getwilds/star repository overview

⁠STAR

This directory contains Docker images for STAR (Spliced Transcripts Alignment to a Reference), an RNA-seq aligner designed for high performance and accuracy.

⁠Available Versions

• latest ( Dockerfile⁠ | Vulnerability Report⁠ )
• 2.7.6a ( Dockerfile⁠ | Vulnerability Report⁠ )
• 2.7.4a ( Dockerfile⁠ | Vulnerability Report⁠ )

⁠Image Details

These Docker images are built from Ubuntu and include:

• STAR: A fast RNA-seq read mapper with high accuracy and support for splice junctions
• 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 STAR with its dependencies.

⁠Usage

⁠Docker

docker pull getwilds/star:latest
# or
docker pull getwilds/star:2.7.6a
# or
docker pull getwilds/star:2.7.4a

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

⁠Singularity/Apptainer

apptainer pull docker://getwilds/star:latest
# or
apptainer pull docker://getwilds/star:2.7.6a
# or
apptainer pull docker://getwilds/star:2.7.4a

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

⁠Example Command

# Docker
docker run --rm -v /path/to/data:/data getwilds/star:latest STAR --runThreadN 4 --genomeDir /data/genome --readFilesIn /data/reads_1.fq /data/reads_2.fq --outFileNamePrefix /data/output/

# Apptainer
apptainer run --bind /path/to/data:/data docker://getwilds/star:latest STAR --runThreadN 4 --genomeDir /data/genome --readFilesIn /data/reads_1.fq /data/reads_2.fq --outFileNamePrefix /data/output/

# Apptainer (local SIF file)
apptainer run --bind /path/to/data:/data star_latest.sif STAR --runThreadN 4 --genomeDir /data/genome --readFilesIn /data/reads_1.fq /data/reads_2.fq --outFileNamePrefix /data/output/

⁠Security Features

The STAR Docker images include:

• Pinned versions for all installed system packages
• A multi-stage build that keeps compilers and development headers out of the final image
• Smoke test during the build to verify the STAR and Samtools installations

⁠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 STAR 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. Installs prerequisites with pinned versions in both stages
5. Copies the compiled STAR and Samtools binaries from the build stage
6. Performs a smoke test to verify the installation

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

⁠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.

⁠Source Repository

These Dockerfiles are maintained in the WILDS Docker Library⁠ repository.