MOSHPIT

MOSHPIT (MOdular SHotgun metagenome Pipelines with Integrated provenance Tracking) is a suite of tools for whole metagenome assembly, annotation, and analysis.

This page contains the official installation instructions for MOSHPIT. MOSHPIT can be installed natively through a conda installation, or used through Docker or Podman. Instructions for both of these installation types follow on this page.

MOSHPIT deployment can occur on a personal computer, institutional high-performance computing (HPC) hardware, cloud-based hardware, or other types of systems. Generally the determining factor for where to install MOSHPIT is the analyses that you want to run: in some cases (e.g., generating visualizations) a personal computer will be sufficient, but for memory or CPU intensive steps (e.g., quality control or taxonomic annotation) an HPC system may be required. If you have questions about what type of system you need for running MOSHPIT, refer to the QIIME 2 Forum.

Version
Links
Documentation Documentation
GitHub Source Code
Conda Channel
Built-in plugins

Installation Instructions

You can install this distribution with either conda or docker.

This release provides an install environment for Linux/WSL only.

Table of Contents
  1. Using Conda
  2. 1. Installing Miniconda
  3. 2. Updating Miniconda
  4. 3. Install the base distribution’s conda environment
  5. 4. Test your install
  6. Using Docker
  7. 1. Install docker
  8. 2. Download base image
  9. 3. Test your install

Using Conda

Steps 1-4 will guide you through installing conda and your selected base distribution.

1. 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. 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 (via installer or manual command), to ensure that your Miniconda installation is fully installed and available for the following commands. On Windows, set up WSL first, then install Miniconda inside WSL.

2. Updating Miniconda

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

   conda update conda

3. Install the base distribution’s conda 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 rachis-moshpit-2026.7 to indicate what QIIME 2 release is installed (i.e. 2026.7).

Instructions
Linux / Windows WSL

Select the tab that fits the operating system that you want QIIME 2 to run on.

(To install an older version, use the dropdown in the distribution details above.)

4. Test your install

Finally, to verify things are working, run:

conda deactivate
conda activate rachis-moshpit-2026.7
qiime info

Using Docker

Steps 1-3 will guide you through installing docker and pulling the image for your selected base distribution.

These steps use the “workshop” image, which contains some conveniences, like a built-in JupyterLab environment with support for viewing .qzv files. You can find details about how to use these features here. If you don’t want these features and prefer a smaller container, you can replace the moshpit-workshop container name in all steps with moshpit (i.e., remove -workshop).

1. Install docker

See https://www.docker.com for instructions for your platform.

2. Download base image

Run the following command to pull the selected image:

docker pull quay.io/qiime2/moshpit-workshop:2026.7

3. Test your install

Finally, to verify things are working, run:

docker run \
  -v $(pwd):/data \
  -it quay.io/qiime2/moshpit-workshop:2026.7 \
  qiime info

This command mounts your current working directory as a volume to /data inside the container, then starts an interactive session (-i) with the command qiime info using the image quay.io/qiime2/moshpit-workshop:2026.7 (-t).

Using Conda

Steps 1-4 will guide you through installing conda and your selected base distribution.

1. 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. 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 (via installer or manual command), to ensure that your Miniconda installation is fully installed and available for the following commands. On Windows, set up WSL first, then install Miniconda inside WSL.

2. Updating Miniconda

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

   conda update conda

3. Install the base distribution’s conda 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 rachis-moshpit-2026.7 to indicate what QIIME 2 release is installed (i.e. 2026.7).

Instructions
Linux / Windows WSL

Select the tab that fits the operating system that you want QIIME 2 to run on.

(To install an older version, use the dropdown in the distribution details above.)

4. Test your install

Finally, to verify things are working, run:

conda deactivate
conda activate rachis-moshpit-2026.7
qiime info

Using Docker

Steps 1-3 will guide you through installing docker and pulling the image for your selected base distribution.

These steps use the “workshop” image, which contains some conveniences, like a built-in JupyterLab environment with support for viewing .qzv files. You can find details about how to use these features here. If you don’t want these features and prefer a smaller container, you can replace the moshpit-workshop container name in all steps with moshpit (i.e., remove -workshop).

