A QIIME 2 plugin developed by Greg Caporaso (gcaporaso@tgen.org). 🔌
q2-tnorth-bot is a tool for testing and developing an automated quality control workflow for sequencing data generated at TGen North.
It is developed as a QIIME 2 plugin for the convenience of adding QIIME 2 actions in the future, but at present it is not intended to be used as a QIIME 2 plugin and just provides some scripts that can be used to facilitate analysis.
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 condaNext, you need to get into the top-level q2-tnorth-bot directory.
If you already have this (e.g., because you just created the plugin), this may be as simple as running cd q2-tnorth-bot.
If not, you'll need the q2-tnorth-bot 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-tnorth-bot-dev --file ./environments/q2-tnorth-bot-qiime2-amplicon-2024.10.ymlAfter this completes, activate the new environment you created by running:
conda activate q2-tnorth-bot-devFinally, run:
make installAs of this writing (11 Sept 2024), the only functionality provided through this plugin is the auto-qc command.
After installation and activation of the conda environment as described above, you should be able to provide a QIIME 2 Fastq Manifest file to automatically create a QIIME 2 "demux artifact" (demux.qza) and a QIIME 2 "demux summary" (demux.qzv).
Both will be created in the user-specified output directory.
This command can be used as follows:
auto-qc <path-to-fq-manifest> <output-directory>Where path-to-fq-manifest is the path to the fastq manifest file, and output-directory is the directory where the output files should be written.
The q2-tnorth-bot Python package was created from template.
To learn more about q2-tnorth-bot, 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-tnorth-bot 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.