QIIME Readme
============

The definitive source for information on QIIME is the QIIME website at `http://www.qiime.org <http://www.qiime.org>`_. The information contained in this document is very minimal in comparison.

:Download: via sourceforge at `http://sourceforge.net/projects/qiime <http://sourceforge.net/projects/qiime>`_.

:Registration: To be informed of bugs, new releases, and new features subscribe to the QIIME blog at `http://qiime.wordpress.com <http://qiime.wordpress.com>`_.

Dependencies
------------

QIIME requires Python_ 2.6, Numpy_ 1.3.0, and PyCogent_ 1.5.1. 

Required
^^^^^^^^

- Python_: the language the toolkit is primarily written in, and in which the user writes control scripts.
- Numpy_: This is a python module used for speeding up matrix computations. It is available as source code for \*nix.
- PyCogent_: the Python Comparative Genomics Toolkit, a library containing core objects commonly used in Bioinformatics applications, wrappers for external applications (e.g., blast), and a lot more.

Note: On some linux platforms (like Ubuntu), you must specifically install a ``python-dev`` package so that the Python_ header files required for building some external dependencies are available.

Documentation
^^^^^^^^^^^^^

Installation instructions, a tutorial, and documentation
--------------------------------------------------------

Installation notes, a tutorial, and documentation is provided at `http://www.qiime.org <http://www.qiime.org>`_.

Testing
-------

``QIIME/tests`` contains all the tests. You can most readily run the tests using the ``QIIME/tests/all_tests.py`` shell script. This is done by typing:

::
    
    $ python Qiime/tests/all_tests.py

Note that if certain optional applications are not installed this will be indicated in the output as test fails beginning with ``ApplicationNotFoundError``.

Tips for use
^^^^^^^^^^^^

All QIIME scripts provide usage information when called with their -h option. This should be the first place to look for information about how to interact with QIIME's scripts. For example, to learn about how QIIME's pick_otus.py script works, call:

::
    
    $ pick_otus.py -h	

.. _Python: http://www.python.org
.. _BLAST: ftp://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/
.. _PyCogent: http://pycogent.sourceforge.net
.. _Cython: http://www.cython.org/
.. _Numpy: http://numpy.scipy.org/
.. _Matplotlib: http://matplotlib.sourceforge.net
.. _Apple: http://www.apple.com
.. _Pyrex: http://www.cosc.canterbury.ac.nz/~greg/python/Pyrex/
.. _`editors go here`: http://www.python.org/cgi-bin/moinmoin/PythonEditors
.. _mpi4py: http://code.google.com/p/mpi4py
.. _`restructured text`: http://docutils.sourceforge.net/rst.html
.. _gcc: http://gcc.gnu.org/
.. _SQLAlchemy: http://www.sqlalchemy.org
.. _`MySQL-python`: http://sourceforge.net/projects/mysql-python
.. _zlib: http://www.zlib.net/
.. _`compiling matplotlib`: http://bioinformatics.anu.edu.au/groups/huttleylab/wiki/da9fe/Building_matplotlib_for_Snow_Leopard.html