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Is this possible? If so how?

The server that I want to copy a ssh key to, only allows authentication with a keyfile rather than username and password.

I am able to login to the server with ssh -i ...

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I just checked and ssh-copy-id supports the -i [identity_file] option just like you would use it for ssh.

If that doesn't work for you, you can see if your version can do this option:

-o ssh -o IdentityFile ~/backups/.ssh/id_dsa

Next you could try updating your version of ssh-copy-id. Lastly, you can simply copy/paste the public key after you ssh in.

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If you have your ssh-agent running and the old key with which you can already log in is loaded it should work like this:

ssh-copy-id -i new-key user@host

or

ssh-copy-id -i new-key host-alias-from-config

I had to add -f but I am not sure if that was an error on my part.

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