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/

⁠Dockerfile Structure

The Dockerfile follows these main steps:

1. Uses Ubuntu 24.04 as the base image
2. Adds metadata labels for documentation and attribution
3. Installs prerequisites with pinned versions
4. Downloads and builds STAR from source
5. Includes Samtools v1.11 built from source
6. Performs cleanup to minimize image size

⁠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.