[pygr-notify] [pygr commit] r27 - wiki

[codesite-noreply at google.com]

Author: cjlee112
Date: Thu Jun 12 14:46:10 2008
New Revision: 27

Added:
   wiki/QuickOverview.wiki

Log:
Created wiki page through web user interface.

Added: wiki/QuickOverview.wiki
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+#summary From the 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.
+
+= Documentation =
+
+Please see our PygrDocumentation page for tutorials, module 
documentation, recipes, and forum.  Within the source code repository, 
you can build the documentation via `cd doc;make`, then point your 
browser at the file *doc/html/pygr/index.html*. You can also check out 
[http://bioinfo.mbi.ucla.edu/pygr/docs/ the older documentation page].
+
+= Prerequisites =
+
+  * Python >= 2.2: Pygr uses Python generators.
+  * C compiler: Pygr includes several C extension modules 
(pygr.cnestedlist, pygr.cdict, pygr.seqfmt), coded in C for high 
performance.  To install Pygr from source code, you need a C compiler.  
(If you don't have a C compiler, you may be able to find a binary 
installer for Pygr on your platform on this site).  Pygr uses the 
Python distutils module to build its extension modules, so any C 
compiler that distutils knows how to find and use is fine.
+
+  * Pyrex: You do not need this if you are installing one of our 
source code releases, because these include the C source code compiled 
by Pyrex. However, if you are compiling from the git repository, you 
will need [http://www.cosc.canterbury.ac.nz/greg.ewing/python/Pyrex/ 
Pyrex], because (currently) the git repository does not include the 
Pyrex-compiled C files.
+
+== Optional, Recommended ==
+While pygr's core functionality only requires a sane python 
environment, some specific features require additional software:
+	
+  * MySQL support: allows Pygr to access MySQL databases using its 
pygr.sqlgraph module.  Also needed for pygr.Data module support for 
storage of pygr.Data resource databases in MySQL.  Requirements: 
*MySQL-python (MySQLdb module) >= 1.2.0; works with any server MySQL >= 3.23.x*
+
+  * NCBI tools: used by the pygr.seqdb.BlastDB class to provide 
convenient blast/megablast search.  Requirements: <B>formatdb, 
blastall, megablast</B>, any recent version; executables must be in 
your $PATH.
+
+= Supported Platforms =
+
+In theory, pygr should work on any platform that adequately supports 
python.  Here are the OS's we've successfully tested on:
+
+  * Linux 2.2.x/2.4.x
+  * Mac OS X
+  * OpenBSD
+  * Windows XP, Vista: please see our page on PygrOnWindows.
+
+= Installation =
+
+Installing pygr is quite simple.
+
+{{{
+cd pygr
+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 =
+Pygr contains several modules imported as follows:
+{{{
+from pygr import seqdb
+}}}
+
+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.
+
+Pygr has a myriad of applications, however, providing a comprehensive 
description of its utility is out of the scope of this document (see PygrDocumentation).
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