Download and install

Prerequisites

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 >= 12.04 and Debian Linux

We suggest install NumPy and the requirements for SciPy and matplotlib through the package manager:

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

Then, upgrade pip and install setuptools:

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

On OS X

In 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 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 (https://github.com/compmetagen/micca/releases):

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 setup.py 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
  • 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' 'matplotlib >=1.3.0' 'biopython >= 1.50' 'cutadapt >=1.9' 'biom-format >=1.3.1'

Download the latest version from https://github.com/compmetagen/micca/releases and complete the installation:

tar -zxvf micca-X.Y.Z.tar.gz
sudo python setup.py 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 setup.py install --prefix=/path/to/modules
export PYTHONPATH=$PYTHONPATH:/path/to/modules/lib/python{version}/site-packages

Note

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 (http://sourceforge.net/projects/rdp-classifier/). The RDP classifier can be used in the classify command (option -m/--method rdp).

Warning

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):

wget https://sourceforge.net/projects/rdp-classifier/files/rdp-classifier/rdp_classifier_2.11.zip
unzip rdp_classifier_2.11.zip

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.

Note

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