snayfach
Installing MIDAS on Mac OS X 10.11 and later
This is not a question but rather a comment to help those in the same situation.
In El Capitan and later, due to System Integrity Protection, the default instructions to install dependencies will not work*. Instead, one must first configure Mac OS X to look for Python packages outside of /System/Library. See instructions from mfripp at StackExchange.
After that, install the dependencies with this command:
sudo -H pip install --upgrade numpy biopython pysam pandas
*the reason why the default instructions will not work is because the version of numpy in Mac OS X is 1.8.0rc1, which doesn't get parsed by the version checker correctly and causes an error. This in itself is potentially a bug, but this issue between pip and SIP occurs with many other programs as well (e.g., Qiime).
