[pygr-notify] [pygr commit] r217 - Edited wiki page through web user interface.

[codesite-noreply at google.com]

Author: marecki
Date: Thu May  7 14:57:03 2009
New Revision: 217

Modified:
    wiki/BuildingAndTestingPygr.wiki

Log:
Edited wiki page through web user interface.

Modified: wiki/BuildingAndTestingPygr.wiki
==============================================================================
--- wiki/BuildingAndTestingPygr.wiki	(original)
+++ wiki/BuildingAndTestingPygr.wiki	Thu May  7 14:57:03 2009
@@ -43,7 +43,7 @@

  Pygr extension code is written in  
[http://www.cosc.canterbury.ac.nz/greg.ewing/python/Pyrex/ Pyrex] rather  
than plain C, making it necessary to have Pyrex code translated into C  
before the compiler can do its job. *Official Pygr packages come with  
pre-build C files* so if you want to install one of these, you may *skip  
this step*. Conversely, you will need Pyrex installed to build Pygr using  
the code from our Git repository.

-Pyrex hasn't been officially declared finished yet, which means two things  
to Pygr users: one is that you'll want the latest available version (as of  
now, 0.9.8.5) in order to avoid bugs, the other is that you'll need to  
build the module by hand. Fortunately the latter is very easy:
+Pyrex hasn't been officially declared finished yet, which means two things  
to Pygr users: one is that you'll want the latest available version (as of  
now, 0.9.8.5) in order to avoid bugs, the other is that unless your  
system's software repositories contain new-enough Pyrex packages (many do -  
look for _pyrex_ or _python-pyrex_), you'll need to build the module by  
hand. Fortunately the latter is very easy:
   * download and unpack the archive;
   * launch a command-line interpreter and enter the newly-created directory;
   * run _python setup.py install_, possibly adding the option _-O_ if you  
want optimised files to be installed too. You may need to be more specific  
than saying just _python_ if multiple versions are present and/or the main  
executable is not in the path. Last but not least, _install_ copies files  
into sytem-wide Python directories so superuser privileges (or at least  
write access) might be needed to run it, in particular under Linux/Unix.
@@ -64,6 +64,32 @@
    * use [http://www.mingw.org/ MinGW], port of GCC and friends to Windows  
bundled with freely-distributable standard header files and import  
libraries.

  Like Pyrex, both the compiler and the header files are build-time  
dependencies only. They can safely be removed afterwards.
+
+
+=== MySQL/SQLite Support ===
+
+The following Python modules must be present in your system in order for  
Pygr to support accessing MySQL and SQLite databases:
+
+ * SQLite - _sqlite3_ (part of the standard library) for Python 2.5 and  
newer, _pysqlite2_ ([http://pysqlite.org/ pysqlite-2.x.y]) for older  
versions;
+
+ * MySQL - _MySQLdb_ (from the  
[http://sourceforge.net/projects/mysql-python MySQL-python] package).
+
+Both are fairly common in package repositories, and if all else fails they  
can be built from the source the same way as Pyrex (then again, note that  
building mysql-python is more complicated than most Python modules,  
especially under Windows - it will be discussed later).
+
+Note that Pygr only checks for SQL-related modules at run time - they  
needn't be present at the time of installation.
+
+
+=== BLAST Support ===
+
+Pygr uses standard command-line BLAST tools to provide BLAST support. To  
have this work:
+
+ * [http://www.ncbi.nlm.nih.gov/BLAST/download.shtml Download the tools];
+
+ * Unpack them somewhere;
+
+ * Add the _bin_ subdirectory of wherever you unpacked the tools to to the  
search path.
+
+Just like with SQL modules, Pygr only looks for BLAST tools at run time.


  === Building and Installing Pygr ===