[pygr-notify] [pygr commit] r191 - Edited wiki page through web user interface.

[codesite-noreply at google.com]

Author: marecki
Date: Fri Apr 17 18:44:01 2009
New Revision: 191

Modified:
    wiki/MegatestSetup.wiki

Log:
Edited wiki page through web user interface.

Modified: wiki/MegatestSetup.wiki
==============================================================================
--- wiki/MegatestSetup.wiki	(original)
+++ wiki/MegatestSetup.wiki	Fri Apr 17 18:44:01 2009
@@ -89,7 +89,7 @@

  == Configuration ==

-== MySQL access ==
+=== MySQL access ===

  Megatests assume the database they use is located on the default MySQL  
server and accessed using default user name/password. If your system-wide  
defaults do not match the desired values of these parameters, you'll need  
to override them - using a standard MySQL option file. Under Linux/Unix you  
will most likely use the per-user option file _$HOME/.my.cnf_ file in your  
home directory

@@ -107,14 +107,14 @@
  XXX


-== Choosing the variant ==
+=== Choosing the variant ===

  As you can see, there are full versions and _chrY(hg18)_ and _chrYh(dm2)_  
versions. Current version of pygr megatest uses only short _(chrY for hg18  
and chrYh for dm2)_ versions in order to reduce overhead (both CPU and  
disc-space). If you want to test full version, you need to change  
*megatest.py* files, i.e. remove all _chrY_/_chrYh_.

  On leelab2 (2.8 GHz dual-core Opteron CPU), the short version of megatests  
runs for about 5 minutes. On the other hand, the full version takes  
approximately 30 hours.


-== The config file ==
+=== The config file ===

  The latest incarnation of megatest code and support scripts is quite  
flexible in terms of where input should come from and output should go to,  
meaning you could basically distribute the relevant directories all over  
the system if you wanted to - but also that regardless of where they go,  
Pygr needs to be told where to look for them. This, along with some other  
megatest-related things, is done using a Pygr configuration file.