getwilds/ollama

Ollama

This directory contains Docker images for Ollama, an LLM inference server, bundled with the https://github.com/stjude-rust-labs/sprocket WDL validator and the Python ollama SDK. Designed for benchmarking LLM-generated WDL scripts.

Available Versions

• latest ( https://github.com/getwilds/wilds-docker-library/blob/main/ollama/Dockerfile_latest | https://github.com/getwilds/wilds-docker-library/blob/main/ollama/CVEs_latest.md )
• 0.21.0 ( https://github.com/getwilds/wilds-docker-library/blob/main/ollama/Dockerfile_0.21.0 | https://github.com/getwilds/wilds-docker-library/blob/main/ollama/CVEs_0.21.0.md )

Image Details

These Docker images are built from ollama/ollama:0.21.0 and include:

• Ollama v0.21.0: LLM inference server for running models locally
• Sprocket v0.23.0: WDL script validator
• Python ollama SDK v0.6.1: Python client library for interacting with Ollama
• Python 3 (system version from base image)

Sprocket is installed from prebuilt binaries published on the https://github.com/stjude-rust-labs/sprocket/releases.

Platform Availability

Available for: linux/amd64, linux/arm64

A GPU is not required to run this image, but is highly encouraged — CPU-only execution of LLMs is significantly slower.

Citation

This image bundles two independent tools. If you use them in your research, please cite the original authors:

• Ollama (LLM inference server): [***]
• Sprocket (WDL execution engine): https://github.com/stjude-rust-labs/sprocket

Usage

Docker

bash
# Pull the latest version
docker pull getwilds/ollama:latest

# Or pull a specific version
docker pull getwilds/ollama:0.21.0

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

Singularity/Apptainer

bash
# Pull the latest version
apptainer pull docker://getwilds/ollama:latest

# Or pull a specific version
apptainer pull docker://getwilds/ollama:0.21.0

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

Example Commands

bash
# Check installed versions
docker run --rm getwilds/ollama:latest ollama --version
docker run --rm getwilds/ollama:latest sprocket --version

# Start the container with GPU access
docker run --rm --gpus all -it getwilds/ollama:latest

# Inside the container, start the Ollama server
ollama serve &

# Pull a model
ollama pull llama3

# Generate a WDL script and validate it with Sprocket
python3 -c "
import ollama
response = ollama.chat(model='llama3', messages=[
    {'role': 'user', 'content': 'Write a WDL task that runs fastqc on a FASTQ file'}
])
with open('/tmp/output.wdl', 'w') as f:
    f.write(response['message']['content'])
"
sprocket lint /tmp/output.wdl

Dockerfile Structure

The Dockerfile follows these main steps:

1. Uses ollama/ollama:0.21.0 as the base image
2. Adds metadata labels for documentation and attribution
3. Installs system dependencies with pinned versions (Python, curl, build tools)
4. Installs the Python ollama SDK via pip
5. Downloads the prebuilt Sprocket binary for the target architecture
6. Runs smoke tests to verify all tools are installed correctly

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 https://github.com/getwilds/wilds-docker-library/blob/main/ollama, which are automatically updated through our GitHub Actions workflow. If a particular vulnerability is of concern, please file an https://github.com/getwilds/wilds-docker-library/issues in the GitHub repo citing which CVE you would like to be addressed.

Source Repository

These Dockerfiles are maintained in the https://github.com/getwilds/wilds-docker-library repository.