is it possible to use variables in remote ssh command?

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In this example

ssh my_server "echo this is my_server; abc=2;"

abc is set on the remote side, so it should be clear why it is not set on your local machine.

In the next example, 

ssh my_server "echo this is my_server; abc=2; echo abc is $abc"

your local shell tries to expand $abc in the argument before it is ever sent to the remote host. A slight modification would work as you expected:

ssh my_server 'echo this is my_server; abc=2; echo abc is $abc'

The single quotes prevent your local shell from trying to expand $abc, and so the literal text makes it to the remote host.

To finally address your real question, try this:

jabref_dir=$( ssh my_server 'jabref_exe=$(which jabref); jabref_dir=$(dirname $jabref_exe);
               java -jar $jabref_dir/../jabref.jar > /dev/null; echo $jabref_dir' )

This will run the quoted string as a command on your remote server, and output exactly one string: $jabref_dir. That string is captured and stored in a variable on your local host.

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