Building Frozen Releases

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Revision as of 19:38, 14 June 2009 by Tharris (talk | contribs)
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Hardware

WormBase frozen releases are hosted on the virtualized server:

wb-dev2.oicr.on.ca

  • 500 GB disk space
  • 4 GB RAM
  • Debian "Lenny"

Server Configuration

All WormBase-specific files are maintained in a shared directory.

ls /usr/local/wormbase
    acedb/
    logs/    // Cross-site logs
    WS100    // WS100 website
    WS110    // WS110 website
    WS120    // WS120 website
    ...

Each frozen release is a separate virtual host running under a single Apache instance. To prevent collision of libraries, version specific Perl modules are maintained in:

  /usr/local/wormbase/VERSION/extlib

@INC is prepended with this path for each virtual host during apache launch.

Users, groups, directories

Set up the basic users, groups, and directories as previously described.

Installing system libraries

Assuming a vanilla Debian installation, install the following libaries via sudo apt-get install. Some of these libraries are discussed below.

     gcc
     curl
     wget
     bzip2
     mysql-server
     mysql-server-5.0
     libgd2-xpm-dev
     libgd2-xpm
     xinetd
     libdbd-mysql
     libdbd-mysql-perl
     apache2
     libapache2-mod-perl2
     libgtk2.0-0
     libgtk2.0-dev
     libglib
     byacc

AceDB

Build AceDB as previously described.

MySQL

Install and configure MySQL as previously described.

Each frozen release will have one or more database of the form species_VERSION or g_species_VERSION. Give access to each of these for the www-data user:

grant select on elegans_WS110.* to www-data@localhost;

Apache2 and mod_perl2

Install and configurate Apache2 and mod_perl2 as described.

Set up name based virtual hosts for each frozen release as follows:

<VirtualHost *:80>
   Include /usr/local/wormbase/VERSION/conf/httpd.conf
   ServerName ws[VERSION].wormbase.org
   UseCanonicalName on
</VirtualHost>

Be certain to remove or comment out the default configuration.

Fetch frozen releases and unpack

$ ssh brie4 
$ cd ~ftp/pub/wormbase
$ screen
$ scp -r data_freezes wb-dev.oicr.on.ca:.
  • Unpack acedb_VERSION.ace.tgz or elegans_VERSION.ace.tgz into /usr/local/wormbase/acedb/
  • Unpack GFF databases into /var/lib/mysql/
  • Prepend the version onto each mysql database: species_VERSION or g_species_VERSION

WHERE DO THE BLAST/BLAT DATABASES GO?

Fix configuration files

perl.startup

  • Insert the VERSION into all appropriate "use lib" statements.
  • Add "use Apache2::compat" for mod_perl1 backwards compatability.

httpd.conf

  • Change all occurrences of /usr/local/wormbase to /usr/local/wormbase/VERSION
  • Change the ServerName as appropriate
  • Prepend the version to both the error and access logs
  • Remove any unnecessary configuration (DAV, mailarch, etc)
  • In the "Location /db/" stanza, replace the PerlHandler line with:
  PerlResponseHandler   ModPerl::Registry

elegans.pm

  • Update the WS200 variable
  • Change the symbolic name of the acedb database to wormbase_VERSION
  • Append the version to all GFF databases

gbrowse.conf

  • Append the version to all GFF databases