[pygr-notify] [pygr commit] r201 - Edited wiki page through web user interface.

[codesite-noreply at google.com]

Author: marecki
Date: Fri May  1 13:28:54 2009
New Revision: 201

Modified:
    wiki/MegatestSetup.wiki

Log:
Edited wiki page through web user interface.

Modified: wiki/MegatestSetup.wiki
==============================================================================
--- wiki/MegatestSetup.wiki	(original)
+++ wiki/MegatestSetup.wiki	Fri May  1 13:28:54 2009
@@ -37,7 +37,7 @@
  Presently there are two distinct classes of megatests, differing in what  
the primary genome used by each class is and therefore named after the  
genome in question: _dm2_ (_Drosophila melanogaster_, or common fruit fly)  
and _hg18_ (_Homo sapiens_, or human). Each class uses its own set of input  
and output data; it is recommended to keep them in separate directories.


-=== BlastDB files ===
+=== BlastDB sequence files ===

  The easiest way of obtaining BlastDB sequence-data files is to fetch them  
using Pygr itself, from the UCLA XML-RPC server - that way downloaded files  
will automatically become registered into the local Pygr resource database.  
Information on how to do this can be found on the PygrResourceDownloader  
page; for your convenience, the lists below provide data-set names in the  
format understood by Pygr.

@@ -138,7 +138,21 @@
  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.


-==== Location of data ====
+==== Location of input ====
+
+Use the following keys to specify directories containing input data:
+
+ # In the _megatests_ section:
+  * _testInputDB_ - name of the database on the server specified above  
containing data imported from our dump files;
+  * _testInputDir_ - directory containing files from  
_input_and_results.tar_.
+ # In the _megatests_SET_ sections:
+  * _axtDir_ - directory containing files from _axt_data_ archives (*hg18  
only*);
+  * _mafDir_ - directory containing files from _maf_data_ archives;
+  * _msaDir_ - directory containing files from _maf_test_ archives;
+  * _seqDir_ - directory containing BlastDB files downloaded using Pygr.
+
+
+==== Location of output ====

  TBA