A QIIME 2 plugin developed by Nicole Sylvester ([email protected]). 🔌
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 condaq2-trimmers provides the trimmer options used by q2-asap
q2-nasp2-types provides custom semantic types and formats used by q2-asap
q2-aligners provides the aligner options used by q2-asap
Next, you need to get into the top-level q2-asap directory.
If you already have this (e.g., because you just created the plugin), this may be as simple as running cd q2-asap.
If not, you'll need the q2-asap directory on your computer.
Since 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-asap-dev --file ./environments/q2-asap-qiime2-tiny-2024.5.ymlAfter this completes, activate the new environment you created by running:
conda activate q2-asap-devFinally, run:
pip install .After completing the install steps above, confirm that everything is working as expected by running:
make testYou 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.
You should be able to review the help text by running:
qiime ASAP --helpHave fun! 😎
The q2-asap Python package was created from template.
To learn more about q2-asap, refer to the project website.
q2-asap is a QIIME 2 version of [ASAP] (https://github.com/TGenNorth/ASAP).
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-asap is a QIIME 2 community plugin, meaning that it is not developed and maintained by the developers of QIIME 2.
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.