Bench-PRS Dock

Bench-PRS Dock is a curated collection of ten Dockerized Polygenic Risk Score (PRS) tools built to make genetic risk prediction analyses reproducible, portable, and easy to benchmark across populations. Each container is versioned, metadata-tracked, and verified for runtime consistency.

Figure 1. Bench-PRS Dock Architecture.

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Quick Start

Pull and run any tool (example PRS-CSx):

docker pull chiomab/prscsx:v1.2
docker run --rm \
    -v ld_ref:/ld_ref \
    -v $(pwd)/test_data:/test_data \
    -v $(pwd)/results:/results \
    chiomab/prscsx:v1.2 \
    python PRScsx.py \
    --ref_dir=/ld_ref \
    --bim_prefix=test_data/test \
    --sst_file=test_data/EUR_sumstats.txt,test_data/EAS_sumstats.txt  \
    --n_gwas=200000,100000 \
    --pop=EUR,EAS \
    --chrom=22 \
    --phi=1e-2 \
    --out_dir=prscsx_results/ \
    --out_name=test \
    --seed=1234

See all tool pages in docs/tool_pages/

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Suite Contents

See the full technical inventory in Bench-PRS Dock Inventory

Bench-PRS Tool Suite

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Tools	Docker Image/ Tags	Image Size	Citation
BridgePRS	chiomab/bridgeprs:v1.5	588.9 MB	Hoggart et al. (2024)
PRS-CSx	chiomab/prscsx:v1.2	118.3 MB	Ruan et al. (2022)
SDPRX	chiomab/sdprx:v1.0	555.8 MB	Zhou et al. (2023)
XPASS/ XPASS+	chiomab/xpass:v1.2	689.1	Cai et al. (2021)
XP-BLUP	chiomab/xpblup:v1.0	51.4 MB	Coram et al. (2017)
GAUDI	chiomab/gaudi-prs:v1.0	577.3 MB	Sun et al. (2024)
PolyFun	chiomab/polyfun:v1.3	2.6 GB	Weissbrod et al. (2022)
SNPNET	chiomab/snpnet:v1.1	811.3 MB	Qian et al. (2020)
TL-PRS	chiomab/tl-prs:v1.2	635.2 MB	Zhao et al. (2022)

Repository Structure

Bench-PRS-Dock/
├─ README.md
├─ CITATION.cff

├─ docs/
│  └─ tool_pages/
│     └─ <tool_name>.md

├─ manifest/
│  ├─ prsdock_inventory.csv
│  └─ verification_log.csv

├─ benchmarking/
│  ├─ scripts/
│  │  ├─ capture_system_info.sh
│  │  ├─ setup/
│  │  │  ├─ measure_time_setup.sh
│  │  │  ├─ run_manual_setup.sh
│  │  │  └─ run_setup_docker.sh
│  │  ├─ execution/
│  │  │  ├─ measure_time_execution.sh
│  │  │  ├─ run_manual_execution.sh
│  │  │  └─ run_docker_execution.sh
│  │  └─ visualization/
│  │  │  ├─ plot_eff_ratio.R
│  │  │  └─ plot_error_barchart.R
│  │      
│  ├─ results/
│  │  ├─ setup_benchmarks/
│  │  │  ├─ docker/
│  │  │  │  └─ <tool>/
│  │  │  └─ manual/
│  │  │     └─ <tool>/
│  │  │
│  │  └─ execution_benchmarks/
│  │     ├─ docker/
│  │     │  └─ <tool>/
│  │     └─ manual/
│  │        └─ <tool>/
│  │
│  └─ figures/

Description:

• Essential: README.md
• Documentation: docs/ - Docker image inventory and Tool-specific pages
• Benchmarking Scripts: benchmarking/scripts/ - To reproduce the benchmarking results reported in this repository, run the scripts located in:
  • setup/ - Setup-time benchmarking scripts
  • execution/ - Execution-time benchmarking scripts
  • visualization/ - R scripts for plotting figures in manuscript
  • capture_system_info.sh - Environment metadata capture
• Benchmark Results: benchmarking/results/ - Organized setup and execution benchmarks for all tools (Docker vs manual)
• Figures: figures/ - Visuals used in README and manuscript

Cite Us

For citation and attribution information, please refer to CITATION.cff.

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