How to install MOSHPIT
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:
These instructions are for users running on Linux or the Windows Subsystem for Linux (WSL v2).
conda env create \
--name qiime2-moshpit-2025.10 \
--file https://raw.githubusercontent.com/qiime2/distributions/refs/heads/dev/2025.10/moshpit/released/qiime2-moshpit-ubuntu-latest-conda.ymlThese instructions are for users with Apple Silicon chips (M1, M2, etc), and configures the installation of QIIME 2 in Rosetta 2 emulation mode.
CONDA_SUBDIR=osx-64 conda env create \
--name qiime2-moshpit-2025.10 \
--file https://raw.githubusercontent.com/qiime2/distributions/refs/heads/dev/2025.10/moshpit/released/qiime2-moshpit-macos-latest-conda.yml
conda activate qiime2-moshpit-2025.10
conda config --env --set subdir osx-64These instructions are for users older Intel-based Apple hardware (NOT M1, M2, etc).
conda env create \
--name qiime2-moshpit-2025.10 \
--file https://raw.githubusercontent.com/qiime2/distributions/refs/heads/dev/2025.10/moshpit/released/qiime2-moshpit-macos-latest-conda.ymlDevelopment version¶
These instructions are for users running on Linux or the Windows Subsystem for Linux (WSL v2).
conda env create \
--name qiime2-moshpit-dev \
--file https://raw.githubusercontent.com/qiime2/distributions/refs/heads/dev/latest/passed/qiime2-moshpit-ubuntu-latest-conda.ymlThese instructions are for users with Apple Silicon chips (M1, M2, etc), and configures the installation of QIIME 2 in Rosetta 2 emulation mode.
CONDA_SUBDIR=osx-64 conda env create \
--name qiime2-moshpit-dev \
--file https://raw.githubusercontent.com/qiime2/distributions/refs/heads/dev/latest/passed/qiime2-moshpit-macos-latest-conda.yml
conda activate qiime2-moshpit-dev
conda config --env --set subdir osx-64These instructions are for users older Intel-based Apple hardware (NOT M1, M2, etc).
conda env create \
--name qiime2-moshpit-dev \
--file https://raw.githubusercontent.com/qiime2/distributions/refs/heads/dev/latest/passed/qiime2-moshpit-macos-latest-conda.yml