I have dowloaded blat from here. I have also added in to executable path:


But I can run the program only from the folder where it is situated and only by typing ./blat and not simple blat, therefore homer does not find it. What should I do in order to be able to run a program just blat?

which blat gave nothing.

echo $PATH

You should add to your PATH the directory in which the executable is located, without the executable name:

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