q2-boots

q2-boots is a QIIME 2 plugin for microbiome rarefaction analysis that is currently in beta testing.

Installation

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 install wget in case you don't already have it.

conda update conda
conda install wget

QIIME 2024.2 release version of q2-boots

The most recent release version of q2-boots is the most stable, and is recommended for use in work that you're intending to publish. It may not contain all of the most recent feature additions, so if you're at an early experimental phase of your analysis you may prefer to install the development version of q2-boots (see those instructions below).

wget https://raw.githubusercontent.com/qiime2/q2-boots/main/environments/q2-boots-qiime2-amplicon-2024.2.yml

conda env create -n q2-boots-2024.2 --file ./q2-boots-qiime2-amplicon-2024.2.yml

conda activate q2-boots-2024.2

QIIME 2024.5 development version of q2-boots

Installing the most recent development version of q2-boots allows you to access the most recent functionality, including some that depends on features being introduced in QIIME 2 2024.5. It is hard to unambiguously reference development versions of software in publications however, so you'll likely want to re-run your boots analyses with a release version prior to publication.

wget https://raw.githubusercontent.com/qiime2/q2-boots/main/environments/q2-boots-qiime2-amplicon-2024.5.yml

conda env create -n q2-boots-2024.5 --file ./q2-boots-qiime2-amplicon-2024.5.yml

conda activate q2-boots-2024.5

Testing and using q2-boots

After completing the install steps above, confirm that everything is working as expected by running:

make test

You should get a report that tests were run, and you should see that all tests passed and none failed. It's usually ok if some warnings are reported.

If all of the tests pass, you're ready to use the plugin. Start by making QIIME 2's command line interface aware of q2-boots by running:

qiime dev refresh-cache

You should then see the plugin in the list of available plugins if you run:

qiime info

You should be able to review the help text by running:

qiime boots --help

Have fun! 😎

Getting help

If you need help with q2-boots, please get in touch on the QIIME 2 Forum.

About

The q2-boots Python package was built using content from the QIIME 2 plugin template. To learn more about q2-boots, refer to the project website. To learn how to use QIIME 2, refer to the QIIME 2 User Documentation. To learn QIIME 2 plugin development, refer to Developing with QIIME 2.

q2-boots is a QIIME 2 community plugin, meaning that it is not necessarily developed and maintained by the developers of QIIME 2. Please be aware that because community plugins are developed by the QIIME 2 developer community, and not necessarily the QIIME 2 developers themselves, some may not be actively maintained or compatible with current release versions of the QIIME 2 distributions. More information on development and support for community plugins can be found here.