Specialized Primary Metabolite Analysis
    From Anaerobic Bacteria
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Download gutSMASH standalone

The most updated gutSMASH version is available from our GitHub page.

The current standalone release is gutSMASH.1.0 (October 2020).

Install from source

First of all, download the gutSMASH python source from our GitHub repo: https://github.com/victoriapascal/antismash/tree/gutsmash

Then, make sure you have the following gutSMASH dependencies installed:

  • hmmer3 (version 3.0)
  • fasttree (version 2.1.7 tested)
  • diamond (0.8.36 tested)
  • muscle (version 3.8.31 tested)
  • prodigal (version 2.6.1 tested)
  • NCBI blast+ (version 2.2.31 tested)
  • python (version 3.7.6 tested, anything >= python 3.0 should work)
  • python-virtualenv (not needed, but highly recommended)

You can use apt-get to install the dependencies in Linux machines:

sudo apt-get install hmmer2 hmmer diamond-aligner fasttree prodigal ncbi-blast+ muscle glimmerhmmsource as3/bin/activate

Or Homebrew for macOS systems:

brew install hmmer2 hmmer diamond fasttree prodigal blast muscle brewsci/science/glimmerhmmsource as3/bin/activate

All the python dependencies can be installed using a simple command:

pip3 install biopython helperlibs bcbio-gff pysvg-py3 scikit-learn matplotlib pyScss Jinja2

To run gutSMASH, there are 3 databases that need to be found in gutsmash/antismash/databases:

  • The latest (processed) Pfam database Pfam-A.hmm.gz available from the Pfam FTP website ( https://pfam.xfam.org/), and hmmpressed using the HMMER suit (http://hmmer.org)
  • The ClusterBlast database, that can be downloaded and uncompressed from here: ClusterBlast.zip
  • The resfam database, that can be downloaded and uncompressed from here: resfam.zip

Next, the smcogs database that needs to be place in gutsmash/antismash/detection/genefunctions/gut_data can be downloaded from here smcogs.hmm.zip. Then, use hmmpress before using it.

Finally, the KnownClusterBlast database that needs to be place in gutsmash/antismash/modules/clusterblast/data/known can be downloaded and uncompressed from here: KnownClusterBlast.zip

For more information on how to run gutSMASH visit the README in our GitHub