Institute Docker Images

This repository contains Dockerfiles for commonly used software at our institute. Each image is optimized for size and built for multiple architectures (amd64 and arm64).

Available Images

| Image Name | Description | Size | Latest Tag | Architectures | Software Version | Image Version | |------------|-------------|------|------------|---------------|------------------|---------------| | plink | PLINK1.9 and PLINK2 for genetic analysis | ~100MB | latest | amd64, arm64 | 1.9 & 2.0 | 1.0.0 | | flashpca2 | Fast PCA implementation for genome-wide data | ~100MB | latest | amd64, arm64 | 2.1 | 1.0.0 | | gcta | Genome-wide Complex Trait Analysis | ~150MB | latest | amd64, arm64 | 1.94.1 | 1.0.0 | | gctb | Bayesian linear mixed models for complex traits | ~120MB | latest | amd64, arm64 | 2.05 | 1.0.0 | | readstat | Statistical data format conversion tool | ~120MB | latest | amd64, arm64 | 1.1.9 | 1.0.0 | | regenie | Whole genome regression for GWAS | ~150MB | latest | amd64 | 3.6 | 1.0.0 |

Versioning Strategy

We use independent versioning for our Docker images: - Software Version: The version of the actual software installed in the container - Image Version: Our internal version for the Docker image (starts at 1.0.0)

This allows us to: - Update the Docker image (bug fixes, optimizations, security updates) while keeping the same software version - Maintain reproducibility by using specific image versions - Track changes independently from software releases

Example: biopsyk/gcta:1.0.0 contains GCTA software version 1.94.1, but if we need to fix the Dockerfile or update dependencies, the next image would be biopsyk/gcta:1.1.0 with the same GCTA 1.94.1 software.

Repository Structure

. ├── README.md ├── images/ │ ├── plink/ │ │ ├── Dockerfile │ │ ├── README.md │ │ └── VERSION │ ├── flashpca2/ │ │ ├── Dockerfile │ │ ├── README.md │ │ └── VERSION │ ├── gcta/ │ │ ├── Dockerfile │ │ ├── README.md │ │ └── VERSION │ ├── gctb/ │ │ ├── Dockerfile │ │ ├── README.md │ │ └── VERSION │ ├── readstat/ │ │ ├── Dockerfile │ │ ├── README.md │ │ └── VERSION │ └── regenie/ │ ├── Dockerfile │ ├── README.md │ └── VERSION └── scripts/ └── build-and-push.sh

Building and Pushing Images

The repository includes a build script that handles multi-architecture builds using Docker BuildX. The script is located in scripts/build-and-push.sh.

To build and push an image:

```bash

Build and push a specific image

./scripts/build-and-push.sh plink

Build and push all images

./scripts/build-and-push.sh all

Examples for the new images

./scripts/build-and-push.sh gcta ./scripts/build-and-push.sh gctb ./scripts/build-and-push.sh readstat ```

Prerequisites

• Docker with BuildX support
• Docker Hub account with access to the institute's organization
• Docker logged in to the registry (docker login)

Building Locally

To build an image locally for your architecture:

```bash cd images/plink docker build -t biopsyk/plink:latest .

Examples for other images

cd images/gcta docker build -t biopsyk/gcta:latest .

cd images/gctb
docker build -t biopsyk/gctb:latest .

cd images/readstat docker build -t biopsyk/readstat:latest . ```

Contributing

To add a new image:

1. Create a new directory under images/
2. Add a Dockerfile and README.md
3. Update the main README.md with image information
4. Test the build locally
5. Submit a pull request

Using with Singularity

To use these Docker images with Singularity (e.g., on an HPC cluster), you can pull them directly from Docker Hub:

```bash

Pull using specific version (recommended for reproducibility)

singularity pull docker://biopsyk/plink:1.0.0

Or pull the latest version (always gets the newest updates)

singularity pull docker://biopsyk/plink:latest

This will create a Singularity Image File (SIF) named 'plink1.0.0.sif' or 'plinklatest.sif'

You can then run PLINK commands using:

singularity exec plink1.0.0.sif plink1.9 --help singularity exec plink1.0.0.sif plink2 --help

Examples for other tools:

singularity pull docker://biopsyk/gcta:1.94.1 singularity exec gcta_1.94.1.sif gcta64 --help

singularity pull docker://biopsyk/gctb:2.05 singularity exec gctb_2.05.sif gctb --help

singularity pull docker://biopsyk/readstat:1.0.0 singularity exec readstat_1.0.0.sif readstat --help

To bind your data directory (replace /path/to/data with your actual data path):

singularity exec -B /path/to/data:/data plink_1.0.0.sif plink2 --help ```

Note: When using Singularity, the container's /data directory is the recommended location for your working files. Use the -B flag to bind your host directory to this location.

License

Please add appropriate license information here.