Upgrading JIRA 5.2.x & Confluence 4.3.x

There is always time during the holidays to do things that you are pushing in front of you. One of such a thing that I pushed for few months was upgrade of JIRA 5.2.2 and Confluence 4.3.5 to latest versions (6.1.1 and 5.4.1 respectively).


I noticed during the upgrade process few glitches. So I made a short tutorial that will cover it.

Whole tutorial is based on the JIRA and Confluence installation that I made a year ago. Basically its is a standalone JIRA / Confluence installation that is behind Apache with SSL. Operating system is CentOS 6.3.


  • JIRA “standalone” installation
  • Confluence “standalone” installation
  • CentOS 6.3
  • Apache >= 2.2 (with mod_ssl & mod_proxy installed)
  • Mysql >= 5.1
  • ssh root access to server
  • All JIRA / Confluence plugins are up to date

Basically I didn’t change anything in configuration from the time I installed it. I only installed new JIRA Agile (GreenHopper) plugin.

Upgrading process


1. Stop JIRA instance
2. Backup JIRA home folder (/opt/atlassian/jira-data) and MySQL DB user for JIRA

Use your favorite tool. I highly recommend to do it. During the upgrading process I made few mistakes and I was happy to have backups to return to previous state.

3. Backup your configuration files
  • /opt/atlassian/jira/5.2.2/conf/server.xml
  • /opt/atlassian/jira/5.2.2/bin/setenv.sh
4. Set JIRA home to jira-application.properties
5. Download JIRA Installer

Download latest JIRA installer from here.

6. Follow the steps from upgrade guide

Follow all steps from the JIRA upgrade guide. Installer is pretty straightforward. It asks few questions but I think that there is no place where you can make a mistake. After the installer is finished it will run JIRA on http://localhost:8080/.

I was running installer as a root so I highly recommend to run it as a jira user or after the installer is finished to change the owner of the JIRA folders:

7. Change configuration from your backup files

You will need to change back setenv.sh (if you changed parameters) and more importantly server.xml:

8. Start JIRA instance with updated configuration

After the JIRA instance is started you will be able to access it on the same adress as before (i.e. https://jira.example.com). After I finished this step I found out that all my issues were gone 🙁

So obviously I panicked and downgraded JIRA. After few another attempts I found out where I made a mistake. I forgot to update all the plugins.

9. Update all your plugins

Go to JIRA administration and update all the plugins that are outdated. This is really crucial if you have JIRA Agile installed.

After I updated all plugins (especially JIRA Agile) all my issues / tasks / … were back.



1. Stop Confluece instance
2. Backup Confluence home folder (/opt/atlassian/confluence-data) and MySQL DB user for confluence
3. Backup your configuration files
  • /opt/atlassian/confluence/4.3.5/confluence/WEB-INF/classes/confluence-init.properties
  • /opt/atlassian/confluence/4.3.5/conf/server.xml
  • /opt/atlassian/confluence/4.3.5/bin/setenv.sh
4. Download Confluence Installer

Download latest Confluence installer from here.

5. Follow the steps from upgrade guide

Follow all steps from the Confluence upgrade guide. After the installer is finished it will run Confluence on http://localhost:8090/. Stop the confluence instance.

Change the owner of the Confluence folders:

6. Change configuration from your backup files

Change back setenv.sh (if you changed parameters) and  server.xml:

7. Start Confluence instance with updated configuration
9. Update all your plugins

I didn’t experienced any data loss with this upgrade. Confluence upgrade was more painless than JIRA upgrade.


There is one disadvantage of this guide. The JIRA and Confluence will be installed on the same place then the previous installation. So if you have version number in your path then it will be a little bit confusing for the “next generations”.

If you have any questions or need help with something feel free to ask.



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