It appears that you must have downloaded the pre-compiled binary for OS X. In that case you do not need to "make"/compile the program. You should be able to run it directly (may need to add execute permissions to bowtie2 binary).
If you are new to command line/would like to pickup some basics of unix from this excellent resource: http://korflab.ucdavis.edu/Unix_and_...ent.html#part1
If you are new to command line/would like to pickup some basics of unix from this excellent resource: http://korflab.ucdavis.edu/Unix_and_...ent.html#part1
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