Getting started

The tutorials in Using QIIME 2 provide basic information on how to use rachis (formerly known as the QIIME 2 Framework), q2cli (i.e., the official rachis command line interface), and the Python 3 API. The tutorials make use of the Tiny Distribution, and the example plugin q2-dwq2. This deployment allows for in-depth learning of how rachis itself works, and the information you learn here will be relevant across all distributions, including QIIME 2, MOSHPIT, and [stand-alone plugins]((xref:rachis-news-target#term-term-stand-alone-plugin) such as genome-sampler. When you’re ready to perform your own data analysis you’ll transition to domain-specific plugins or distributions and their documentation.

Before attempting to run the Using QIIME 2 tutorials, configure your learning environment following the steps here.

Install the “Tiny Distribution”¶

The “Tiny Distribution” is a minimal set of functionality for building and using plugins through the command line or Python 3 API. Install the most recent release version of the Tiny Distribution using the instructions on the QIIME 2 Library.

Activate the conda environment and test your installation¶

You can now activate the environment you just created using conda activate, as described in the installation instructions.

To test your environment, run:

qiime info

You should see something like the following, though the version numbers you’ll see may be different:

System versions
Python version: 3.10.14
QIIME 2 release: 2025.4
QIIME 2 version: 2025.4.0
q2cli version: 2025.4.0

Installed plugins
metadata: 2025.4.0
types: 2025.4.0

...

At this stage you have a working environment, but it doesn’t do a whole lot. To add some bioinformatics functionality, we’ll next add the example plugin q2-dwq2.

Install q2-dwq2¶

All domain-specific functionality comes in the form of plugins. Sometimes you’ll install these directly, and sometimes you’ll install distributions like QIIME 2 or MOSHPIT which are bundles of plugins intended to be used together. In this case, we’re going to install one specific plugin. Run the following command from your using-qiime2 conda environment (i.e., after having run conda activate using-qiime2).

pip install https://github.com/caporaso-lab/q2-dwq2/archive/refs/heads/main.zip

If you run qiime info again, you should now see a new plugin, dwq2, in the list of Installed Plugins.

System versions
Python version: 3.10.14
QIIME 2 release: 2025.4
QIIME 2 version: 2025.4.0
q2cli version: 2025.4.0

Installed plugins
dwq2: 0+unknown
metadata: 2025.4.0
types: 2025.4.0

...

Exploring the available functionality¶

To see the list of available plugins, along with some additional information, run:

qiime --help

To see what functionality, or Actions a plugin defines, call help on that plugin:

qiime dwq2 --help

To learn how to use a specific action, call help on it:

qiime dwq2 nw-align --help

Take a few minutes now to explore q2-dwq2. What is this plugin intended to do? What is some of the functionality that it provides?