Download and install


micca requires Python >=2.7, NumPy (>= 1.8.0) and the software required in order to install SciPy (>= 0.13.0) through pip.

On Ubuntu Linux >=12.04

In Linux, we suggest install NumPy and requirements for SciPy through the package manager. In Ubuntu Linux you can use apt-get install:

sudo apt-get install python-numpy
sudo apt-get install gcc gfortran python-dev libblas-dev liblapack-dev cython


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

  1. Install Xcode;

  2. Install Homebrew;

  3. Install Python and gfortran:

    brew update
    brew install python
    brew install gfortran

Install NumPy:

pip install numpy

Install micca using pip

The easiest way to install micca is to using pip, from PYPI:

sudo pip install micca

or from the tarball (

sudo pip install micca-X.Y.Z.tar.gz

Install micca from source

In order to install micca from sources (with the standard procedure python install), in addition to Python (>=2.7, <3.0), NumPy (>= 1.8.0) and SciPy (>= 0.13.0), the following Python packages must be installed:

  • Pandas >=0.17.0, <0.18.0
  • 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 'pandas >=0.17.0, <0.18.0' '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
python build
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 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 .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.

Download and unzip the file (RDP cladssifier v2.11 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.