Git ​

Git is a version control system for tracking changes in files and coordinate work across your lab.

Depending on your lab's Data Safety Level (DSL), your data controller may allow access to hosted git repository managers such as GitLab, GitHub and Bitbucket.

Add remote Git repositories ​

Log into your lab home machine in HUNT Cloud and add the following lines to your SSH configuration file ~/.ssh/config:

TIP

If the SSH configuration file ~/.ssh/config does not exist, you have to create it.

How to access GitHub ​

Copy paste github configuration into SSH config on your lab machine:

ini
Host github.com
  Hostname ssh.github.com
  User git
  Port 443
  IdentityFile ~/.ssh/git

Then you should be able to clone using the git@github.com format.

See GitHub's documentation for more details.

How to access GitLab ​

ini
Host gitlab.com
  Hostname altssh.gitlab.com
  User git
  Port 443
  PreferredAuthentications publickey
  IdentityFile ~/.ssh/git

See GitLab's documentation for more details.

How to access Bitbucket ​

ini
Host bitbucket.org
  Hostname altssh.bitbucket.org
  User git
  Port 443
  IdentityFile ~/.ssh/git

See Atlassian's documentation for more details.

Set up ​

Generate a new SSH key for the connection ​

From your lab home machine:

  • Generate a new key to be used with your git-repository manager: ssh-keygen -f ~/.ssh/git. You may change the key-name, git in this example, to whatever you like.

  • View the content of your new public key, and copy the content to your clipboard: cat ~/.ssh/git.pub

Add your new key ​

Test your connection ​

  • In GitHub, test if you are allowed to connect to GitHub from port 443 (ssh -T -p 443 git@ssh.github.com -i ~/.ssh/git). GitHub should greet you if successful, if not, you need to talk to your lab technical contact to learn about the network restrictions of your lab.
  • In GitLab, test if you are allowed to connect to GitLab from port 443 (ssh -T -p 443 git@altssh.gitlab.com -i ~/.ssh/git). GitLab should greet you if successful, if not, you need to talk to your lab technical contact to learn about the network restrictions of your lab.
  • In GitHub, test your new connection with ssh -T git@github.com. You should see a greeting.
  • In GitLab, test your new connection with ssh -T git@gitlab.com. You should see a greeting.

Troubleshooting ​

Connection does not work ​

You may have noticed that things do not work when you attempt to use the regular git@github.com: format, for example:

bash
git clone git@github.com:samtools/htslib.git

This is due to our restriction on port 22 which is used for the git clone command.

The above guides demonstrate how you can use a different port, such as port 443, for this communication.