Installation

Existing QIIME 2 environment¶

The q2-ena-uploader plugin can be installed into any QIIME 2 conda environment (see here for more specific installation instructions). To install the plugin, run the following commands:

conda activate <your QIIME 2 environment>

pip install git+https://github.com/bokulich-lab/q2-ena-uploader.git

Refresh the QIIME 2 cache and check if the plugin is available:

qiime dev refresh-cache
qiime ena-uploader --help

New QIIME 2 environment¶

Alternatively, you can also create a dedicated environment by executing:

conda env create -n uploader-env --file https://raw.githubusercontent.com/bokulich-lab/q2-ena-uploader/main/environment-files/q2-ena-uploader-qiime2-tiny-2025.4.yml