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

  • Using the Bioconda distribution.
  • 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.

Bioconda#

Note: Bioconda at the moment still provides antiSMASH 4.1.0, not the new version 5. We are hoping to fix this soon.

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
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 Linux 9#

Note: We are still working on an antiSMASH 5 installer script.

For 64bit AMD/Intel Debian 9 machines, all the required dependencies are available either from the official Debian repositories, or from the custom antiSMASH repository. If you are allowed to sudo, installing antiSMASH is as easy as:

curl -q https://bitbucket.org/antismash/antismash/downloads/install_deb.sh > install_deb.sh
bash install_deb.sh

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#

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, create a python virtualenv for installing the antiSMASH python dependencies. This is not required, but highly recommended.

virtualenv --python $(which python3) as5
source as5/bin/activate

Next, obtain a copy of the antiSMASH source code. We don't have any final release of antiSMASH 5 yet, so either clone the antiSMASH 5 git repository:

git clone https://github.com/antismash/antismash.git
cd antismash

or grab a zip file of the development tree by opening https://github.com/antismash/antismash/ in your browser, clicking the "clone or download" button and selecting "Download ZIP" there.

All the python dependencies are specified in the setup.py file, so you can just run the install from the antiSMASH source code directory:

pip install .

Then, run download-antismash-databases to grab and prepare the databases:

download-antismash-databases

To check all of the dependencies are installed and antiSMASH can find them, run:

antismash --check-prereqs

If antiSMASH prints "All prerequisites satisfied", you're good to go.