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Best practice in science is to use version control when doing any programming. To use Git version control, go to the root directory of your folder of interest and create a new repository with:

git init

You can read more about this workflow with the GitHub interactive tutorial and the Software Carpentry lesson.

git push gives fatal: HTTP request failed

GitHub recommends using HTTPs when pushing to their repo. However on the HPC Cluster, this returns an error:

$ git push -u origin master
error: The requested URL returned error: 403 Forbidden while accessing https://github.com/<username>/<repo>.git/info/refs

fatal: HTTP request failed

To get around this, one should instead use git@ instead of https:// and : instead of the trailing / in github.com. You can do both these things but just running this command in the root of your git repo:

sed -ie '/url[ \t]*=[ \t]*/s/https:\/

...

\/github.com\//git@github.com:/' .git/config
grep url .git/config  # See the change

Alternatively, when cloning the repository just use ssl instead:

$ git clone git@github.com:<user>/<repository>.git

git push gives Permission denied (publickey)

$ git push -u origin master
Warning: Permanently added 'github.com,192.30.252.130' (RSA) to the list of known hosts.
Permission denied (publickey).
fatal: The remote end hung up unexpectedly

Follow the GitHub instructions to setup your ssh keys and add the public key to your GitHub repository.