[pygr-notify] [pygr commit] r190 - Edited wiki page through web user interface.

[codesite-noreply at google.com]

Author: marecki
Date: Fri Apr 17 18:43:02 2009
New Revision: 190

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 18:43:02 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 (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 MySQL server (version 5 is recommended), with write access during  
set-up and read access during running. 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;

@@ -86,11 +86,14 @@

  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 ==
+== Configuration ==
+
+== MySQL access ==
+
+Megatests assume the database they use is located on the default MySQL  
server and accessed using default user name/password. If your system-wide  
defaults do not match the desired values of these parameters, you'll need  
to override them - using a standard MySQL option file. Under Linux/Unix you  
will most likely use the per-user option file _$HOME/.my.cnf_ file in your  
home directory

-Next step is to prepare MySQL database in which all above txt input files  
are saved. First, you need to make the _.my.cnf_ file in your HOME  
directory.
+have it contain something like this:
  {{{
  [client]
  port=3306
@@ -98,7 +101,10 @@
  user=your_account
  password=your_password
  }}}
-Pygr will automatically try to load ~/.my.cnf to connect MySQL database.
+
+For more information on the subject of MySQL option files, see  
http://dev.mysql.com/doc/refman/5.1/en/option-files.html.
+
+XXX


  == Choosing the variant ==