When using the Linux installer for JIRA, the bundled JIRA Configuration Tool does not start, unless you have a local Java installation properly configured on your system. This is problematic, as the Linux installer does bundle Java, but config.sh never picks up those variables.
You will notice the following error on the console:
In addition, the configuration tool is not launched.
Note: If you have a working java command, the tool may still launch while seeing the above warning.
This is recommended anyways, as generally new Java versions bring security and performance improvements.
You can invoke setenv.sh from the same bin directory where config.sh can be found. This should set the bundled Java's environment variables. Best is to invoke setenv.sh in config.sh.