bwa-docker-singularity

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

BWA is a software package for mapping DNA sequences against a large reference genome, such as the human genome.
https://bio-bwa.sourceforge.net/bwa.shtml

Requirements:

To building: build-essential zlib1g-dev

Build docker container:

1. For BWA installation instructions:

https://github.com/lh3/bwa

2. Build the Docker Image

To build image from the command line:

# Assumes current working directory is the top-level bwa-docker-singularity directory
docker build -t bwa:0.7.17 . # tag should match software version

• Can do this on Google shell

To test this tool from the command line:

docker run --rm -it bwa:0.7.17 bwa 

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 bwa0.7.17-docker.tar && gzip bwa0.7.17-docker.tar # = IMAGE_ID of <tool> image
docker run -v "$PWD":/data --rm -it singularity:1.1.5 bash -c "singularity build /data/bwa0.7.17.sif docker-archive:///data/bwa0.7.17-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 bwa0.7.17.sif file to the system on which you want to run BWA from the Singularity container

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

# set up path to the Singularity container
BWA_SIF=path/to/bwa0.7.17.sif

# Test that <tool> can run from Singularity container
singularity run $BWA_SIF bwa # depending on system/version, singularity may be called apptainer