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The home page for QIIME is here:

To find the documentation that describes how to install QIIME 2 go to the QIIME 2 homepage then from the menu at the top click on “Docs”. From that page click on the link “Natively installing QIIME 2”.

This explains that you need to first install Miniconda (this is a small Python distribution) and then under that python distribution install Qiime.

Install Miniconda

See our Python Miniconda install page, then return to here. Then we are set to install Qiime 2.

Install QIIME 2

Check what is the latest QIIME2. These instructions use a QIIME2 2023 “tiny” version.

Continue to follow the install notes. Those notes suggest to call your QIIME 2 environment based on the QIIME 2 release date. This is a good idea, though you can name it anything you like.

Make sure your in your base conda environment:

~/$ source miniconda3/bin/activate
(base) ~/$

Download the qiime2 definition file:

(base)$ wget

Create a miniconda environment named “qiime2-tiny-2023.9” based on this definition file:

(base)$ conda env create -n qiime2-tiny-2023.9 --file qiime2-tiny-2023.9-py38-linux-conda.yml

... it will take a while ...

Once the install has finished you can optionally remove the definition file:

$ rm qiime2-tiny-2023.9-py38-linux-conda.yml

We can “source” the new QIIME 2 environment to enable it like this:

$ conda activate qiime2-tiny-2023.9

Run Qiime’s help command to check it works:

(qiime2-tiny-2023.9)$ qiime --help

We can also deactivate this environment and reactivate it later with.

(qiime2-tiny-2023.9)$ conda deactivate
(base) ~/$

$ conda activate qiime2-tiny-2023.9