From your list of tools:
Jenkins and Github have apt/yum repositories you can use to install and upgrade.
For Atlassian products, best up to date information about repositories I can found is This ShipIt experiment and it seems unlikely to change from this forum post
But:
Basically, continuous deployment to production without human interaction for these tools.
You should NOT, this is likely to break your workflow and eventually corrupt your datas and repositories, an update to critical systems like CI/CD support must have to be controlled to avoid breaking something for hours or days.
Now if you really want something automated to handle the installation and configuration of your tools, you can try a Configuration Management System like Chef/Puppet/Ansible/Salt.
For Chef I know better, there's cookbooks for Jira and Confluence maintained.
For the rest you'll be on your own writing the bits to deploy and configure.