Please follow the below steps to install the certificate on the tomcat server
You might receive a single file or a bunch of files from the SSL vendor. Certificates can be of different extensions (such as crt, cer, p7b, txt, etc.) but the commands remain the same.
Steps to perform this activity will be available on the site of respective certifying authority's website. However you can use the below standard commands to perform the same. Considering the files you have received are root.crt, inter.crt and mydomain.crt
keytool -import -trustcacerts -alias root -file root.crt -keystore your_site_name.keystore
keytool -import -trustcacerts -alias inter -file inter.crt -keystore your_site_name.keystore
Note: In case of multiple intermediate certificates use the same command with different alias names (i.e inter1, inter2, etc.)
keytool -import -trustcacerts -alias tomcat -file mydomain.crt -keystore your_site_name.keystore