anyone has advise on how to properly deploy jira in a server? with this I mean changes in the config files, security and best practices. I tried to look at the atlassian docs but, was not helpful. I'm trying to deploy multiple instances with same configurations and reduce time spend doing this.
For both of my JIRA and Confluence instances, I use Apache as a reverse proxy for the purpose of SSL. I've found this method to be so much easier to maintain than doing SSL through Tomcat.
I edit the setenv.sh file and set both Xms and Xmx to the same value (I use 2048m). If your systems have enough memory, this dedicates a block and increases performance by allowing JIRA/Confluence to not have to request more memory each time it needs it. You may also want to adjust the MaxPermSize as your needs require - I've up'ed it to 512m and things are running smooth.
If you are using LDAP for user management (I'm synch'ing with an Active Directory server) I recommend turning on SSL for this. If you don't, all of your user information, including passwords, will be sent in the clear from the LDAP server to JIRA/Confluence. To use SSL for LDAP you'll need to install the LDAP server's certification to Tomcat java key store. Atlassian has documentation for this on their site.
There are many other things you can do, but these are just some highlights.
1. Create database for JIRA and give r/w to JIRA user
2. Install JIRA to the server (if Linux, just follow the instructions in their docs)
3. Go to localhost and follow the setup wizard
You do not need to deal with config files or security initially as all done in UI. If you want to go SSL, just install Apache and setup proxy, also detailed in docs for extra security. Alternatively, you can just use JIRA Tomcat and turn on SSL if you want, but Apache always is the suggested method and things work much faster in Linux environment.
You can do the same for multiple instances.
Hope that helps.
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