# Natively installing QIIME 2¶

This guide describes how to natively install the QIIME 2 Core 2018.2 distribution.

Note

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 2018.2 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 qiime2-2018.2 to indicate what QIIME 2 release is installed (i.e. 2018.2).

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

wget https://data.qiime2.org/distro/core/qiime2-2018.2-py35-osx-conda.yml
conda env create -n qiime2-2018.2 --file qiime2-2018.2-py35-osx-conda.yml
# OPTIONAL CLEANUP
rm qiime2-2018.2-py35-osx-conda.yml
wget https://data.qiime2.org/distro/core/qiime2-2018.2-py35-linux-conda.yml
conda env create -n qiime2-2018.2 --file qiime2-2018.2-py35-linux-conda.yml
# OPTIONAL CLEANUP
rm qiime2-2018.2-py35-linux-conda.yml

Tip

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 qiime2-2018.2 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 qiime2-2018.2


To deactivate an environment, run source deactivate.

qiime --help