Difference between revisions of "Building Frozen Releases"

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       libglib
 
       libglib
 
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== AceDB ==
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Build AceDB as [[OICR-Configuring_the_development_machine#AceDB previously described]].
  
 
== Fetch frozen releases and unpack ==
 
== Fetch frozen releases and unpack ==

Revision as of 19:23, 14 June 2009

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

Please refer to OICR-Configuring_the_development_machine for details.

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 OICR-Configuring_the_development_machine#AceDB previously described.

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