multiqc-docker-singularity

Build Docker container for MultiQC and (optionally) convert to Apptainer/Singularity.

MultiQC is a reporting tool that parses summary statistics from results and log files generated by other bioinformatics tools.

Requirements:

Python, Matplotlib, others managed by pip install

Build docker container:

1. For MultiQC installation instructions:

https://multiqc.info/docs/

2. Build the Docker Image

To build image from the command line:

# Assumes current working directory is the top-level multiqc-docker-singularity directory
docker build -t multiqc:1.14 . # tag should match software version

• Can do this on Google shell

To test this tool from the command line:

docker run --rm -it multiqc:1.14 multiqc --help 

Optional: Conversion of Docker image to Singularity

3. Build a Docker image to run Singularity

(skip if this image is already on your system)
https://github.com/mattgalbraith/singularity-docker

4. Save Docker image as tar and convert to sif (using singularity run from Docker container)

docker images
docker save <IMAGE ID> -o multiqc1.14-docker.tar && gzip multiqc1.14-docker.tar # = IMAGE_ID of multiqc image
docker run -v "$PWD":/data --rm -it singularity:1.1.5 bash -c "singularity build /data/multiqc1.14.sif docker-archive:///data/multiqc1.14-docker.tar.gz"

NB: On Apple M1/M2 machines ensure Singularity image is built with x86_64 architecture or sif may get built with arm64

Next, transfer the multiqc1.14.sif.sif file to the system on which you want to run MultiQC from the Singularity container

5. Test singularity container on (HPC) system with Singularity/Apptainer available

# set up path to the Singularity container
MULTIQC_SIF=path/to/multiqc1.14.sif.sif

# Test that MultiQC can run from Singularity container
singularity run $MULTIQC_SIF multiqc --help # depending on system/version, singularity may be called apptainer