[pygr-notify] [pygr] r259 committed - Edited wiki page through web user interface.

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Revision: 259
Author: marecki
Date: Wed Aug 26 18:59:19 2009
Log: Edited wiki page through web user interface.
http://code.google.com/p/pygr/source/detail?r=259

Modified:
  /wiki/MegatestSetup.wiki

=======================================
--- /wiki/MegatestSetup.wiki	Wed Aug 26 17:16:39 2009
+++ /wiki/MegatestSetup.wiki	Wed Aug 26 18:59:19 2009
@@ -120,7 +120,7 @@
    * maf_data.tar
    * maf_test.tar
   # NLMSA for _hg18_ megatests
-  * axt_data.tar
+  * axt_data3.tar
    * maf_data3.tar
    * maf_test3.tar
   # Miscellaneous files, needed by both classes
@@ -173,19 +173,20 @@

  ==== Choosing the variant ====

-Both data sets used by megatests are quite large, making running tests  
over them in their entirely quite time consuming - for example, on a  
machine with a 2.8 GHz dual-core Opteron CPU and a SATA-2 RAID disc a  
single such run takes approximately 30 hours! Therefore, it may be  
desirable to run megatests only on subsets of the two data sets. In order  
to do this, specify appropriate subsets using the _smallSampleKey_ keyword  
in data set-specific sections. For example, to only use _chrYh_ in  
_dm2_-based megatests and _chrY_ in _hg18_-based ones, specify:
+Both data sets used by megatests are quite large, making running tests  
over them in their entirely quite time consuming - for example, on a  
machine with a 2.8 GHz dual-core Opteron CPU and a SATA-2 RAID disc a  
single such run takes approximately 30 hours! Therefore, it may be  
desirable to run megatests only on subsets of the two data sets. In order  
to do this, specify appropriate subsets using the _smallSampleKey_ keyword  
in data set-specific sections. For example, to only use _chrYh_ in the  
_annotation_dm2_ megatest, _chr4h_ in _nlmsa_dm2_ and _chrY_ in  
_hg18_-based ones, specify:

  {{{
  [megatests_dm2]
  smallSampleKey = chrYh
+smallSampleKey_nlmsa = chr4h

  [megatests_hg18]
  smallSampleKey = chrY
  }}}

-On the aforementioned machine this reduces the running time of megatests  
to approximately 10 minutes per run.
-
-Note that in principle any valid subsets could be used here, then again we  
only provide reference output files for the two subsets shown in the  
example.
+On the aforementioned machine this reduces the running time of megatests  
to approximately 12 minutes per run.
+
+In principle, any valid subsets could be used to have "quick" megatests.  
Then again, we only provide reference output files for the configuration  
shown above.


  ==== Location of input ====