Server Certification

Checking Passphrase for private key:  openssl rsa -check -in keyfilename
Changing Passphrase: openssl rsa -des3 -in keyfilename -out newkeyfilename

Installing or trusting certificates:
Extensions .crt, .pem and .cer are interchangeable, just change the file name extension, they have the same form. Try this:

sudo cp mycert.cer /usr/share/ca-certificates/mycert.pem
sudo dpkg-reconfigure ca-certificates
sudo update-ca-certificates

Getting the RSA public and private key from conf file.

openssl req -new -keyout userkey.pem -out usercert_request.pem -config agnis-dev.conf

Exporting signed public key file (.pem) to .p12

openssl pkcs12 -export -out dev-JagritiInnovations-11171-usercert.p12 -inkey userkey.pem -in dev-JagritiInnovations-11171-usercert.pem

Exporting signed public key file (.p12) to .jks

keytool -importkeystore -srckeystore dev-JagritiInnovations-11171-usercert.p12 -destkeystore dev-JagritiInnovations-11171-usercert.jks -srcstoretype PKCS12 -deststoretype JKS