The command is "bowtie2", not "bowtie". A command will (almost) always be the name of a file, which you could have double checked by just looking in your bin folder. Setting up your PATH and such is outside the purview of installation documents, so they'll generally not be included (you'd be well served to just buy a book on using Linux).
Since you downloaded the precompiled version, you don't need to compile anything. We can't see your computer, so we can't know whether you need to add the bin directory to your path or not (and how to do that will depend on your shell, though odds are good that editing .bashrc or .bash_profile will do it).
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Bowtie Troubles
I'm a Linux/command line novice having trouble getting bowtie to work at all. I've downloaded bowtie2-2.2.3-linux-x86_64.zip (26.4 MB) from sourceforge. I extracted it in my builds folder and copied it to my bin folder. Now what? The manual seems very vague. Do I need to compile? If so, how? Do I need to set it to my path? If so, how? When I open up a terminal and type 'bowtie' I get: The program 'bowtie' is currently not installed. To run 'bowtie' please ask your administrator to install the package 'bowtie'
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