How to install MOSHPIT - MOSHPIT documentation

MOSHPIT is available as a QIIME 2 distribution. You can find detailed installation instructions on the QIIME 2 Library page.

Quick start¶

Below you will find a quick installation guide for different operating systems:

Linux (Ubuntu)

macOS (Apple Silicon)

These instructions are for users running on Linux or the Windows Subsystem for Linux (WSL v2).

conda env create \
  --name rachis-moshpit-2026.4 \
  --file https://raw.githubusercontent.com/qiime2/distributions/refs/heads/dev/2026.4/moshpit/released/rachis-moshpit-linux-64-conda.yml

These instructions are for users with Apple Silicon chips (M1, M2, etc) using Docker. Run the following command to pull the selected image:

docker pull quay.io/qiime2/moshpit:2026.4

Verify things are working by running:

docker run \
  -v $(pwd):/data \
  -it quay.io/qiime2/moshpit:2026.4 \
  qiime info

Development version¶

Linux (Ubuntu)

These instructions are for users running on Linux or the Windows Subsystem for Linux (WSL v2).

conda env create \
  --name rachis-moshpit-dev \
  --file https://raw.githubusercontent.com/qiime2/distributions/refs/heads/dev/latest/passed/rachis-moshpit-linux-64-conda.yml

Tutorials

Contig-based AMR abundance estimation

How-To Guides

How to use parsl parallelization