To generate a CSR for StartSSL whilst using a Linux computer, simply use the following command:
MY_SITE="www.domain.com" openssl req -new -newkey \ rsa:2048 \ -keyout $MY_SITE.key \ -out $MY_SITE.csr
Copy and paste the contents of the newly generated
.csr file into the web form and select "PKI" before entering the password you used to encrypt the CSR.
Copy the private key given to you by StartCom, and replace the contents of your
.key file with it.
Now decrypt the private key file with:
MY_SITE="www.domain.com" openssl rsa \ -in $MY_SITE.key \ -out $MY_SITE.decrypted.key
Now download the certificate bundle from StartCom. You will need the certificates provided by the site, along with the decrypted file in your Apache/Nginx configuration.