[pygr-notify] [pygr] r275 committed - Edited wiki page through web user interface.

[pygr at googlecode.com]

Revision: 275
Author: marecki
Date: Thu Dec 10 12:40:22 2009
Log: Edited wiki page through web user interface.
http://code.google.com/p/pygr/source/detail?r=275

Modified:
  /wiki/MegatestSetup.wiki

=======================================
--- /wiki/MegatestSetup.wiki	Wed Aug 26 19:09:23 2009
+++ /wiki/MegatestSetup.wiki	Thu Dec 10 12:40:22 2009
@@ -37,9 +37,9 @@
  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 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.
+=== SequenceFileDB sequence files ===
+
+The easiest way of obtaining SequenceFileDB 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.

  The following sequences must be obtained:

@@ -134,6 +134,11 @@
  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.


+==== The download test ====
+
+Since version 0.8.1 Pygr uses a new version of the download megatest which  
uses a local HTTP server to provide the desired file, thus reducing the  
test's dependence on a fast and stable network connection. Of course that  
means you will have to download the necessary file, i.e. a text dump of an  
NLMSA, first... We recommend  
http://biodb.bioinformatics.ucla.edu/PYGRDATA/dm2_multiz9way.txt.gz - it's  
the same file as what the older versions of this test used, it's large but  
not too large and building it can take advantage of sequence data required  
by other megatests.
+
+
  === MySQL data ===

  You can find gzip-compressed MySQL dump files (produced with version 5) at  
http://biodb.bioinformatics.ucla.edu/MEGATEST/. Simply create a new  
database on your server, download all the _.sql.gz_ files and import them  
into the said database using e.g. the standard MySQL client (_mysql_).
@@ -168,7 +173,20 @@

  All of the keywords listed below can be found in any of these files. They  
are read in the order listed here, overriding old values with new ones  
should a keyword appear in more than one.

-The config files follow standard syntax understood by Python's  
[http://docs.python.org/library/configparser.html ConfigParser module],  
i.e. very similar to that of Windows INI files. Among other things this  
means keywords in a file are divided into sections. Megatests use keywords  
from three sections: _megatests_ for general configuration, _megatests_dm2_  
and _megatests_hg18_ for settings pertaining to specific input data sets.
+The config files follow standard syntax understood by Python's  
[http://docs.python.org/library/configparser.html ConfigParser module],  
i.e. very similar to that of Windows INI files. Among other things this  
means keywords in a file are divided into sections. Megatests use keywords  
from four sections: _megatests_ for general configuration, _megatests_dm2_  
and _megatests_hg18_ for settings pertaining to specific input data sets  
and _megatests_download_ for downloader-specific options.
+
+
+==== The download test ====
+
+The version of the download megatest made available since Pygr 0.8.1  
requires one to specify where the test's built-in HTTP server is to find  
the NLMSA file to serve for downloading. This can be done by setting the  
_httpdServedFile_ keyword in _megatest_download_ to the path and name of  
that file. One can also optionally specify _httpdPort_ to override the  
default TCP port (28145) to be occupied by the built-in HTTP server.
+
+*Note: the download megatest in 0.8.1 has a bug in parsing _httpdPort_  
which prevents the test from running.* To work around that problem, set  
_httpdPort_ in the config file and change line 38 of  
_tests/downloadNLMSA_megatest.py_ from
+
+server_addr = ('127.0.0.1', httpdPort)
+
+to
+
+server_addr = ('127.0.0.1', int(httpdPort))


  ==== Choosing the variant ====