Easiest way I know to import a PEM format cert or key file into your Java keystore involves two steps.
1- Convert your PEM format certificate into DER format by using the following command syntax:
openssl x509 -outform der -in yourcert.pem -out yourcert.der
2- Import your resulting DER format certificate into your "cacerts" keystore using this syntax:
keytool -import -alias youralias -keystore cacerts -file yourcert.der
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