getwilds/bwa repository overview

⁠BWA

This directory contains Docker images for the Burrows-Wheeler Aligner (BWA), a software package for mapping low-divergent sequences against a large reference genome.

⁠Available Versions

• latest ( Dockerfile⁠ | Vulnerability Report⁠ )
• 0.7.17 ( Dockerfile⁠ | Vulnerability Report⁠ )

⁠Image Details

These Docker images are built from Ubuntu 24.04 and include:

• BWA v0.7.17: A software package for mapping DNA sequences against a reference genome
• Samtools v1.11: A suite of programs for interacting with high-throughput sequencing data

The images are designed to be minimal and focused on a specific version of BWA with its dependencies.

⁠Platform Availability

Note: This image is only built for linux/amd64 architecture. BWA contains x86-specific optimizations that are not compatible with ARM64 platforms.

⁠Usage

⁠Docker

docker pull getwilds/bwa:latest
# or
docker pull getwilds/bwa:0.7.17

# Alternatively, pull from GitHub Container Registry
docker pull ghcr.io/getwilds/bwa:latest

⁠Singularity/Apptainer

apptainer pull docker://getwilds/bwa:latest
# or
apptainer pull docker://getwilds/bwa:0.7.17

# Alternatively, pull from GitHub Container Registry
apptainer pull docker://ghcr.io/getwilds/bwa:latest

⁠Example Commands

# Docker
docker run --rm -v /path/to/data:/data getwilds/bwa:latest bwa mem -t 4 reference.fa reads_1.fq reads_2.fq > aligned_reads.sam

# Apptainer
apptainer run --bind /path/to/data:/data docker://getwilds/bwa:latest bwa mem -t 4 reference.fa reads_1.fq reads_2.fq > aligned_reads.sam

# Apptainer (local SIF file)
apptainer run --bind /path/to/data:/data bwa_latest.sif bwa mem -t 4 reference.fa reads_1.fq reads_2.fq > aligned_reads.sam

⁠Security Features

The BWA Docker images include:

• Dynamic versioning for all dependencies to ensure the latest security patches
• Pinned versions for reproducibility
• Minimal installation with only required dependencies
• Health check to verify the BWA installation

⁠Security Scanning and CVEs

These images are regularly scanned for vulnerabilities using Docker Scout. However, due to the nature of bioinformatics software and their dependencies, some Docker images may contain components with known vulnerabilities (CVEs).

Use at your own risk: While we strive to minimize security issues, these images are primarily designed for research and analytical workflows in controlled environments.

For the latest security information about this image, please check the CVEs_*.md files in this directory⁠, which are automatically updated through our GitHub Actions workflow. If a particular vulnerability is of concern, please file an issue⁠ in the GitHub repo citing which CVE you would like to be addressed.

⁠Dockerfile Structure

The Dockerfile uses a multi-stage build to keep the final image minimal:

1. Build stage: Uses Ubuntu 24.04 with build tools and dev headers to compile BWA v0.7.17 and Samtools v1.11 from source
2. Final stage: Uses a fresh Ubuntu 24.04 base with only the runtime libraries needed to run the compiled binaries
3. Adds metadata labels for documentation and attribution
4. Dynamically determines and pins the latest security-patched versions of dependencies in both stages
5. Copies the compiled BWA and Samtools binaries from the build stage
6. Sets up a working directory at /data for workflow execution
7. Implements a health check to verify the BWA installation

This approach keeps compilers and development headers out of the final image, reducing its size and attack surface.

⁠Source Repository

These Dockerfiles are maintained in the WILDS Docker Library⁠ repository.