Using Docker (that is, on MS Windows, Mac OS X and Linux!)

The easiest way to run micca is through Docker. Docker works similarly to a virtual machine image, providing a container in which all the software has already been installed, configured and tested.

  1. Install Docker for Linux, Mac OS X or Windows.

  2. Run the Docker Quickstart Terminal (Mac OS X, Windows) or the docker daemon (Linux, sudo service docker start).

  3. Download the latest version:

    docker pull compmetagen/micca
  4. Run an instance of the image, mounting the host working directory (e.g. /Users/davide/micca) on to the container working directory /micca:

    docker run --rm -t -i -v /Users/davide/micca:/micca -w /micca compmetagen/micca /bin/bash

    You need to write something like -v //c/Users/davide/micca:/micca if you are in Windows or -v /home/davide/micca:/micca in Linux. The --rm option automatically removes the container when it exits.

  5. Now you can use micca:

    root@68f6784e1101:/micca# micca -h


The RDP classifier is preinstalled in the Docker image, so you can check the software version by typing echo $RDPPATH

Using pip

At the moment, only Python 2.7 is supported.

On Ubuntu >= 12.04 and Debian >=7

We suggest to install the following packages through the package manager:

sudo apt-get update
sudo apt-get install build-essential python-numpy gcc gfortran python-dev libblas-dev liblapack-dev cython pkg-config libfreetype6 libfreetype6-dev libpng-dev

Then, upgrade pip and install setuptools:

pip install --upgrade pip
pip install 'setuptools >=14.0'

Finally, install micca:

sudo pip install micca

On Mac OS X

In Mac OS X, we recommend to install Python from Homebrew:

  1. Install Xcode;

  2. Install Homebrew;

  3. Make sure the environment variable PATH is properly setted in your ~/.bash_profile or ~/.bashrc:

    .. code-block:: sh

    export PATH=/usr/local/bin:$PATH

  4. Install Python:

    brew update
    brew install python

Install the GNU Fortran and the NumPy package:

brew install gcc
pip install numpy

Finally, install micca:

sudo pip install micca

Installation problems

  • BIOM fatal error: ‘numpy/arrayobject.h’. If the installation process returns a message like this:

    biom/_filter.c:258:10: fatal error: 'numpy/arrayobject.h' file not found
    #include "numpy/arrayobject.h"
    1 error generated.
    error: command 'clang' failed with exit status 1

    then you need to run:

    pip install --global-option=build_ext --global-option="-I/usr/local/lib/python2.7/site-packages/numpy/core/include/" biom-format

    After that you can install the micca package.

Install micca from source

In order to install micca from sources (with the standard procedure python install), in addition to Python (>=2.7) and NumPy (>=1.8.0), the following Python packages must be installed:

  • SciPy >=0.13.0
  • Pandas >=0.17.0
  • matplotlib >=1.3.0
  • Biopython >=1.50
  • cutadapt >=1.9
  • biom-format >=1.3.1

The easiest way to install these packages is to is using pip:

sudo pip install 'scipy >=0.13.0' 'pandas >=0.17.0' 'matplotlib >=1.3.0' 'biopython >= 1.50' 'cutadapt >=1.9' 'biom-format >=1.3.1'

Download the latest version from and complete the installation:

tar -zxvf micca-X.Y.Z.tar.gz
sudo python install

If you don’t have root access

Install micca in a local directory by specifying the --prefix argument. Then you need to set the environment variable PYTHONPATH:

python install --prefix=/path/to/modules
export PYTHONPATH=$PYTHONPATH:/path/to/modules/lib/python{version}/site-packages


In order to export the variable permanently add the command at the bottom of your ~/.bash_profile or ~/.bashrc file.

Testing the installation

micca -h

Install RDP classifier (optional)

The RDP Classifier is a naive bayesian classifier for taxonomic assignments ( The RDP classifier can be used in the classify command (option -m/--method rdp).


Only RDP Classifier version >2.8 is supported. Install the standard Java or Java compatible runtime (sudo apt-get install default-jre in Ubuntu/Debian or go to the Oracle Java homepage for OS X)

Download and unzip the file (RDP classifier 2.11 2015-09-14):


Now you must set the environment variable RDPPATH by typing:

$ export RDPPATH=/path-to-rdp-classifier/rdp_classifier_2.11/

e.g. export RDPPATH=/Users/David/rdp_classifier_2.11.


In order to export the variable permanently add the latest command at the bottom of your .bashrc file.