For those of you running MacQIIME on OSX El Capitan or higher, you may (like me) find that the MacQIIME executable is no longer in your path.
I was a little confused:I couldn’t find it on my system, although I still had my MacQIIME installation in the default location. What gives?
After reinstalling MacQIIME with no luck, I finally looked at the documentation (serves me right for being lazy). Turns out that the developers are aware of this issue, and plan to fix it soon. For now, they offer the below line of code to execute the MacQIIME shell:
<span class="hljs-keyword">source</span> <span class="hljs-regexp">/macqiime/</span>configs<span class="hljs-regexp">/bash_profile.txt </span>
More permanent solutions are also posted on their install page. Thanks to the Werner lab for maintaining MacQIIME.