The general format for setting properties on the command-line is -Dname=value. For example, here is how the Orion application server is started, where the file.encoding property is set to utf-8:
java -Dfile.encoding=utf-8 -jar orion.jar -userThreads
Other app servers have startup and shutdown scripts. The same -Dname=value options are set under the covers, but the means of setting properties varies.
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Setting properties and options on startup
In some versions of Windows, there is no option to add Java variables to the service. In these cases, you must add the properties by viewing the option list in the registry. Go to Start -> Run, and run "regedt32.exe". For JIRA, there should be an entry at HKEY_LOCAL_MACHINE -> SOFTWARE -> Apache Software Foundation -> Procrun 2.0 -> JIRA ( or HKEY_LOCAL_MACHINE -> SOFTWARE -> Wow6432Node -> Apache Software Foundation -> Procrun 2.0 -> JIRA -> Parameters -> Java if on 64 bit ). See more at at Increasing JIRA Memory.
Tomcat on Windows, running startup.bat:
Right-click 'My Computer', go to Properties -> Advanced -> Environment Variables and set JAVA_OPTS to the desired value:
export JAVA_OPTS=-Dname1=value1 -Dname2=value2 ...
on the command-line before starting Tomcat, in your ~/.bash_profile or at the beginning of the the startup script (bin/setenv.sh for Linux or bin\setenv.bat for Windows).
JIRA also has a few internal startup options that can be set, some of these are used for debugging but a few may come in handy. Note that some of these are configurable via the Administration sections of JIRA.
java -Dmail.debug=false -Djira.jelly.on=true -Datlassian.mail.fetchdisabled=true -Djira.trackback.senddisabled=true
-Dmail.debug=(true|false) — will enable/disable SMTP mail debugging (but note this will only work in 3.7.2+).
-Djira.jelly.on=(true|false) — will enable/disable Jelly scripting
-Datlassian.mail.fetchdisabled=(true|false) — will enable/disable mail fetching services for IMAP and POP
-Datlassian.mail.senddisabled=(true|false) — will enable/disable JIRA sending mail
-Djira.trackback.senddisabled=(true|false) — will enable/disable
-Djira.i18n.texthighlight=(true|false) — will show text elements of JIRA that are internationalised