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If you want to create a certificate chain to be used in PEM format directly the order of the certificates needs to be changed:
cat intermediate/certs/client1.cert.pem intermediate/certs/intermediate.cert.pem certs/ca.cert.pem> ../keystores/new-client1.chain.pem;

Importing pem files to jks

Code Block
openssl pkcs12 -export -in user.pem -inkey user.key -certfile user.pem -out testkeystore.p12
keytool -importkeystore -srckeystore testkeystore.p12 -srcstoretype pkcs12 -destkeystore wso2carbon.jks -deststoretype JKS

Import the certificate chain and the private key in to a PKCS12 container

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