PMET Shiny App

www.PMET.online

PMET (Promoter Motif Enrichment Tool) identifies cooperative transcription factor (TF) activity by evaluating both homotypic and heterotypic motif combinations across promoter sets.

Project Structure

pmet-shiny-app/
├── app.R                         # Shiny entry point
├── R/                            # Shiny application code (UI, Server, modules, utils)
├── data/
│   ├── configure/                # Runtime config (email, CPU, nginx link)
│   ├── demo_*/                   # Demo datasets
│   ├── indexing/                 # Pre-computed motif hits (21 species, downloaded at build)
│   ├── genome_n_annotation.json
│   └── motif_db_meta.json
├── scripts/
│   ├── pmet/                     # Core PMET analysis scripts (shell + Python)
│   └── download_pmet_indexing.sh # Downloads indexing data from Zenodo
├── www/                          # Frontend assets (CSS, JS, images)
├── config/                       # Runtime config (mounted as volumes)
│   ├── nginx.conf                # Nginx results file server config
│   └── shiny-server.conf         # Shiny Server config (timeouts, etc.)
├── Dockerfile
├── docker-compose.yml
├── pmet.sh                       # Docker management script
├── .dockerignore
└── .env.example                  # ** THE ONLY FILE to edit for deployment **

Quick Start (Docker)

1. Configure

cp .env.example .env
# Edit .env — ports, CPU threads, SMTP credentials, server hostname.
# That's the ONLY file you need to touch.

2. Build & Run

./pmet.sh build
./pmet.sh start

Or use the interactive menu: ./pmet.sh

This will:

1. Build the Shiny image (install R packages, compile PMET, download indexing data)
2. Start Shiny Server on port 3838
3. Start Nginx results server on port 3080

3. Access

Service	URL
Shiny App	http://localhost:3838/pmet/
Results (Nginx)	http://localhost:3080/results/

Configuration

All settings are in .env:

SHINY_PORT=3838                        # Shiny host port
NGINX_PORT=3080                        # Nginx host port
NGINX_HOST=your-server.example.com     # Public hostname (for email links)
PMET_NCPU=4                            # CPU threads
SMTP_HOST=smtp.gmail.com               # Leave empty to skip email
SMTP_PORT=465
SMTP_USERNAME=you@gmail.com
SMTP_PASSWORD=app-password
SMTP_FROM=you@gmail.com

Then ./pmet.sh restart.

pmet.sh commands: build, rebuild, start, stop, restart, logs, logs-app, shell, status, clean, purge.

Architecture

┌──────────┐     ┌──────────┐
│  Shiny   │────▶│  Results  │◀──── Nginx (:80 internal, NGINX_PORT on host)
│  Server  │     │  Volume   │      (file download)
│  (:3838) │     └──────────┘
└──────────┘
└──────────┘
     User submits task
       → PMET analysis runs
         → Results saved to shared volume
           → Email sent with download link

Pre-computed Indexing Data

21 plant species with motif hits from 5 databases are downloaded during Docker build from Zenodo.

To add new species or databases, copy indexing results to data/indexing/. The app auto-detects new additions.

PMET Workflow