The documentation says JIRA needs JAVA and implies it needs to be installed on the machine. However, there is a jre directory under the Atlassian/jira folder and JIRA works fine. However the wizard for database connection doesn't work for me. I'm going to upgrade shortly. do I need to install the JAVA JRE from Oracle?
JIRA 4.4+ comes with embedded Java when you use the installer. The docs are not entirely lying - you do need it... but the installer will do it for you.
Do you have the right JDBC jar installed for your database?
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