Installation via Github repository#

To install epsSMASH via Github, you first need to clone the epsSMASH GitHub repository to your local machine. Then you need to install all the dependencies which epsSMASH relies on, which can be found in a YAML file at epssmash/config/. Once the dependencies are installed, epsSMASH can be installed using pip. Databases needed for Clusterblast and Pfam annotation of clusters can then be downloaded using the download-epssmash-databases command. The commands needed to perform the complete install are listed below:

git clone https://github.com/AOHD/epsSMASH.git # Clone repo

conda env create -f epssmash/config/config.yaml # Create conda environment with dependencies

conda activate antismash_dependencies # Activate conda environment

pip install . # Install epsSMASH with pip

download-epssmash-databases # Download databases needed for Clusterblast and Pfam annotation

epsSMASH --help-showall # Test installation

Using Docker#

epsSMASH is available on the Docker Hub. In the epsSMASH Github repository, two Docker wrapper scripts can be found at epssmash/docker/: run_epssmash and download_epssmash_databases. Moving these wrappers to your bin folder and running them will allow you to run epsSMASH without going through the installation above. Note that you must specify the input file and output directory when using run_epssmash:

run_antismash <input file> <output directory> [epsSMASH options]

If download_epssmash_dependencies is run before run_epssmash it will create the epsSMASH Docker image before attempting to download the databases.