Install

micca is composed by several executable Python scripts and wraps lots of external applications.

Requirements

micca requires Python (http://www.python.org/) >= 2.7.

External Applications

Python Modules

The easiest way to install the Python dependencies is by using pip:

$ pip install numpy scipy matplotlib pandas biopython cutadapt dendropy

Install micca

  1. Untar micca-X.Y.tar.gz, creating micca-X.Y folder (where X.Y is the current version of micca)

  2. Go into micca-X.Y folder and from a terminal run:

    $ sudo python setup.py install
    
  3. If you don’t have root access, installing 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
    
  4. Test the installation. From the command line run:

    $ micca-test
    

    If all the required software is installed, you should see something like this:

    Checking for dependencies...
    DNACLUST... OK
    BLAST+... OK
    CUTADAPT... OK
    PyNAST... OK
    T-Coffee... OK
    MUSCLE... OK
    SICKLE... OK
    FastTree... OK
    UCHIME... OK
    Biopython... OK
    matplotlib... OK
    SciPy... OK
    DendroPy... OK
    NumPy... OK
    pandas... OK
    RDP Classifier... OK

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