1. Install docker

See https://www.docker.com for instructions for your platform.

2. Download base image

Run the following command to pull the selected image:

docker pull quay.io/qiime2/moshpit-workshop:2026.7

3. Test your install

Finally, to verify things are working, run:

docker run \
  -v $(pwd):/data \
  -it quay.io/qiime2/moshpit-workshop:2026.7 \
  qiime info

This command mounts your current working directory as a volume to /data inside the container, then starts an interactive session (-i) with the command qiime info using the image quay.io/qiime2/moshpit-workshop:2026.7 (-t).

Using Conda

Steps 1-4 will guide you through installing conda and your selected base distribution.

1. 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. 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 (via installer or manual command), to ensure that your Miniconda installation is fully installed and available for the following commands. On Windows, set up WSL first, then install Miniconda inside WSL.

2. Updating Miniconda

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

   conda update conda

3. Install the base distribution’s conda 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 rachis-moshpit-2026.7 to indicate what QIIME 2 release is installed (i.e. 2026.7).

Instructions
Linux / Windows WSL

Select the tab that fits the operating system that you want QIIME 2 to run on.

(To install an older version, use the dropdown in the distribution details above.)

4. Test your install

Finally, to verify things are working, run:

conda deactivate
conda activate rachis-moshpit-2026.7
qiime info

Using Docker

Steps 1-3 will guide you through installing docker and pulling the image for your selected base distribution.

These steps use the “workshop” image, which contains some conveniences, like a built-in JupyterLab environment with support for viewing .qzv files. You can find details about how to use these features here. If you don’t want these features and prefer a smaller container, you can replace the moshpit-workshop container name in all steps with moshpit (i.e., remove -workshop).

1. Install docker

See https://www.docker.com for instructions for your platform.

2. Download base image

Run the following command to pull the selected image:

docker pull quay.io/qiime2/moshpit-workshop:2026.7

3. Test your install

Finally, to verify things are working, run:

docker run \
  -v $(pwd):/data \
  -it quay.io/qiime2/moshpit-workshop:2026.7 \
  qiime info

This command mounts your current working directory as a volume to /data inside the container, then starts an interactive session (-i) with the command qiime info using the image quay.io/qiime2/moshpit-workshop:2026.7 (-t).

Using Conda

Steps 1-4 will guide you through installing conda and your selected base distribution.

1. 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. 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 (via installer or manual command), to ensure that your Miniconda installation is fully installed and available for the following commands. On Windows, set up WSL first, then install Miniconda inside WSL.

2. Updating Miniconda

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

   conda update conda

3. Install the base distribution’s conda 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 rachis-moshpit-2026.7 to indicate what QIIME 2 release is installed (i.e. 2026.7).

Instructions
Linux / Windows WSL

Select the tab that fits the operating system that you want QIIME 2 to run on.

(To install an older version, use the dropdown in the distribution details above.)

4. Test your install

Finally, to verify things are working, run:

conda deactivate
conda activate rachis-moshpit-2026.7
qiime info

Using Docker

Steps 1-3 will guide you through installing docker and pulling the image for your selected base distribution.

These steps use the “workshop” image, which contains some conveniences, like a built-in JupyterLab environment with support for viewing .qzv files. You can find details about how to use these features here. If you don’t want these features and prefer a smaller container, you can replace the moshpit-workshop container name in all steps with moshpit (i.e., remove -workshop).

1. Install docker

See https://www.docker.com for instructions for your platform.

2. Download base image

Run the following command to pull the selected image:

docker pull quay.io/qiime2/moshpit-workshop:2026.7

3. Test your install

Finally, to verify things are working, run:

docker run \
  -v $(pwd):/data \
  -it quay.io/qiime2/moshpit-workshop:2026.7 \
  qiime info

This command mounts your current working directory as a volume to /data inside the container, then starts an interactive session (-i) with the command qiime info using the image quay.io/qiime2/moshpit-workshop:2026.7 (-t).