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To run a cron job that connects to an RDS database from an Elastic Beanstalk application, you can use a .ebextensions configuration file.
Place a file such as 01_cronjob.config in a .ebextensions directory at the root of your application source code.
The file should contain:
files:
"/etc/cron.d/cronjob" :
mode: "000644"
owner: root
group: root
content: |
*/5 * * * * root cd /var/app/current && ./script.sh >> /var/log/cronjob.log 2>&1
This will run the script.sh file inside your application directory every 5 minutes.
The script can then connect to the RDS database using the RDS_HOSTNAME, RDS_USERNAME, RDS_PASSWORD environment variables provided by Elastic Beanstalk.
Make sure to grant access to the security group of your EC2 instances to connect to the RDS port from its IP range.