[pygr-notify] [pygr commit] r114 - wiki

[codesite-noreply at google.com]

Author: marecki
Date: Thu Dec 18 18:28:34 2008
New Revision: 114

Added:
    wiki/MegatestSetup.wiki

Log:
Created wiki page through web user interface.

Added: wiki/MegatestSetup.wiki
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+#summary How to set everything up to be able to run megatests.
+
+= Introduction =
+
+The purpose of this page will be to, as soon as it's complete, provide  
complete instructions for everyone wishing to run megatests on his/her  
machine - from obtaining the necessary data to actual running of megatests.  
Note that right now this is work in progress.
+
+= Details =
+
+== Downloading and preparing data ==
+
+In order to setup pygr megatest on your machines, first step is to  
download _seqdb.BlastDB_. You can download all seqdb.BlastDB via  
_biodb2.bioinformatics.ucla.edu_, see the PygrResourceDownloader page for  
more details.
+
+These are lists of _seqdb.BlastDBs_ to download from  
_biodb2.bioinformatics.ucla.edu_:
+
+# for dm2 megatest (annotation database, NLMSA MAF format)
+ msaSpeciesList =  
['anoGam1', 'apiMel2', 'dm2', 'dp4', 'droAna3', 'droEre2', 'droGri2', 'droMoj3', 'droPer1', 'droSec1', 'droSim1', 'droVir3', 'droWil1', 'droYak2', 'triCas2']
+
+# for hg18 megatest (annotation database, NLMSA MAF format)
+ msaSpeciesList =  
['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 megatest, pairwise alignment, axtNet format input
+ msaSpeciesList = ['canFam2', 'hg18', 'mm8', 'panTro2', 'rn4']
+
+
+_PYGRDATADOWNLOAD_ should be set to your own directory in which all  
_seqdb.BlastDBs_ will be saved.
+
+ os.environ['PYGRDATADOWNLOAD'] = '/my/seqdb/path'
+
+At the top of each dm2/hg18 megatest files in tests directory, you can see  
following lines. You may need to change following lines to  
_PYGRDATADOWNLOAD_ path. If you want to maintain original *megatest.py*  
files intact, you may need to create following directory in your megatest  
machine.
+
+ seqDir = '/result/pygr_megatest/seq_data'
+
+ seqDir = '/result/pygr_megatest/seq_data3'
+
+All the necessary pre-built NLMSA and pre-calculated results are available  
at http://biodb.bioinformatics.ucla.edu/MEGATEST/
+
+And, there are some sets of pre-build NLMSA. These pre-built NLMSA files  
should be saved in your machine.
+
+ msaDir = '/result/pygr_megatest/maf_test'  # maf_test.tar in biodb  
MEGATEST URL.
+
+ msaDir = '/result/pygr_megatest/maf_test3' # maf_test3.tar in biodb  
MEGATEST URL.
+
+All the test results and NLMSA will be saved subdirectory of  
_/usr/tmp/deepreds_. You can find _/usr/tmp/deepreds_ path in all of  
*megatest.py*. You may need to change this directory or create one for  
megatest.
+
+
+
+*TBC*
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