MCP Server Configuration Examples

This guide provides practical configuration examples and best practices for setting up MCP servers with Pylee. Each example includes security considerations and common customizations.

Configuration File Structure

MCP servers are configured through JSON configuration files. The basic structure includes server definitions with command execution parameters:

{
  "mcpServers": {
    "server-name": {
      "command": "executable",
      "args": ["argument1", "argument2"],
      "env": {
        "VARIABLE": "value"
      },
      "cwd": "/working/directory"
    }
  }
}

File System Server Configurations

Basic File Access

{
  "mcpServers": {
    "filesystem": {
      "command": "npx",
      "args": [
        "-y",
        "@modelcontextprotocol/server-filesystem",
        "/Users/username/Documents"
      ]
    }
  }
}

Restricted File Access

{
  "mcpServers": {
    "secure-filesystem": {
      "command": "npx",
      "args": [
        "-y",
        "@modelcontextprotocol/server-filesystem",
        "/opt/app/data",
        "--allowed-extensions",
        ".txt,.md,.json",
        "--max-file-size",
        "10MB",
        "--read-only"
      ],
      "env": {
        "NODE_ENV": "production"
      }
    }
  }
}

Multiple Directory Access

{
  "mcpServers": {
    "docs-filesystem": {
      "command": "npx",
      "args": [
        "-y",
        "@modelcontextprotocol/server-filesystem",
        "/Users/username/Documents"
      ]
    },
    "projects-filesystem": {
      "command": "npx",
      "args": [
        "-y",
        "@modelcontextprotocol/server-filesystem",
        "/Users/username/Projects"
      ]
    }
  }
}

Database Server Configurations

PostgreSQL Server

{
  "mcpServers": {
    "postgres": {
      "command": "uvx",
      "args": [
        "mcp-server-postgres",
        "--host", "localhost",
        "--port", "5432",
        "--database", "myapp"
      ],
      "env": {
        "POSTGRES_USER": "readonly_user",
        "POSTGRES_PASSWORD": "secure_password",
        "POSTGRES_SSL_MODE": "require"
      }
    }
  }
}

SQLite Server

{
  "mcpServers": {
    "sqlite": {
      "command": "python",
      "args": [
        "-m", "mcp_server_sqlite",
        "/path/to/database.db",
        "--read-only"
      ]
    }
  }
}

MySQL Server

{
  "mcpServers": {
    "mysql": {
      "command": "uvx",
      "args": [
        "mcp-server-mysql",
        "--host", "localhost",
        "--port", "3306",
        "--database", "production_db"
      ],
      "env": {
        "MYSQL_USER": "mcp_reader",
        "MYSQL_PASSWORD": "${MYSQL_PASSWORD}",
        "MYSQL_SSL_CA": "/etc/ssl/certs/ca-certificates.crt"
      }
    }
  }
}

API Integration Servers

GitHub Server

{
  "mcpServers": {
    "github": {
      "command": "npx",
      "args": [
        "-y",
        "@modelcontextprotocol/server-github"
      ],
      "env": {
        "GITHUB_PERSONAL_ACCESS_TOKEN": "${GITHUB_TOKEN}",
        "GITHUB_API_BASE_URL": "https://api.github.com"
      }
    }
  }
}

REST API Server

{
  "mcpServers": {
    "api-server": {
      "command": "node",
      "args": ["/path/to/custom-api-server.js"],
      "env": {
        "API_BASE_URL": "https://api.example.com",
        "API_KEY": "${API_KEY}",
        "API_TIMEOUT": "30000",
        "RATE_LIMIT": "100"
      }
    }
  }
}

Slack Integration

{
  "mcpServers": {
    "slack": {
      "command": "uvx",
      "args": ["mcp-server-slack"],
      "env": {
        "SLACK_BOT_TOKEN": "${SLACK_BOT_TOKEN}",
        "SLACK_APP_TOKEN": "${SLACK_APP_TOKEN}",
        "SLACK_WORKSPACE": "your-workspace"
      }
    }
  }
}

Development vs Production Configurations

Development Configuration

{
  "mcpServers": {
    "dev-filesystem": {
      "command": "npx",
      "args": [
        "-y",
        "@modelcontextprotocol/server-filesystem",
        "/Users/dev/workspace",
        "--allow-symlinks",
        "--verbose"
      ],
      "env": {
        "NODE_ENV": "development",
        "DEBUG": "mcp:*"
      }
    },
    "dev-database": {
      "command": "uvx",
      "args": [
        "mcp-server-postgres",
        "--host", "localhost",
        "--database", "myapp_dev"
      ],
      "env": {
        "POSTGRES_USER": "dev_user",
        "POSTGRES_PASSWORD": "dev_password"
      }
    }
  }
}

