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Executable files (built programs and shell scripts) normally go in /bin or /usr/bin but what about a jar file? It is a 'program' making me think it should go in bin, but on the other hand it requires a script to start it.

I have a very simply script to start the jar.

java -jar myapp.jar

But where should I put the jar file its self?

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    /usr/share/java could be one place. Though if it's a user .jar it belongs more in one directory in your $HOME – solsTiCe Jun 9 '15 at 22:24
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It depends on you, i would suggest not to use any place designated to store system wide binary files. Although you can put it in /usr/local/bin or any other designated place to store system wide binary files but as it is not a regular binary file you better put somewhere else. Your home directory may be a good place too.

Actually it does not matter where you are putting this as long as you are going to use full path to call it:

java -jar /path/to/myapp.jar

Whereas if you want to put it somewhere in your PATH, you can add the path to the directory containing the file to the PATH (put it in ~/.bashrc):

export PATH=$PATH:/path/to/directory

Make sure the directory does not contain anything else (otherwise it would be a great place for running random malicious commands !!).

Now you can also create an alias of the command, for example:

alias myapp='java -jar /path/to/myapp.jar'

put it in ~/.bash_aliases. Now you can run the application by just typing:

myapp
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There is no definite location that you 'should' store your executable jars in. It is based solely on user preference. I find that keeping my executable jars on the desktop works best so i don't need to continuously travel through my file system to use them which can sometimes get lost if your memory isn't the best.

Also little sidenote, if you install Java 8 then you can use Oracles Java 8 Runtime so you can just double click on the jar.
Hope I helped answer your dilemma.

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