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q2-usearch

Test and lint

A QIIME 2 plugin developed by Core Bioinformatics, QIB.

Installation instructions

The following instructions are intended to be a starting point and should be replaced when q2-usearch is ready to share with others. They will enable you to install the most recent development version of q2-usearch. Remember that release versions should be used for all "real" work (i.e., where you're not testing or prototyping) - if there aren't instructions for installing a release version of this plugin, it is probably not yet intended for use in practice.

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:

conda update conda

Install development version of q2-usearch

Next, you need to get into the top-level q2-usearch directory. If you already have this (e.g., because you just created the plugin), this may be as simple as running cd q2-usearch. If not, you'll need the q2-usearch directory on your computer. How you do that will differ based on how the package is shared, and ideally the developer will update these instructions to be more specific (remember, these instructions are intended to be a starting point). For example, if it's maintained in a GitHub repository, you can achieve this by cloning the repository. Once you have the directory on your computer, change (cd) into it.

If you're in a conda environment, deactivate it by running conda deactivate.

Then, run:

conda env create -n q2-usearch-dev --file ./environments/qiime2-tiny-2024.5-py38-linux-conda.yml

After this completes, activate the new environment you created by running:

conda activate q2-usearch-dev

Install the plugin in dev mode:

make dev

Testing and using the most recent development version of q2-usearch

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-usearch 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 usearch --help

Have fun! 😎

About

The q2-usearch Python package was created from this template. To learn more about q2-usearch, 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-usearch 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. If you need help with a community plugin, first refer to the project website. If that page doesn't provide information on how to get help, or you need additional help, head to the Community Plugins category on the QIIME 2 Forum where the QIIME 2 developers will do their best to help you.

Authors

  • Thanh Le Viet (thanh.le-viet[at]quadram[dot]ac[dot]uk).