Natively installing QIIME 2

This guide describes how to natively install the available QIIME 2 2024.2 distribution.

Miniconda

Installing Miniconda

Miniconda provides the conda environment and package manager, and is
the recommended way to install QIIME 2. Follow the Miniconda 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. It is important to follow all of the directions
provided in the Miniconda instructions, particularly ensuring that you run
conda init at the end of the installation process, to ensure that your
Miniconda installation is fully installed and available for the following
commands.

Updating Miniconda

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

Install QIIME 2 within a conda environment

Once you have Miniconda installed, create a conda environment and install
the QIIME 2 2024.2 distribution of your choice within the environment.
We highly recommend creating a new environment specifically for the
QIIME 2 distribution and 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 environments qiime2-<distro>-2024.2
to indicate what QIIME 2 release is instal ( i.e.2024.2).

QIIME 2 Amplicon Distribution

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

wget https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.2-py38-osx-conda.yml 
 conda env create -n qiime2 - amplicon-2024.2 --file qiime2-amplicon-2024.2-py38-osx-conda.yml

OPTIONAL cleanup

rm qiime2-amplicon-2024.2-py38-osx-conda.yml

These instructions is are are for user with Apple Silicon chip ( M1 , m2 , etc ) , and configure the installation of QIIME 2 in Rosetta 2 emulation mode .

wget https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.2-py38-osx-conda.yml
CONDA_SUBDIR=osx-64 conda env create -n qiime2-amplicon-2024.2 --file qiime2-amplicon-2024.2-py38-osx-conda.yml
conda activate qiime2-amplicon-2024.2
conda config --env --set subdir osx-64

OPTIONAL cleanup

rm qiime2-amplicon-2024.2-py38-osx-conda.yml

wget https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.2-py38-linux-conda.yml 
 conda env create -n qiime2 - amplicon-2024.2 --file qiime2-amplicon-2024.2-py38-linux-conda.yml

OPTIONAL cleanup

rm qiime2-amplicon-2024.2-py38-linux-conda.yml

These instructions is are are identical to the Linux instruction and are intend for user of the Windows Subsystem for Linux .

wget https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.2-py38-linux-conda.yml 
 conda env create -n qiime2 - amplicon-2024.2 --file qiime2-amplicon-2024.2-py38-linux-conda.yml

OPTIONAL cleanup

rm qiime2-amplicon-2024.2-py38-linux-conda.yml

QIIME 2 Shotgun distribution

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

wget https://data.qiime2.org/distro/shotgun/qiime2-shotgun-2024.2-py38-osx-conda.yml
conda env create -n qiime2-shotgun-2024.2 --file qiime2-shotgun-2024.2-py38-osx-conda.yml

OPTIONAL cleanup

rm qiime2-shotgun-2024.2-py38-osx-conda.yml

These instructions is are are for user with Apple Silicon chip ( M1 , m2 , etc ) , and configure the installation of QIIME 2 in Rosetta 2 emulation mode .

wget https://data.qiime2.org/distro/shotgun/qiime2-shotgun-2024.2-py38-osx-conda.yml
CONDA_SUBDIR=osx-64 conda env create -n qiime2-shotgun-2024.2 --file qiime2-shotgun-2024.2-py38-osx-conda.yml
conda activate qiime2-shotgun-2024.2
conda config --env --set subdir osx-64

OPTIONAL cleanup

rm qiime2-shotgun-2024.2-py38-osx-conda.yml

wget https://data.qiime2.org/distro/shotgun/qiime2-shotgun-2024.2-py38-linux-conda.yml
conda env create -n qiime2-shotgun-2024.2 --file qiime2-shotgun-2024.2-py38-linux-conda.yml

OPTIONAL cleanup

rm qiime2-shotgun-2024.2-py38-linux-conda.yml

These instructions is are are identical to the Linux instruction and are intend for user of the Windows Subsystem for Linux .

wget https://data.qiime2.org/distro/shotgun/qiime2-shotgun-2024.2-py38-linux-conda.yml
conda env create -n qiime2-shotgun-2024.2 --file qiime2-shotgun-2024.2-py38-linux-conda.yml

OPTIONAL cleanup

rm qiime2-shotgun-2024.2-py38-linux-conda.yml

QIIME 2 tiny distribution

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

wget https://data.qiime2.org/distro/tiny/qiime2-tiny-2024.2-py38-osx-conda.yml
conda env create -n qiime2-tiny-2024.2 --file qiime2-tiny-2024.2-py38-osx-conda.yml

OPTIONAL cleanup

rm qiime2-tiny-2024.2-py38-osx-conda.yml

These instructions is are are for user with Apple Silicon chip ( M1 , m2 , etc ) , and configure the installation of QIIME 2 in Rosetta 2 emulation mode .

wget https://data.qiime2.org/distro/tiny/qiime2-tiny-2024.2-py38-osx-conda.yml
CONDA_SUBDIR=osx-64 conda env create -n qiime2-tiny-2024.2 --file qiime2-tiny-2024.2-py38-osx-conda.yml
conda activate qiime2-tiny-2024.2
conda config --env --set subdir osx-64

OPTIONAL cleanup

rm qiime2-tiny-2024.2-py38-osx-conda.yml

wget https://data.qiime2.org/distro/tiny/qiime2-tiny-2024.2-py38-linux-conda.yml
conda env create -n qiime2-tiny-2024.2 --file qiime2-tiny-2024.2-py38-linux-conda.yml

OPTIONAL cleanup

rm qiime2-tiny-2024.2-py38-linux-conda.yml

These instructions is are are identical to the Linux instruction and are intend for user of the Windows Subsystem for Linux .

wget https://data.qiime2.org/distro/tiny/qiime2-tiny-2024.2-py38-linux-conda.yml
conda env create -n qiime2-tiny-2024.2 --file qiime2-tiny-2024.2-py38-linux-conda.yml

OPTIONAL cleanup

rm qiime2-tiny-2024.2-py38-linux-conda.yml

Activate the conda environment

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

conda activate qiime2-<distro>-2024.2

To deactivate an environment, run conda deactivate.

test your installation

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

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

Next steps

Now that you have a QIIME 2 distribution instal , check out theq2cli
docs to get familiar with the QIIME 2 command – line
interface ( it is used extensively in thetutorials) . After that , try out theQIIME 2 tutorials for examples of using QIIME 2 to analyze microbiome
datasets. You might also try installing other QIIME 2 interface.

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.

(Re-)Activating QIIME 2

If at any point during the analysis the QIIME 2 conda environment is closed
or deactivated, QIIME 2 2024.2 can be activated (or reactivated) by running
the following command:

conda activate qiime2-<distro>-2024.2

To determine the currently active conda environment, run the following
command and look for the line that starts with “active environment”: