Some of the application "run" files do not come with icons, such as Foxit, Mendeley Desktop, etc. In order to put the image as the icon so you know what to click to run the file, as in Windows tradition, simply right click the file, go to preferences, double-click the icon in the top-left corner and insert the image file, usually a .png file. You may have to go to the internet and right-click and save image as in order to get the icon.
Here is the process for Scilab, a free, open-source math software similar to MathWorks MATLAB and Wolfram Mathematica. Note that I have already done this with the screen shots so your original icon will look different. It will look like the "scilab-cli" file. Actually, Scilab is in the Ubuntu software repositories so this install wasn't even necessary, :/.
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