The command line is the following :

java -Xmx800m -Xms800m -jar solverpatat08.jar -file ./Track2/comp-2007-2-8.tim -t 420 -seed 1 -nbruns 1

where the main arguments are respectively :
-file A : the path of the instance (name) or a directory. In that case all files with .tim extension will be loaded and all the .sln files will be produced.
-t B : the time limit in seconds
-nbruns C : the number of runs (by default 1)
-seed D :  the seed (by default 0 and is incremented by one for each run)
-feas : the solveur is only searching for a feasible solution (ignoring the optimization stage)
-saph : the predication of the cooling is made in a deterministic manner. this degrades the performances but is reproductible. the cooling is otherwise predicting based on a dynamic evaluation of the speed of the solver which always slightly vary from one execution to another.
-colost : use another strategy for the optimization stage called the coloring strategy.

A file "name_seed.sln" is produced in the directory containing the instance so the solution can be checked. 

The -file and -t arguments are mandatory. More options are available for the command line. To get all the details on the command line, just run it without any arguments :
java -Xmx800m -Xms800m -jar solver.jar

Notice that the jvm 1.6.0 is needed to run the code. the version of the jvm on your machine can be checked with : 
java -version