ran config.sh

[HENRY]

If I configure only with http, it works fine. If I tried with http/HTTPS,  it complains as follows

Setup: Tomcat is misconfigured

The server.xml file is missing parameters needed by Jira to handle requests that contain special characters.

Can you please discuss with me this issue.

[Andy Heinzer]

I'm suspecting your using a version of Jira 7.12.0 or newer. If so there is an update to Tomcat here that requires your server.xml to contain some additional parameters to make Jira work.  Details are in Jira Software 7.12 upgrade notes

What's the problem?

The Apache Tomcat server is filtering out requests that contain special characters, making them fail. That's because Tomcat is using a different encoding and URI standard than most browsers (details here). The problem is most visible when searching with JQL as you’d use a number of special characters when doing it (e.g. []<>), but it can also affect other pages in Jira. 

Steps to take:

To solve the problem, edit the server.xml file, and add properties that make Tomcat accept special characters in the requests.

1. Go to <Jira-installation-directory>/conf, and edit the server.xml file.
2. Find all connectors your application is using. Just search for Connector in the file, or look at the example below.

3. Add relaxedPathChars="[]|" relaxedQueryChars="[]|{}^\`"<>" to the connector properties in server.xml. For example:

   <Connector port="8080" relaxedPathChars="[]|" relaxedQueryChars="[]|{}^&#x5c;&#x60;&quot;&lt;&gt;" maxThreads="150" minSpareThreads="25" connectionTimeout="20000" enableLookups="false" maxHttpHeaderSize="8192" protocol="HTTP/1.1" useBodyEncodingForURI="true" redirectPort="8443" acceptCount="100" disableUploadTimeout="true" bindOnInit="false"/>

4. Restart Jira.
5. (Data Center) Repeat these steps on each node.

It's possible that the config tool has not yet been updated to account for this change in your specific version.

[Nic Brough -Adaptavist-]

You'll need to edit the server.xml - add the parameters for SSL as described in https://confluence.atlassian.com/adminjiraserver/running-jira-applications-over-ssl-or-https-938847764.html - it is probably the "connector" settings.