From your application create a source bundle and you can refer the below link:
http://docs.aws.amazon.com/elasticbeanstalk/latest/dg/applications-sourcebundle.html
Create a new version from your application using AWS CLI and deploy it in an application environment. The CLI documentation for EBS here.
For creating source bundle:
zip MyCodeBundle.zip <source files>
For uploading it to S3:
aws s3 cp MyCodeBundle.zip s3://a-bucket-where-you-store-your-source-bundles/
Refer here for creating a new application using the uploaded source bundle.
aws elasticbeanstalk create-application-version --application-name YourEBSAppName --version-label YourVersionLabel --source-bundle S3Bucket="a-bucket-where-you-store-your-source-bundles",S3Key="MyCodeBundle.zip"
Update the environment to use the version
aws elasticbeanstalk create-application-version --application-name YourEBSAppName --version-label YourVersionLabel --source-bundle S3Bucket="a-bucket-where-you-store-your-source-bundles",S3Key="MyCodeBundle.zip"
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You can also refer elastic beanstalk.