[pygr-notify] [pygr] r258 committed - Edited wiki page through web user interface.

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Revision: 258
Author: marecki
Date: Wed Aug 26 17:16:39 2009
Log: Edited wiki page through web user interface.
http://code.google.com/p/pygr/source/detail?r=258

Modified:
  /wiki/MegatestSetup.wiki

=======================================
--- /wiki/MegatestSetup.wiki	Wed Aug 26 16:54:43 2009
+++ /wiki/MegatestSetup.wiki	Wed Aug 26 17:16:39 2009
@@ -88,7 +88,7 @@
    * Bio.Seq.Genome.TETNG.tetNig1
    * Bio.Seq.Genome.TUPGB.tupBel1
    * Bio.Seq.Genome.XENTR.xenTro2
- # For the _restartIterator_ megatest
+ # For the _restartIterator_ megatest (note significant overlap with _dm2_  
megatests; also see the comment in the next section)
    * Bio.Seq.Genome.ANOGA.anoGam1
    * Bio.Seq.Genome.APIME.apiMel3
    * Bio.Seq.Genome.DROAN.droAna3
@@ -110,6 +110,10 @@

  === NLMSA and other files ===

+Pygr megatests can be divided into two classes depending on whether they  
require NLMSA to be pre-built in a controlled environment or not. The first  
class consists of all _dm2_ and _hg18_ megatests, the second - of the  
_restartIterator_ megatest.
+
+==== If pre-built NLMSA are required ====
+
  The necessary files are available (as tar archives) on the Web, at  
http://biodb.bioinformatics.ucla.edu/MEGATEST/ . Download the archives and  
unpack them into directories of your choice. You need the following files:

   # NLMSA for _dm2_ megatests
@@ -119,12 +123,15 @@
    * axt_data.tar
    * maf_data3.tar
    * maf_test3.tar
- # NLMSA for the _restartIterator_ megatests
-  * *FIXME*: TBA
- # Miscellaneous files
+ # Miscellaneous files, needed by both classes
    * input_and_results.tar (note: doesn't create its own directory!)

-This time some post-installation steps are necessary before the data can  
be used: the files _dm2_multiz15way.seqDictP_ (from maf_test.tar),  
_hg18_multiz28way.seqDictP_ (from maf_test3.tar) and  
_dm3_multiz15way.seqDictP_ (from *FIXME*: TBA) contain hardcoded paths  
which will need to be changed to reflect your directory structure. Assuming  
the final path components are to stay the same (i.e. you keep the data in  
the directories in which they came in the archives), simply open the files  
in question using an ordinary text editor and replace all the occurrences  
of _/result/pygr_megatest_ (*FIXME*: double-check this!) with the path of  
your choice.
+This time some post-installation steps are necessary before the data can  
be used: the files _dm2_multiz15way.seqDictP_ (from maf_test.tar) and  
_hg18_multiz28way.seqDictP_ (from maf_test3.tar) contain hardcoded paths  
which will need to be changed to reflect your directory structure. Assuming  
the final path components are to stay the same (i.e. you keep the data in  
the directories in which they came in the archives), simply open the files  
in question using an ordinary text editor and replace all the occurrences  
of _result/pygr_data_ and _/result/pygr_megatest_ with the path(s) of your  
choice.
+
+
+==== If pre-built NLMSA are not required ====
+
+Simply download the _Bio.MSA.UCSC.dm3_multiz15way_ alignment using Pygr,  
the same way you have downloaded all the sequence files. This has the added  
benefit of Pygr being able to resolve sequence dependencies of the  
alignment - in other words, should any required sequences be missing from  
the local resource database they shall be downloaded automatically.


  === MySQL data ===