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I am normally a linux user and therefore I generated all my rsa-keypairs there. Now I have to use a windows system to do some work, and therefore need to get my repositories via ssh, but unfortunately pageant (which is somehow a have-to if you use tortoise) won't accept my ssh key-files as they are no ppk files.

Any solutions, as I must not generate new key-pairs?

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There is no such thing as "normal" keys. Neither format is more "normal" than the other.

You can convert the OpenSSL private keys to PuTTY .ppk format using PuTTYgen, which, like Pageant, is part of the PuTTY package. Use the "Import OpenSSH key" command, then "Save private key".

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