Install

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

Note

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 setup.py 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 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 the environment variable 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.