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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:

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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

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Right-click 'My Computer', go to Properties -> Advanced -> Environment Variables and set JAVA_OPTS to the desired value:

In Linux/*nix:

Set:

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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).

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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.

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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 trackback linking
-Djira.i18n.texthighlight=(true|false) — will show text elements of JIRA that are internationalised