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README.txt
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Pygr README
===========
Introduction
------------
Pygr is an open source software project used to develop graph database
interfaces for the popular Python language, with a strong emphasis
on bioinformatics applications ranging from genome-wide analysis of
alternative splicing patterns, to comparative genomics queries of
multi-genome alignment data.
For more information see
http://pygr.org
Latest Release
--------------
http://code.google.com/p/pygr/downloads/list
Documentation
-------------
This distribution includes the full Pygr documentation source,
but you will need the Sphinx documentation tool to build the
formatted docs. You can get Sphinx via:
easy_install -U Sphinx
To build HTML versions of the docs using Sphinx:
cd doc
make html
The docs are also available online:
http://pygr.org/docs/latest-release/
Core Prerequisites
-----------------
1) Python >= 2.3
To build Pygr from source code, you need Pyrex
Apps Prerequiites
-----------------
MySQL-python >= 1.2.0
MySQL >= 3.23.x
Note: While pygr's core functionality is solely dependent on a sane python environment, the aformentioned apps requirements must be installed if one wishes to utilize the apps modules and test code.
Supported Platforms
-------------------
In theory, pygr should work on any platform that adequately supports python.
Here are the OS's we've successfully tested on:
o Linux 2.2.x/2.4.x
o OS X
o OpenBSD
o Windows XP
Installation
------------
Installing pygr is quite simple.
1) tar -xzvf pygr-0.3.tar.gz
2) cd pygr
3) python setup.py install
Once the test framework has completed successfully, the setup script
will install pygr into python's respective site-packages directory.
If you don't want to install pygr into your system-wide site-packages,
replace the "python setup.py install" command with
"python setup.py build". This will build pygr but not install it
in site-packages.
Using Pygr
----------
Check out the tutorials in the online docs!
Pygr contains several modules imported as follows:
from pygr import seqdb # IMPORT SEQUENCE DATABASE MODULE
If you did not install pygr in your system-wide site-packages, you
must set your PYTHONPATH to the location of your pygr build.
For example, if your top-level pygr source directory is PYGRDIR then
you'd type something like:
setenv PYTHONPATH PYGRDIR/build/lib.linux-i686-2.3
where the last directory name depends on your specific architecture.
License
-------
New BSD license.
Author
------
Chris Lee <[email protected]> and the rest of the Pygr developer team.
Please see http://code.google.com/p/pygr for a current list
of the participating developers.
Also see http://github.com/cjlee112/pygr/ for a list of other
developers who have created their own branches of the Pygr
git repository.