[pygr-notify] [pygr commit] r187 - Edited wiki page through web user interface.

[codesite-noreply at google.com]

Author: marecki
Date: Wed Apr 15 17:42:07 2009
New Revision: 187

Modified:
    wiki/MegatestSetup.wiki

Log:
Edited wiki page through web user interface.

Modified: wiki/MegatestSetup.wiki
==============================================================================
--- wiki/MegatestSetup.wiki	(original)
+++ wiki/MegatestSetup.wiki	Wed Apr 15 17:42:07 2009
@@ -23,7 +23,7 @@

   * _(optional)_ A local pygr.Data XML-RPC server, so that the  
data-download test is not affected by the quality of your connection to the  
UCLA one;

- * sequence data and other input used by megatests along with reference  
output; obtaining and installing these will be described below.
+ * Sequence data, miscellaneous input and reference output used by  
megatests; obtaining and installing these will be described below.


  == Downloading and preparing data ==
@@ -55,9 +55,9 @@
    * Bio.Seq.Genome.DROWI.droWil1
    * Bio.Seq.Genome.DROYA.droYak2
    * Bio.Seq.Genome.TRICA.triCas2
- # For _hg18_ "annotation" and "NLMSA" megatests (FIXME - verify and  
reformat!)
+ # For _hg18_ "annotation" and "NLMSA" megatests (*FIXME* - verify and  
reformat!)
     
* 'anoCar1', 'bosTau3', 'canFam2', 'cavPor2', 'danRer4', 'dasNov1', 'echTel1', 'equCab1', 'eriEur1', 'felCat3', 'fr2', 'galGal3', 'gasAcu1', 'hg18', 'loxAfr1', 'mm8', 'monDom4', 'ornAna1', 'oryCun1', 'oryLat1', 'otoGar1', 'panTro2', 'rheMac2', 'rn4', 'sorAra1', 'tetNig1', 'tupBel1', 'xenTro2'
- # For _hg18_ "pairwise alignment" megatest (FIXME - verify and reformat!)
+ # For _hg18_ "pairwise alignment" megatest (*FIXME* - verify and  
reformat!)
    * 'canFam2', 'hg18', 'mm8', 'panTro2', 'rn4'

  Once the files have been downloaded they require no further attention.
@@ -77,7 +77,7 @@
   # Miscellaneous files
    * 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) 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_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_megatest_ (*FIXME*: double-check this!) with the path of  
your choice.


  XXX