At the moment, there are thre options available to install antiSMASH:

  • Using the Bioconda package.
  • Using one of the pre-built Docker images. A slightly larger download, but zero-fuss install on any system that can run Docker.
  • A manual install, with three options to get the required dependencies:
    • Using the pre-built Debian installer. This obviously is limited to Debian and related distributions.
    • Using the Bioconda distribution.
    • Full manual install. Most work, but most options to customise your install.

Using Bioconda#

Bioconda is a channel for the conda package manager with a focus on bioinformatics software. Once you have bioconda installed, installing antiSMASH is as easy as running

conda create -n antismash antismash
conda activate antismash
download-antismash-databases
conda deactivate

Later, if you want to run antiSMASH, simply call

conda activate antismash
antismash my_input.gbk

Using Docker#

If you're not on Debian, but don't want to bother with the full-blown manual installation, there are two docker images you can use.

antiSMASH standalone#

This image includes all the required databases, no further configuration needed. It is a ~9 GB download at the moment. If you have docker installed, just grab the wrapper script and get going:

mkdir ~/bin    # not required if you already have that
curl -q https://dl.secondarymetabolites.org/releases/latest/docker-run_antismash-full > ~/bin/run_antismash
chmod a+x ~/bin/run_antismash
run_antismash <input file> <output directory> [antismash options]

Note that due to the nature of the wrapper script having to do some magic mapping between your system and the container, you always need to provide input file and output directory first, and in that order.

antiSMASH standalone-lite#

This image includes everything but the PFAM and ClusterBlast databases, meaning you still have to install those. The wrapper script assumes those databases will live in /data/databases, make sure to tweak the script and the rest of the install instructions if you want to change this location.

First, grab the wrapper script:

mkdir ~/bin    # not required if you already have that
curl -q https://dl.secondarymetabolites.org/releases/latest/docker-run_antismash-lite > ~/bin/run_antismash
chmod a+x ~/bin/run_antismash

The easiest way to download the antiSMASH databases is using the database downloader script. Again the wrapper script assumes your databases live in /data/databases. If you want to use a different location, just provide that to the download_antismash_databases script as the parameter.

curl -q https://dl.secondarymetabolites.org/releases/latest/download_antismash_databases > ~/bin/download_antismash_databases
chmod a+x ~/bin/download_antismash_databases
download_antismash_databases

Note that due to the nature of the wrapper script having to do some magic mapping between your system and the container, you always need to provide input file and output directory first, and in that order:

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

Manual install#

antiSMASH relies on a number of external tools to perform its analyses. You need to install those before installing antiSMASH. Use one of the methods mentioned below to get all relevant dependencies, then continue with installing the latest antiSMASH release to install antiSMASH itself.

Dependencies via Debian/Ubuntu#

For 64bit AMD/Intel Debian or Ubuntu machines, all the required dependencies are available either from the official Debian repositories, or from the custom antiSMASH repository.

First add the antiSMASH debian repository:

sudo apt-get update
sudo apt-get install -y apt-transport-https
sudo wget http://dl.secondarymetabolites.org/antismash-stretch.list -O /etc/apt/sources.list.d/antismash.list
sudo wget -q -O- http://dl.secondarymetabolites.org/antismash.asc | sudo apt-key add -
sudo apt-get update

then install the binaries themselves

sudo apt-get install hmmer2 hmmer diamond-aligner fasttree prodigal ncbi-blast+ muscle glimmerhmm

If you want to use CASSIS or the full RODEO analysis for RiPPs and agree to the MEME license, add meme-suite to that list.

After the dependencies are installed, create a Python virtual environment.

Dependencies via Bioconda#

Bioconda is a channel for the conda package manager with a focus on bioinformatics software. Once you have bioconda installed, install the dependencies:

conda create -n antismash
conda activate antismash
conda install hmmer2 hmmer diamond fasttree prodigal blast muscle glimmerhmm

If you want to use CASSIS or the full RODEO analysis for RiPPs and agree to the MEME license, also run conda install meme==4.11.2.

Later, if you want to run antiSMASH, simply call

conda activate antismash
antismash my_input.gbk

After the dependencies are installed, continue with installing the latest antiSMASH release.

Dependencies via Homebrew#

Homebrew is a package manager for macOS (and Linux). It comes with a great selection of bioinformatics packages.

First, add the brewsci/bio tap to get access to the bioinformatics packages.

brew tap brewsci/bio

then install the binaries themselves

brew install hmmer2 hmmer diamond fasttree prodigal blast muscle brewsci/science/glimmerhmm

Unfortunately, Homebrew doesn't fix the file name conflicts between the hmmer and hmmer2 packages, so to have both tools available, run the following:

export HMMER2_BINDIR="$(brew --prefix)/opt/hmmer2/bin"
export BREW_BINDIR="$(dirname $(brew link -n hmmer2 | head -n2 | tail -n1))"
pushd ${BREW_BINDIR}
for FNAME in ${HMMER2_BINDIR}/*; do
    BINARY=$(basename $FNAME)
    ln -s $FNAME ${BINARY/hmm/hmm2}
done
popd
unset HMMER2_BINDIR BREW_BINDIR

If you want to use CASSIS or the full RODEO analysis for RiPPs and agree to the MEME license, run

brew install https://raw.githubusercontent.com/brewsci/homebrew-bio/12b4ef4679c5c6ed21ab7c046c2709c4cefb4338/Formula/meme.rb

to install MEME in version 4.11.2

After the dependencies are installed, create a Python virtual environment.

Full manual install#

Install the following dependencies:

  • diamond (versions 0.8.36, 0.9.17, and 0.9.24 tested, we recommended the 0.9 series)
  • fasttree (version 2.1.9 tested)
  • GlimmerHMM (version 3.0.4 tested)
  • hmmer2 (version 2.3.2 tested, append a 2 to all hmmer2 executables to avoid conflict with hmmer3 executable names, like hmmalign -> hmmalign2)
  • hmmer3 (3.1b2 tested)
  • meme (version 4.11.2 tested. Version 4.11.4 changes output file formats, so don't use that.)
  • muscle (version 3.8.31 tested)
  • NCBI blast+ (version 2.6.0 tested)
  • prodigal (version 2.6.3 tested)
  • python (version 3.5.3 tested, any version >= 3.5.0 should work)
  • python-virtualenv (not needed, but highly recommended)

After the dependencies are installed, create a Python virtual environment.

Create a Python virtual environment#

Not strictly necessary, but highly recommended if you're not already using conda.

  • Create and activate a virtual environment (this can be skipped, but is highly recommended)
virtualenv -p $(which python3) ~/as5env
source ~/as5env/bin/activate

Later, if you want to run antiSMASH, simply call

source ~/as5env/bin/activate
antismash my_input.gbk

Now, continue with installing the latest antiSMASH release.

Installing the latest antiSMASH release#

  • Download and extract the antiSMASH source (using version 5.1 as an example):
wget https://dl.secondarymetabolites.org/releases/5.1.1/antismash-5.1.1.tar.gz
tar -zxf antismash-5.1.1.tar.gz
  • Install antiSMASH (again, using 5.1 as an example, the name will match the download step):
pip install ./antismash-5.1.1
download-antismash-databases

We recommend running the prerequisite check to make sure everything is as expected with

antismash --check-prereqs

If you want to see the available command line options, use

antismash --help

or, for a full list of all available options, including debug options

antismash --help-showall