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Natively installing QIIME 2

This guide describes how to natively install the QIIME 2 Core 2019.1 distribution.


QIIME 2 does not currently support Windows. We recommend using one of the QIIME 2 virtual machines.

Install Miniconda

Miniconda provides the conda environment and package manager, and is the recommended way to install QIIME 2. Follow the instructions for downloading and installing Miniconda. You may choose either Miniconda2 or Miniconda3 (i.e. Miniconda Python 2 or 3). QIIME 2 will work with either version of Miniconda.

After installing Miniconda and opening a new terminal, make sure you’re running the latest version of conda:

conda update conda
conda install wget

Install QIIME 2 within a conda environment

Once you have Miniconda installed, create a conda environment and install the QIIME 2 Core 2019.1 distribution within the environment. We highly recommend creating a new environment specifically for the QIIME 2 release being installed, as there are many required dependencies that you may not want added to an existing environment. You can choose whatever name you’d like for the environment. In this example, we’ll name the environment qiime2-2019.1 to indicate what QIIME 2 release is installed (i.e. 2019.1).

From the above tabs, please choose the installation instructions that are appropriate for your platform.

conda env create -n qiime2-2019.1 --file qiime2-2019.1-py36-osx-conda.yml
rm qiime2-2019.1-py36-osx-conda.yml
conda env create -n qiime2-2019.1 --file qiime2-2019.1-py36-linux-conda.yml
rm qiime2-2019.1-py36-linux-conda.yml


If you receive errors during the installation process, such as gfortran errors, please ensure you are following the installation instructions that are compatible with your platform. Other errors are often resolved by running conda env remove -n qiime2-2019.1 to remove the failed environments, then running conda clean -y --all to clean the local conda installation, and finally re-running the installation instructions above.

Activate the conda environment

Now that you have a QIIME 2 environment, activate it using the environment’s name:

source activate qiime2-2019.1

To deactivate an environment, run source deactivate.

Test your installation

You can test your installation by activating your QIIME 2 environment and running:

qiime --help

If no errors are reported when running this command, the installation was successful!

Next steps

Now that you have the Core distribution installed, check out the q2cli docs to get familiar with the QIIME 2 command-line interface (it is used extensively in the tutorials). After that, try out the QIIME 2 tutorials for examples of using QIIME 2 to analyze microbiome datasets. You might also try installing other QIIME 2 interfaces.

How do I update to the newest version of QIIME 2?

In order to to update/upgrade to the newest release, you simply install the newest version in a new conda environment by following the instructions above. Then you will have two conda environments, one with the older version of QIIME 2 and one with the newer version.