Download plantiSMASH Standalone#

Stand-alone versions of plantiSMASH are available through our GitHub page.

Current Release#

The current standalone release is plantiSMASH 2.0-beta (December 16th, 2024).

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Installation Options#

There are two ways to install plantiSMASH:

1. Downloading the standalone release – Suitable for users who want to install plantiSMASH from a zip package and ensure dependencies are installed separately.
2. Cloning from GitHub – Recommended for users who want the latest development version and prefer managing dependencies in a virtual Conda environment.

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Option 1: Downloading the standalone release#

1. Download the latest plantiSMASH standalone release from our GitHub repo:
   https://github.com/plantismash/plantismash/releases

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

   • Glimmer (3.02)
   • GlimmerHMM (3.0.4)
   • HMMER3 (3.3.2)
   • HMMER2 (version 2.3.2 tested). plantiSMASH requires hmmpfam2, a legacy tool from HMMER 2. This binary is no longer included in HMMER 3.x and must be installed manuallyappend a 2 to all hmmer2 executables to avoid conflict with hmmer3 executable names, like hmmalign -> hmmalign2
   • FastTree (2.1.8)
   • DIAMOND (2.0.15)
   • MUSCLE (3.8.31)
   • Prodigal (2.6.3)
   • NCBI Blast+ (2.12.0)
   • CD-HIT (4.8.1)
   • LibXML2 (2.10.3)
   • pplacer
   • NCBI Datasets CLI (16.40.1)
   • Unzip
   • Helperlibs (0.2.1)
   • Biopython (1.76)

3. Once all dependencies are installed, plantiSMASH should be ready to use.

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Option 2: Cloning from GitHub#

Using Windows? Click here for the full Windows Setup Guide.

1. Clone the latest version from GitHub:

   git clone -b dev https://github.com/plantismash/plantismash.git
   cd plantismash

2. If not installed already, conda/mamba can be installed by following these instructions:

   # 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
   # follow instructions and let it run `conda init`
   
   # set default channels
   source ~/.bashrc
   conda config --set auto_activate_base false
   source ~/.bashrc
   conda config --add channels bioconda
   conda config --add channels conda-forge
   conda config --set channel_priority strict  

3. Create and activate a Conda environment using the provided environment.yml file

   conda env create -f environment.yml
   conda activate plantismash

4. Download the required databases:

   python download_databases.py

5. Verify the installation

   python run_antismash.py -h

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