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.. _quick-install:
Quick installation
==================
PyCogent.app for OSX 10.6
-------------------------
`Download PyCogent.app <http://sourceforge.net/projects/pycogent/files/PyCogent.app/>`_. This native OSX app comes bundled with all required dependencies and is a download, decompress and go experience! It also implements the novel script form system that controls command line scripts via a form based input mechanism.
By virtual machine
------------------
One way to install PyCogent is to install the QIIME virtual machine using VirtualBox. The installation instructions can be found `here <http://qiime.sourceforge.net/install/virtual_box.html>`_.
Please, note that this is the only installation method supported for Windows and that natively Windows does not support gz files properly so to uncompress a gz file in Windows use `7-zip <http://www.7-zip.org/>`_.
For systems with ``easy_install``
---------------------------------
For the list of dependencies see the :ref:`required` software list.
The following assumes you have ``easy_install`` on your system (this comes standard with new Macs for instance), that you have administrator privileges and that you're connected to the internet. See below if you don't have ``easy_install``.
The key steps for the minimal install are:
1. Download the :download:`requirements file <../cogent-requirements.txt>`.
2. Install pip ::
$ sudo easy_install -U pip
3. Use pip to download, build and install PyCogent plus the numpy dependency. ::
$ DONT_USE_PYREX=1 sudo pip install -r path/to/cogent-requirements.txt
.. note:: The ``DONT_USE_PYREX=1`` statement is required if you have Pyrex installed due to a conflict between setuptools and later versions of Pyrex. If you don't have Pyrex, this will still work.
If the above fails to download PyCogent you can `download the tarball <http://sourceforge.net/projects/pycogent>`_ to your hard drive and replace the first line of the :download:`requirements file <../cogent-requirements.txt>` with the full path to the tarball, e.g. ``/Users/my_user_name/Downloads/cogent-1.5.3.tgz``.
Optional installs
^^^^^^^^^^^^^^^^^
To use the Ensembl querying code
""""""""""""""""""""""""""""""""
Add the following lines to the requirements file ::
MySQL-python>=1.2.2
SQLAlchemy>=0.5
.. note:: The MySQL-python module requires that you have MySQL installed.
To use the parallel capabilities
""""""""""""""""""""""""""""""""
Add the following to the requirements file ::
mpi4py>=1.0
To build the documentation
""""""""""""""""""""""""""
Add the following to the requirements file ::
Sphinx>=0.6
To use the development version of PyCogent
""""""""""""""""""""""""""""""""""""""""""
Just replace the first line of the requirements file with ``https://pycogent.svn.sourceforge.net/svnroot/pycogent/trunk``.
To use the graphics capabilities
""""""""""""""""""""""""""""""""
You need to install matplotlib_ (version 1.1.0+) to use the drawing code. However, compiling matplotlib can be a challenge. We therefore suggest you obtain a prebuilt binary for your platform from the matplotlib_ project page rather than modify the requirements file. For OSX, we suggest reading the following instructions on `compiling matplotlib`_.
.. _pip: http://pypi.python.org/pypi/pip
.. _matplotlib: http://matplotlib.sourceforge.net/
.. _`compiling matplotlib`: http://sourceforge.net/projects/pycogent/forums/forum/651121/topic/5635916
.. todo::
**FOR RELEASE:** update the tarball name for the version.
Installing ``easy_install``
---------------------------
If your system doesn't have ``easy_install``, you can execute the following::
$ sudo curl http://peak.telecommunity.com/dist/ez_setup.py | python
or, if you are on a linux system that has a package manager, you may only need to do something like::
$ sudo apt-get install python-setuptools
Use the approach to getting ``easy_install`` that best suites your system, then follow the (above) instructions for the ``pip`` based installation.
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