qiime2/distributions/dev/latest/passed/qiime2-amplicon-macos-latest-conda.yml
CONDA_SUBDIR=osx-64 conda env create -n q2dev-amplicon --file qiime2-amplicon-macos-latest-conda.yml
rm qiime2-amplicon-macos-latest-conda.yml
conda config --env --set subdir osx-64
Metagenome distribution#
wget https://raw.githubusercontent.com/qiime2/distributions/dev/latest/passed/qiime2-metagenome-macos-latest-conda.yml
conda env create -n q2dev-metagenome --file qiime2-metagenome-macos-latest-conda.yml
rm qiime2-metagenome-macos-latest-conda.yml
wget https://raw.githubusercontent.com/qiime2/distributions/dev/latest/passed/qiime2-metagenome-ubuntu-latest-conda.yml
conda env create -n q2dev-metagenome --file qiime2-metagenome-ubuntu-latest-conda.yml
rm qiime2-metagenome-ubuntu-latest-conda.yml
wget https://raw.githubusercontent.com/qiime2/distributions/dev/latest/passed/qiime2-metagenome-macos-latest-conda.yml
CONDA_SUBDIR=osx-64 conda env create -n q2dev-metagenome --file qiime2-metagenome-macos-latest-conda.yml
rm qiime2-metagenome-macos-latest-conda.yml
conda config --env --set subdir osx-64