Running anvi'o in Singularity containers

Ryan Bartelme, PhD

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Preparation

If you want to test anvi'o on an HPC system, here are a few strategies:

Pulling anvi'o docker image into Singularity

Start by using singularity to pull the latest version of the anvi'o image from dockerhub:

singularity pull docker://meren/anvio

After seeing the standard output of the docker pull command, Singularity will print out something like:

INFO:    Creating SIF file...

And the *.sif file should appear in the directory:

$ ls
anvio_latest.sif

The latest docker image of anvi'o will NOT have the databases configured. This is also an opportune time to create your own customized docker image from the meren/anvio:latest docker image tag.

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Making your own Dockerfile to customize your anvi'o runtime

See an example: Dockerfile this runs through the database configurations for anvi'o. (As of 03-25-21 this does not properly compile the 3d structure db's)

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Configuring anvi'o Singularity containers

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Docker container image customization

In this case I used a Dockerfile, where I am building off the anvio-dbconfig image. The modifications include an installation of ncbi-genome-download using the anvio conda environment pip and setting the entrypoint to the conda environment of anvio for the docker runtime. Note profile is included to make sure the container sources the .bashrc for the conda path.

Building Singularity images

Our local cluster singularity version:

singularity-ce version 3.8.0

Building from the Docker image above:

NOTE: This required sudo su on our local cluster, which I have access to, this has not been tested with --fakeroot yet.

sudo su

1. Singularity build statement, using Singularity recipe:

   singularity build anvio-pangenomics.sif Singularity

2. Get ownership of Singularity *.sif file and set group permissions.

   sudo chown rbartelme:iplant-everyone anvio-pangenomics.sif

3. Read up on job scheduling with your HPC's IT team documentation

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Example with SLURM, Singularity, and Snakemake

Snakemake Workflows with Singularity

Anvi'o has awesome snakemake workflows built in! This is the "end-to-end" approach for all your HPC or cloud compute needs.

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Comparative Genomics

Example json input for Comparative Genomics Workflow:

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