1. When classpath is used, jar command is ignored . So use "classpath" with class file and "cp" with jar file
2. NEVER FORGET TO PUT : even you use only 1 external jar. In some cases you will get compilation error if you don't put :
java -classpath /media/Data/eclipseWorkspace/myExternalJar/commons-math-1.2.jar: com.cbrc.motifmap.CombinationOfTF
java -cp /media/Data/eclipseWorkspace/myExternalJar/commons-math-1.2.jar: -jar myJar.jar
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