Trying to fix basic functionality again.

DOCKER_README.md

@@ -0,0 +1,104 @@
+# Synthea Disease Module Generator
+
+This package provides Docker and Nextflow integrations for Synthea to:
+1. Generate disease modules using Claude AI
+2. Look up existing disease modules by name
+3. Run both functions in a containerized environment
+
+## Prerequisites
+
+- Docker
+- Nextflow (will be installed automatically if not present)
+- Anthropic API key (Claude)
+
+## Setup
+
+1. **Clone the repository and navigate to it**:
+   ```bash
+   git clone https://github.com/yourusername/synthea-alldiseases.git
+   cd synthea-alldiseases
+   ```
+
+2. **Set your Anthropic API key**:
+   
+   Option 1: Environment variable:
+   ```bash
+   export ANTHROPIC_API_KEY=your_api_key_here
+   ```
+   
+   Option 2: You'll be prompted to enter it when you run the script if it's not set.
+
+## Usage
+
+### Running the Module Generator
+
+Use the provided script:
+
+```bash
+./run_module_generator.sh --disease_name "Disease Name Here"
+```
+
+Additional options:
+```
+--modules_dir      Path to modules directory (default: src/main/resources/modules)
+--output_dir       Output directory for generated modules (default: output)
+--help             Show help information
+```
+
+### Examples
+
+Generate a module for Multiple Sclerosis:
+```bash
+./run_module_generator.sh --disease_name "Multiple Sclerosis"
+```
+
+Generate a module and save it to a custom location:
+```bash
+./run_module_generator.sh --disease_name "Parkinson's Disease" --output_dir ./custom_modules
+```
+
+### Using Docker Compose (Alternative)
+
+You can also run the entire environment using Docker Compose:
+
+```bash
+docker-compose up -d
+docker-compose exec synthea bash
+```
+
+Once inside the container:
+```bash
+./run_module_generator.sh --disease_name "Disease Name"
+```
+
+## How It Works
+
+The pipeline follows these steps:
+
+1. Check if a module already exists for the disease
+2. Look up the disease in the disease list for ICD-10 codes and other metadata
+3. If the module exists, copy it to the output directory
+4. If the module doesn't exist, generate it using Claude AI
+5. Save the module to the specified output directory
+6. For new modules, also update the modules directory
+
+## Modifying the Docker Configuration
+
+If you need to customize the Docker environment:
+
+1. Edit `Dockerfile` to add dependencies or change the configuration
+2. Rebuild the Docker image:
+   ```bash
+   docker build -t synthea-module-generator .
+   ```
+
+## Troubleshooting
+
+- **API Key Issues**: Ensure your ANTHROPIC_API_KEY is set correctly
+- **Docker Permission Issues**: You may need to run Docker commands with sudo
+- **Memory Issues**: For large modules, you may need to increase Docker's memory allocation
+- **Pipeline Errors**: Check execution_report.html for detailed error information
+
+## License
+
+This project is licensed under the same license as Synthea.