I have this in an ActiveMQ config:
Based on the answers above, here is how to create a brand new keystore for your java based web server, out of an independently created Comodo cert and private key using keytool (requires JDK 1.6+)
Issue this command and at the password prompt enter somepass - 'server.crt' is your server's cert and 'server.key' is the private key you used for issuing the CSR:
openssl pkcs12 -export -in server.crt -inkey server.key -out server.p12 -name www.yourdomain.com -CAfile AddTrustExternalCARoot.crt -caname "AddTrust External CA Root"
Then use keytool to convert the p12 keystore into a jks keystore:
keytool -importkeystore -deststorepass somepass -destkeypass somepass -destkeystore keystore.jks -srckeystore server.p12 -srcstoretype PKCS12 -srcstorepass somepass
Then import the other two root/intermediate certs you received from Comodo:
Import COMODORSAAddTrustCA.crt:
keytool -import -trustcacerts -alias cert1 -file COMODORSAAddTrustCA.crt -keystore keystore.jks
Import COMODORSADomainValidationSecureServerCA.crt:
keytool -import -trustcacerts -alias cert2 -file COMODORSADomainValidationSecureServerCA.crt -keystore keystore.jks