Install Anvio

Written on June 2nd , 2022 by Andrea Telatin

Anvi’o workshop requisites

If you cannot have a working Anvi’o installation, please join as auditor, we can pair you with other participants!

1. Install Anvi’o

In general, follow Anvio’s instructions

  1. On Windows, you will need the Windows Subsystem for Linux (WSL) installed (and possibly the permission to install software from Computing, if you do not already have it).
  2. Install Miniconda
    • on Windows, install the Linux version inside WSL!
    • on Mac, you might need to install XCode and other prerequisites, see here
    • Ensure to install the latest stable version (v8) and not the development version
  3. Follow the instructions on Anvi’o website to install https://anvio.org/install
  4. Test the installation typing: 
    conda activate anvio-8
anvi-self-test --suite mini

2. Install the databases

  1. Download some extra databases, typing these commands from the command line (from the anvio-8 environment)
    • Run anvi-setup-scg-taxonomy, to setup SCG taxonomy data using GTDB genomes.
    • Run anvi-setup-ncbi-cogs, to setup NCBI’s COG database for quick annotation of genes with functions,
    • Run anvi-setup-kegg-data, so anvi-estimate-metabolism and anvi-reaction-network find the database of KEGG orthologs ready when you need it.
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