You can do a git clone to copy this repository:
git clone https://github.com/nextgenusfs/mhc_cluster.git
And then you will need to add to your $PATH or always include the entire path to the scripts at runtime.
export PATH="/location/of/packages/mhc_cluster:$PATH"
You will also need to install USEARCH9 - get it here: http://www.drive5.com/usearch/download.html. One way to make the program executable and move into your path:
#make executable
sudo chmod +x /path/to/usearch9.2.64_i86osx32
#create softlink to folder in $PATH
sudo ln -s /path/to/usearch9.2.64_i86osx32 /usr/local/bin/usearch9
You will also need VSEARCH, which you can download with homebrew/bioconda or directly from GitHub repo.
#install with homebrew
brew tap homebrew/science
brew install vsearch
You will also need to have HMMer3 installed, simpliest way on MacOSX is with Homebrew (http://brew.sh). And then you can tap the homebrew/science rep (https://github.com/Homebrew/homebrew-science)
brew tap homebrew/science
brew install hmmer
python, biopython, VSEARCH, AMPtk, USEARCH9 (accessible in PATH; alternatively you can pass in the variable -u /path/to/usearch8 to scripts requiring USEARCH8).