[pygr-notify] [pygr commit] r189 - Edited wiki page through web user interface.

[codesite-noreply at google.com]

Author: marecki
Date: Fri Apr 17 15:54:18 2009
New Revision: 189

Modified:
    wiki/MegatestSetup.wiki

Log:
Edited wiki page through web user interface.

Modified: wiki/MegatestSetup.wiki
==============================================================================
--- wiki/MegatestSetup.wiki	(original)
+++ wiki/MegatestSetup.wiki	Fri Apr 17 15:54:18 2009
@@ -15,7 +15,7 @@

   * A computer system you don't mind placing under heavy load, particularly  
I/O-wise, on a regular basis. Instructions on this page assume a box  
running Linux, which so far is the only operating system we have tried  
running megatests on; Unix(-based) systems should also be supported out of  
the box, Windows should in principle work but will need either Cygwin or a  
custom runner script. _Please let us know about the outcome of attempts of  
running on non-Linux boxes!_

- * A MySQL server with write access to. You'll probably want to use a  
local, dedicated instance to minimise security implications of the above as  
well as possible influence of database-access delays on test results;
+ * A MySQL server (version 5 is recommended) with write access to. You'll  
probably want to use a local, dedicated instance to minimise security  
implications of the above as well as possible influence of database-access  
delays on test results;

   * A (relative) lot of disc space. At present megatests take up about 200  
GB when idle and up to 600 GB while running;

@@ -30,6 +30,8 @@

  Data files need by Pygr megatests can be divided into three categories:  
sequence data in Pygr's _seqdb.BlastDB_ format, NLMSA files for different  
tests, and miscellaneous input/output files. The latter two are installed  
differently from the former one; both procedures will be described here.

+Last but not least, since NLMSA-building megatests are run for both file  
and SQL storage back-ends it is necessary to import data from the last  
category above into a MySQL database. For your convenience we have provided  
MySQL dump-files which can be used for this purpose.
+
  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.


@@ -80,6 +82,10 @@
  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.


+=== 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_).
+
  XXX

  == Setting up the Database ==
@@ -93,12 +99,6 @@
  password=your_password
  }}}
  Pygr will automatically try to load ~/.my.cnf to connect MySQL database.
-
-Then create a database named PYGRDB_JAN06. Files created by _mysqldump_  
are available at http://biodb.bioinformatics.ucla.edu/MEGATEST/ . You can  
import all these .sql files by _mysql_ command. MySQL version 5 or higher  
is recommended for compatability.
-
-Same NLMSA building Megatest will run twice, one for file-saving version  
and
-the other for MySQL version. In each step, text-to-binary conversion test
-is included.


  == Choosing the variant ==