Download plantiSMASH Standalone#

Stand-alone releases are available on
GitHub Releases and PyPI.

Current Release#

Latest tag:
GitHub Release PyPI

Installation Options#

There are two supported ways to install plantiSMASH:

  1. Recommended: Clone from GitHub and install via Conda – creates a full reproducible environment with all external tools and the latest stable code.
  2. Alternative: Install the Python package only (from PyPI) – for developers or integration use; external dependencies must be installed manually.

This option gives you a fully functional standalone version of plantiSMASH.

💡 Windows users: If you don’t already have a Linux environment,
follow our Windows setup guide to install WSL (Windows Subsystem for Linux).
This lets you run plantiSMASH natively inside Ubuntu on Windows before proceeding with the steps below.

  1. Clone the latest release from Github 

    git clone https://github.com/plantismash/plantismash.git
# navigate to that directory 
cd plantismash

  2. Create the Conda environment

    🧩 Don’t have Conda or Mamba installed yet? Click to expand setup instructions.

    To create a reproducible plantiSMASH environment, you’ll need a Conda-based package manager such as Miniforge (recommended) or Mambaforge.

    Follow these steps to install it on Linux (or inside WSL on Windows):

    # 1. Download and install Miniforge
curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh"
bash Miniforge3-$(uname)-$(uname -m).sh

# 2. Initialize Conda
source ~/.bashrc
conda init bash

# 3. Set default configuration
conda config --set auto_activate_base false
conda config --add channels bioconda
conda config --add channels conda-forge
conda config --set channel_priority strict
    💡 You only need to do this once — future plantiSMASH environments will reuse this configuration. 

    
# Using mamba (recommended)
mamba env create -f environment.yml
conda activate plantismash

  3. Verify your installation: 

    
# check Python entry points
plantismash --help
plantismash_download_databases --help

  4. Download the required databases 

    # default location is created automatically (uses appdirs)
plantismash_download_databases

    Tip: to test on an example genome, you can fetch A. thaliana with the NCBI Datasets CLI and run plantiSMASH:

    mkdir -p test_datasets/Arabidopsis_thaliana && cd $_

datasets download genome accession GCF_000001735.4 --include gbff

unzip -o ncbi_dataset.zip

plantismash --taxon plants --limit -1 --outputfolder result/ \
ncbi_dataset/data/GCF_000001735.4/genomic.gbff

Option 2 - Python package only (advanced users)#

  1. Download the latest plantiSMASH standalone release from our GitHub page

    GitHub Release

  2. Ensure you have the following dependencies installed (tested versions in parentheses):

  3. Once all dependencies are installed and available on your PATH, install the Python package:

    pip install plantismash

  4. Verify the installation: 

    plantismash --help
plantismash_download_databases --help

    ⚠️ This installs only the Python code, not the external binaries. To run full analyses, the required tools (HMMER, BLAST, DIAMOND, etc.) must be available on your PATH.

Notes and FAQs#

•   Why Python 3.8?

This release currently targets Python >=3.8,<3.9 for compatibility with some dependencies. Use the provided environment.

•   HMMER2 note

plantiSMASH requires hmmpfam2 from legacy HMMER 2 in addition to HMMER 3. The line bioconda/label/cf201901::hmmer2 installs the legacy binaries under distinct names to avoid conflicts.

•   PyPI vs Conda

PyPI provides the Python package only. All native/CLI tools are installed via Conda in environment.yml.

•   Reproducibility

The environment.yml pins versions of external tools; PyPI pins Python libs in pyproject.toml. This combination reproduces the tested setup.