Installing MacQIIME

Generally, the MacQIIME page by Jeff Werner seems like a reasonable start. The installation instructions are reasonably clear, but these directions are not for an absolute beginner using a Mac. Particularly it is probably best if the user has some knowledge of *NIX flavor operating systems.

My journey started by following Jeff Werner’s instructions, but I deviated.

I had a problem with the installation because the script wants to place the macqiime file in /usr/bin. This folder is restricted in this OS X El Capitan (10.11.1) version. Therefore, I modified the install.s file to put macqiime in /usr/local/bin:

cd [PATH to]/MacQIIME_1.9.1-20150604_OS10.7

nano install.s

Change all instances of /usr/bin to /usr/local/bin and save (write out) and exit.

I had already added /usr/local/bin to my PATH

To check the PATH

echo $PATH

If it is not in the path add to path with

export PATH=”/usr/local/bin:$PATH”


An important part is probably at the bottom of his MacQIIME page:

Not included, but may be needed: You’ll probably have to install or update XQuartz; Legacy NCBI blast is not installed (assuming many people have their own install of this); AmpliconNoise is not installed (it requires custom compilation, dependent on MPI, specific to your system); USEARCH is not installed, due to licensing; R and associated functions are not installed.

I walked through the addons. XQuartz had a dmg. Java installation was pretty straight forward. I had an install of R and adding packages was no trouble at all. But some addons require some work in the terminal.

I choose NCBI blast-2.2.25-universal-macosx.tar.gz and used option 2 and put it in my machines opt folder instead of my document folder. These instructions were fairly clean.

USEARCH installation instructions rely on those of the USEARCH site and are not as clean.  Keeping a window or tab open to the blast install instructions from Jeff Werner’s site helped with the terminal commands necessary to accomplish moving the files and renaming them at the same time. Because I chose to place them in opt I had to preface the copy (cp) command  and the change permission command (chmod) with sudo and run it as administrator:

sudo cp Download/usearch5.2.236_i86osx32 /opt/usearch

sudo cp Download/usearch6.1.544_i86osx32 /opt/usearch61

sudo chmod +x /opt/usearch

sudo chmod +x /opt/usearch61

Adding these locations to the path:

export PATH=$PATH:~/opt/usearch

export PATH=$PATH:~/opt/usearch61

Check that the PATH has these added

echo $PATH

The AmpliconNoise installation in Jeff Werner’s instructions are non-existent.

I chose to install Homebrew and let it due the heavy lifting.

First Xcode needed to be installed from the Apple Applications Menu.
Then start Xcode and accept the agreement or Homebrew will moan.
I installed Homebrew using the terminal command at their site.

Following the Homebrew installation run:

brew update

brew doctor

Fix the items mentioned in brew doctor. For this installation:

sudo chown -R $(whoami) /usr/local/share/man/mann

Install GNU Science Library with Homebrew

brew install gsl

The next addon is AmpleconNoise. When downloaded and unpackaged it contained a Doc.pdf that stated it had dependencies.

It needs open-mpi and that is available from Homebrew:

brew install open-msi

It needs GNU Science Library and that is already installed. But it also requires mafft. This formula was found in a tap. To install it, run:

brew install homebrew/science/mafft

AmpliconNoise make fails with

FCluster.c:675:3: error: non-void function ‘outputCluster’ should return a value [-Wreturn-type]

A report of this is was at

This may be related to Xcode so I went to and downloaded the Command Line Tools (OS X 10.11) for Xcode 7.2 beta and installed Command_Line_Tools_OS_X_10.11_for_Xcode_7.2_beta_2.dmg manually. However, running ‘make’ on the ApliconNoise folder still returns this error.

With some help from Yoshiki Vázquez Baeza at the QIIME help group with a solution.

Can you try going to the FCluster folder and opening the file named makefile to change the second line to look like this:

CFLAGS = -O3 -Wno-error=return-type

This should show you a warning instead of the error you are seeing. Try re-running the make command again from the Ampliconnoise folder and if a similar issue raised, proceed in the same manner.

Success with the ApliconNoise after repairing several makefile.

The addon TopiaryExplorer installation instructions were likewise tough to trackdown. They are at

-To be continued