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