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Anvio

Anvi’o is a comprehensive platform that brings together many aspects of today’s cutting-edge computational strategies of data-enabled microbiology in an integrated and easy-to-use fashion through extensive interactive visualization capabilities.

BUT, Anvi’o isn't a regular software, it provides a framework to data within web applications. The web applications are interactive, and allow users to explore their data in a dynamic way.

BUT, opening a website on a HPC environment isn't trivial.

Here some solution to run Anvi'o and access the web applications in a HPC environment.

SSH Tunnel#

1. Launch the Anvi'o CLI method#

# Log in to the HPC cluster
$ <username>@core.cluster.france-bioinformatique.fr

# Load the Anvio module
[login:~]$ module load anvio/8

# Open an interactive session on a compute node
[slurm1:~]$ srun --mem 2G --cpus-per-task 1 --pty /bin/bash

# Launch the Anvio CLI method. For exemple, this demo:
[cpu-node-051:~]$ anvi-self-test --suite pangenomics

[•••]

* The server is up and running 🎉

Server address ...............................: http://0.0.0.0:8081

☝️ There are 2 important information to note here:

  • The compute node name (here cpu-node-051) where the Anvi'o web server is running.
  • The port number (here 8081) where the Anvi'o web server is listening

2. Open a SSH tunnel#

⚠️ In parallel, in a new terminal.

  1. From your local machine, open a SSH tunnel to the compute node where the Anvi'o web server is running.

    ssh -N -L 8080:cpu-node-051:8081 chucknorris@core.cluster.france-bioinformatique.fr

    This part will change depending of the compute node name and the port number where the Anvi'o web server is running: cpu-node-051:8081

  2. Open your web browser and go to the following URL: http://localhost:8080

Enjoy 🎉