Import certificate and key into java key store using keytool

If you have the certificate and key in pkcs12 format you can directly import it into an existing java key store:

keytool -importkeystore -srckeystore server.p12 -srcstoretype pkcs12 -destkeystore server.jks -deststoretype jks

If you have it in PEM you can convert it to pkcs12 first:
cat server_key.pem server_cert.pem server_cacert.pem > server.pem
openssl pkcs12 -export -out server.p12 -in server.pem