At the moment, there are three options available to install antiSMASH:
- Using the Bioconda distribution (currently limited to version 4.1).
- Using the pre-built Debian installer. This obviously is limited to Debian and related distributions.
- Using one of the pre-built Docker images. A slightly larger download, but zero-fuss install on any system that can run Docker.
- Manual install. Most work, but most options to customise your install.
Note: Bioconda at the moment still provides antiSMASH 4.1.0, not the new version 5.
conda create -n antismash antismash source activate antismash download-antismash-databases source deactivate antismash
This will install antiSMASH in a dedicated conda environment and download the PFAM and ClusterBlast databases required for antiSMASH.
Then, if you want to run antiSMASH, simply call
source activate antismash antismash my_input.gbk
You can use
antismash --help to show all available options.
On Debian/Ubuntu Linux#
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.
- Install binary dependencies: 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.
- Download and extract the antiSMASH source (using version 5.1 as an example):
wget https://dl.secondarymetabolites.org/releases/5.1.0/antismash-5.1.0.tar.gz tar -zxf antismash-5-1-0.tar.gz
- Create and activate a virtual environment (this can be skipped, but is highly recommended)
virtualenv -p $(which python3) as5env source as5env/bin/activate
- Install antiSMASH (again, using 5.1 as an example, the name will match the download step):
pip install antismash-5-1-0 download-antismash-databases
We recommend running the prerequisite check to make sure everything is as expected with
If you want to see the available command line options, use
or, for a full list of all available options, including debug options
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.
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.
This image includes everything but the PFAM and ClusterBlast databases, meaning
you still have to install those. The wrapper script assumes those databases will
/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]
First, make sure you have the following antiSMASH dependencies installed:
- 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)
Then follow the instructions from the Debian install section, starting after the binary installation step.