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.
Note: Bioconda at the moment still provides antiSMASH 4.1.0, not the new version 5. We are hoping to fix this soon.
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
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, 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 .
download-antismash-databases to grab and prepare the
To check all of the dependencies are installed and antiSMASH can find them, run:
If antiSMASH prints "All prerequisites satisfied", you're good to go.