Can I assume that you are deploying your custom application on top of a lamp stack? If so, please check this guide as it might be helpful.
If you followed that guide, in order to access your application at domain.com/store instead of domain.com/myapp you need to change the
alias directive in the file /opt/bitnami/apps/myapp/conf/httpd-prefix.conf. The guide suggests:
Alias /myapp/ "/opt/bitnami/apps/myapp/htdocs/"
Alias /myapp "/opt/bitnami/apps/myapp/htdocs/"
but you should use:
Alias /store/ "/opt/bitnami/apps/myapp/htdocs/"
Alias /store "/opt/bitnami/apps/myapp/htdocs/"
I hope it helps,