Production Configuration

{
  "mcpServers": {
    "prod-filesystem": {
      "command": "npx",
      "args": [
        "-y",
        "@modelcontextprotocol/server-filesystem",
        "/opt/app/data",
        "--read-only",
        "--max-file-size", "5MB",
        "--allowed-extensions", ".txt,.json,.csv"
      ],
      "env": {
        "NODE_ENV": "production",
        "LOG_LEVEL": "error"
      }
    },
    "prod-database": {
      "command": "uvx",
      "args": [
        "mcp-server-postgres",
        "--host", "${DB_HOST}",
        "--port", "${DB_PORT}",
        "--database", "${DB_NAME}",
        "--connection-pool-size", "10",
        "--read-only"
      ],
      "env": {
        "POSTGRES_USER": "${DB_USER}",
        "POSTGRES_PASSWORD": "${DB_PASSWORD}",
        "POSTGRES_SSL_MODE": "require",
        "POSTGRES_SSL_CERT": "/etc/ssl/client-cert.pem",
        "POSTGRES_SSL_KEY": "/etc/ssl/client-key.pem"
      }
    }
  }
}

Security-Focused Configurations

Sandboxed File Server

{
  "mcpServers": {
    "sandboxed-fs": {
      "command": "docker",
      "args": [
        "run", "--rm",
        "--user", "1000:1000",
        "--read-only",
        "--tmpfs", "/tmp",
        "--volume", "/opt/app/data:/data:ro",
        "--network", "none",
        "mcp-filesystem-server:latest",
        "/data"
      ]
    }
  }
}

Authenticated API Server

{
  "mcpServers": {
    "secure-api": {
      "command": "node",
      "args": ["/opt/mcp/secure-api-server.js"],
      "env": {
        "API_BASE_URL": "https://api.internal.company.com",
        "CLIENT_ID": "${OAUTH_CLIENT_ID}",
        "CLIENT_SECRET": "${OAUTH_CLIENT_SECRET}",
        "REFRESH_TOKEN": "${OAUTH_REFRESH_TOKEN}",
        "TOKEN_ENDPOINT": "https://auth.company.com/oauth/token",
        "ALLOWED_SCOPES": "read:data,read:users"
      }
    }
  }
}

Network-Isolated Database

{
  "mcpServers": {
    "isolated-db": {
      "command": "docker",
      "args": [
        "run", "--rm",
        "--network", "mcp-internal",
        "--env-file", "/etc/mcp/db.env",
        "mcp-postgres-server:latest"
      ]
    }
  }
}

Custom Server Configurations

Python Custom Server

{
  "mcpServers": {
    "custom-python": {
      "command": "python",
      "args": [
        "-m", "my_custom_server",
        "--config", "/etc/mcp/custom-config.json"
      ],
      "cwd": "/opt/my-mcp-server",
      "env": {
        "PYTHONPATH": "/opt/my-mcp-server",
        "CONFIG_PATH": "/etc/mcp/custom-config.json",
        "LOG_LEVEL": "INFO"
      }
    }
  }
}

Node.js Custom Server

{
  "mcpServers": {
    "custom-node": {
      "command": "node",
      "args": [
        "dist/server.js",
        "--port", "3001",
        "--host", "127.0.0.1"
      ],
      "cwd": "/opt/custom-mcp-server",
      "env": {
        "NODE_ENV": "production",
        "PORT": "3001",
        "HOST": "127.0.0.1",
        "CONFIG_FILE": "/etc/mcp/server-config.json"
      }
    }
  }
}

Environment-Specific Examples

Docker Compose Integration

{
  "mcpServers": {
    "compose-db": {
      "command": "docker",
      "args": [
        "compose",
        "-f", "/opt/mcp/docker-compose.yml",
        "exec", "-T", "postgres",
        "mcp-server-postgres"
      ],
      "cwd": "/opt/mcp",
      "env": {
        "COMPOSE_PROJECT_NAME": "mcp-stack"
      }
    }
  }
}

Kubernetes Pod Execution

{
  "mcpServers": {
    "k8s-server": {
      "command": "kubectl",
      "args": [
        "exec", "-n", "mcp-namespace",
        "deployment/mcp-server",
        "--", "mcp-server-postgres"
      ],
      "env": {
        "KUBECONFIG": "/etc/kubernetes/admin.conf"
      }
    }
  }
}

Advanced Configuration Patterns

Multi-Environment Setup

{
  "mcpServers": {
    "primary-db": {
      "command": "uvx",
      "args": [
        "mcp-server-postgres",
        "--host", "${PRIMARY_DB_HOST}",
        "--database", "${PRIMARY_DB_NAME}"
      ],
      "env": {
        "POSTGRES_USER": "${PRIMARY_DB_USER}",
        "POSTGRES_PASSWORD": "${PRIMARY_DB_PASSWORD}"
      }
    },
    "analytics-db": {
      "command": "uvx",
      "args": [
        "mcp-server-postgres",
        "--host", "${ANALYTICS_DB_HOST}",
        "--database", "${ANALYTICS_DB_NAME}",
        "--read-only"
      ],
      "env": {
        "POSTGRES_USER": "${ANALYTICS_DB_USER}",
        "POSTGRES_PASSWORD": "${ANALYTICS_DB_PASSWORD}"
      }
    }
  }
}

