Normally a git clone would be via HTTPS, with prompts for GitHub credentials:

$ git clone https://github.com/MyOrg/MyRepo.git

To automate GitHub pull/push requests, need to use SSH w/ key authentication.

Start by setting up a ~/.gitconfig file and specify your primary GitHub e-mail address:

[core]
 editor = nano
[user]
 name = Johnny Five
 email = johnny5@shortcircuit.com

Upload the SSH public key to GitHub.  This will be ~/.ssh/id_rsa.pub by default.  To specify a different private key for GitHub,  add an entry in ~/.ssh/config like this:

Hostname github.com
User git
IdentityFile ~/.ssh/mySpecialGitHubKey.pem

Then do clone via SSH.  Note “git” should be username, not GitHub username.

$ git clone ssh://git@github.com/MyOrg/MyRepo.git