Load-Balanced Configuration

{
  "mcpServers": {
    "api-primary": {
      "command": "node",
      "args": ["/opt/api-server/server.js"],
      "env": {
        "API_ENDPOINT": "https://api1.example.com",
        "INSTANCE_ID": "primary"
      }
    },
    "api-secondary": {
      "command": "node",
      "args": ["/opt/api-server/server.js"],
      "env": {
        "API_ENDPOINT": "https://api2.example.com",
        "INSTANCE_ID": "secondary"
      }
    }
  }
}

Configuration Management

Environment Variables File

Create a .env file for your configuration:

# Database Configuration
DB_HOST=localhost
DB_PORT=5432
DB_NAME=production
DB_USER=mcp_user
DB_PASSWORD=secure_password

# API Configuration
API_KEY=your-secret-api-key
GITHUB_TOKEN=your-github-token

# File System Configuration
DATA_DIRECTORY=/opt/app/data
LOG_DIRECTORY=/var/log/mcp

# Security Configuration
SSL_CERT_PATH=/etc/ssl/certs/server.crt
SSL_KEY_PATH=/etc/ssl/private/server.key

Configuration Validation

{
  "mcpServers": {
    "validated-server": {
      "command": "node",
      "args": [
        "/opt/mcp/server.js",
        "--validate-config"
      ],
      "env": {
        "CONFIG_SCHEMA": "/opt/mcp/schema.json",
        "STRICT_VALIDATION": "true"
      }
    }
  }
}

Monitoring and Logging

Enhanced Logging Configuration

{
  "mcpServers": {
    "monitored-server": {
      "command": "node",
      "args": ["/opt/server.js"],
      "env": {
        "LOG_LEVEL": "info",
        "LOG_FORMAT": "json",
        "LOG_FILE": "/var/log/mcp/server.log",
        "METRICS_ENABLED": "true",
        "METRICS_PORT": "9090"
      }
    }
  }
}

Health Check Configuration

{
  "mcpServers": {
    "health-checked-server": {
      "command": "node",
      "args": [
        "/opt/server.js",
        "--health-check-port", "8080",
        "--health-check-path", "/health"
      ],
      "env": {
        "HEALTH_CHECK_INTERVAL": "30000",
        "SHUTDOWN_TIMEOUT": "10000"
      }
    }
  }
}

Best Practices

Security Best Practices

Use environment variables for sensitive data
Enable read-only mode when possible
Restrict file access to specific directories
Use strong authentication for database connections
Enable SSL/TLS for network connections
Run servers with minimal privileges
Use container isolation when available

Performance Best Practices

Configure connection pooling for databases
Set appropriate timeouts for network operations
Enable caching when beneficial
Monitor resource usage and set limits
Use efficient serialization formats
Optimize query patterns for data access

Operational Best Practices

Use descriptive server names
Document configuration choices
Implement proper logging
Set up health checks
Plan for graceful shutdowns
Version your configurations
Test configurations thoroughly

Configuration File Locations

System-wide Configuration

# Linux/macOS
/etc/mcp/config.json
/usr/local/etc/mcp/config.json

# Windows
C:\ProgramData\MCP\config.json

User-specific Configuration

# Linux/macOS
~/.mcp/config.json
~/.config/mcp/config.json

# Windows
%APPDATA%\MCP\config.json

Project-specific Configuration

# In your project directory
./mcp.config.json
./.mcp/config.json

Troubleshooting Configuration Issues

Common Problems

Invalid JSON syntax - Use a JSON validator
Missing environment variables - Check variable names and values
Incorrect file paths - Verify paths exist and are accessible
Permission issues - Check file and directory permissions
Port conflicts - Ensure ports are available
Command not found - Verify executables are in PATH

Debug Configuration

{
  "mcpServers": {
    "debug-server": {
      "command": "node",
      "args": ["/opt/server.js", "--debug"],
      "env": {
        "DEBUG": "mcp:*",
        "NODE_ENV": "development",
        "VERBOSE": "true"
      }
    }
  }
}

For more information, see:

Get Started

Using Pylee

Understanding Pylee

MCP Servers

Support

​MCP Server Configuration Examples

​Configuration File Structure

​File System Server Configurations

​Basic File Access

​Restricted File Access

​Multiple Directory Access

​Database Server Configurations

​PostgreSQL Server

​SQLite Server

​MySQL Server

​API Integration Servers

​GitHub Server

​REST API Server

​Slack Integration

​Development vs Production Configurations

​Development Configuration

​Production Configuration

​Security-Focused Configurations

​Sandboxed File Server

​Authenticated API Server

​Network-Isolated Database

​Custom Server Configurations

​Python Custom Server

​Node.js Custom Server

​Environment-Specific Examples

​Docker Compose Integration

​Kubernetes Pod Execution

​Advanced Configuration Patterns

​Multi-Environment Setup

​Load-Balanced Configuration

​Configuration Management

​Environment Variables File

​Configuration Validation

​Monitoring and Logging

​Enhanced Logging Configuration

​Health Check Configuration

​Best Practices

​Security Best Practices

​Performance Best Practices

​Operational Best Practices

​Configuration File Locations

​System-wide Configuration

​User-specific Configuration

​Project-specific Configuration

​Troubleshooting Configuration Issues

​Common Problems

​Debug Configuration