Address

wb-dev.oicr.on.ca

Hardware

The WormBase development server at OICR is a virtual server with the following stats:

Debian Linux
500 GB disk space (mounted at /dev/hda1)
4 GB RAM

Server Configuration

All WormBase components are collected under a single directory: /usr/local/wormbase

$ ls /usr/local/wormbase
  acedb/   // The Acedb database (including bin directory)
  util/    // Utility components such as e-pcr and wublast
  extlib/  // Third party Perl libraries   
  website-classic  // The classic WormBase website
  website  // The new-and-improved website!

Installing Libraries

Assuming a vanilla Debian installation, install the following libaries and all of their dependencies 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
     libreadline5-dev
     flex
     libdb4.6
     libdb-dev
     emacs

Preparing directories and users

WormBase uses several user accounts for directory and server permissions. You will need to create these users and several preliminary directories. Creating a new user and group varies among Unix flavors. On most Linux systems, the following commands will create the new groups. You should have sudo privilege to execute these commands.

User and group accounts

These users should not have a login password. They are to establish privileges only.

acedb group

This is the group that will have write privileges to the acedb directory tree. Acedb administrators should be added to this group.

$ /usr/sbin/groupadd acedb

acedb user

This is the user that the acedb server will run as. It should be a member of the acedb group.

$ /usr/sbin/useradd -g acedb -d /usr/local/wormbase/acedb acedb

This useradd command also adds the new acedb user to the acedb group. Note that the acedb user's home directory was set to /usr/local/acedb, a directory which will be created in the next step.

wormbase group

This is a group that will have write privileges to the wormbase directory tree. WormBase administrators and authors should be added to this group.

$ /usr/sbin/groupadd wormbase

This would be a good time to add yourself to the acedb and wormbase groups.

$ /usr/sbin/usermod -a -G acedb,wormbase [your_login_name]

[The '-a' argument keeps this command from deleting other, preexisting group memberships.]

You may need to re-login for these changes to take effect. Use the groups command to check which groups you are a member of:

% groups

Directories

The root container for all things WormBase:

/usr/local/wormbase, owner=root group=wormbase mode=drwxrwsr-x

$ mkdir /usr/local/wormbase
$ chgrp wormbase /usr/local/wormbase
$ chmod 2775 /usr/local/wormbase

External Perl libraries: /usr/local/wormbase/extlib, owner=tharris group=wormbase mode=drwxrwsr-x

$ mkdir /usr/local/wormbase/extlib
$ chgrp wormbase /usr/local/wormbase/extlib
$ chmod 2775 /usr/local/wormbase/extlib

The "classic" website: /usr/local/wormbase/website-classic, owner=root group=wormbase mode=drwxrwsr-x

$ mkdir /usr/local/wormbase/website-classic
$ chgrp wormbase /usr/local/wormbase/website-classic
$ chmod 2775 /usr/local/wormbase/website-classic

/usr/local/wormbase/website-classic/logs, owner=root group=wormbase mode=drwxrwsr-x

$ mkdir /usr/local/wormbase/website-classic/logs
$ chgrp wormbase /usr/local/wormbase/website-classic/logs
$ chmod 2775 /usr/local/wormbase/website-classic/logs

/usr/local/wormbase/website-classic/cache, owner=nobody group=nobody mode=drwxrwsr-x

$ mkdir /usr/local/wormbase/website-classic/cache
$ chown nobody:nobody /usr/local/wormbase/website-classic/cache
$ chmod 2775 /usr/local/wormbase/website-classic/cache

The "util" directory contains components that apply to both the classic and updated site, like wublast and e-pcr.

/usr/local/wormbase/util/wublast, owner=root group=wormbase mode=drwxrwsr-x

$ mkdir /usr/local/wormbase/util/wublast
$ chgrp wormbase /usr/local/wormbase/util/wublast
$ chmod 2775 /usr/local/wormbase/util/wublast

/usr/local/wormbase/acedb, owner=acedb group=acedb,mode=drwxrwsr-x

$ mkdir /usr/local/wormbase/acedb
$ chown acedb:acedb /usr/local/wormbase/acedb
$ chmod 2775 /usr/local/wormbase/acedb

Configure the FTP/Mirroring directory THIS IS NOT DONE YET

~ftp/pub/wormbase, owner=root group=wormbase mode=drwxrwsr-x

$ mkdir ~ftp/pub/wormbase
$ chgrp wormbase ~ftp/pub/wormbase
$ chmod 2775 ~ftp/pub/wormbase

You may ignore this step if you do not plan to mirror the WormBase FTP site. In the examples below, the -p option is used to create the intermediate parents of directories if they don't already exist. If your mkdir doesn't support this option, you will need to create the intermediate directories manually.

Perl modules

CPAN / Environment configuration

I maintain a suite of Perl modules common to WormBase at:

 /usr/local/wormbase/extlib

If you need to over-ride the default version of a module, place it in the extlib directory of either the classic or rearchitecure site:

 /usr/local/wormbase/website-classic/extlib
   OR
 /usr/local/wormbase/website/extlib

Set up CPAN to build modules in the local library path (/usr/local/wormbase/extlib):

 perl -MCPAN -e shell   // Note that you DO NOT need to be sudo...
 cpan> o conf init (only necessary if not prompted)

For the Makefile.PL arguments, enter

 INSTALL_BASE=/usr/local/wormbase/extlib

And for Build.PL enter

 --install_base /usr/local/wormbase/extlib

Prepare/update your CPAN:

cpan> install CPAN
cpan> reload CPAN

Before installing modules, you may need to set your PERL5LIB environment variable to point to include the extlib directory.

 emacs ~/.bash_profile
 export PERL5LIB /usr/local/wormbase/extlib:/usr/local/wormbase/extlib/lib:/usr/local/wormbase/extlib/lib/perl5

Basic required modules

Install the following Perl modules via CPAN. Note that you DO NOT AND SHOULD NOT be sudo..

perl -I/usr/local/wormbase/extlib/lib -MCPAN -e shell

YAML
LWP
ExtUtils::MakeMaker
Bundle::CPAN
Cache::Cache
Cache::FileCache
CGI
CGI::Session     // CPAN installation fails in local dirs; tries to install man3 in system path.
CGI::Cache
CGI::Toggle
Date::Calc
Date::Manip      // CPAN installation fails in local dirs; tries to install man3 in system path.
DB_File
DBI
DBD::mysql   (mysql must be installed first)
Digest::MD5
GD 
GD::SVG
GD::Graph
GD::Graph::pie
HTML::TokeParser
IO::Scalar
IO::String
Image::GD::Thumbnail
MIME::Lite
Net::FTP
Proc::Simple
readline
Search::Indexer
SOAP::Lite
Statistics::OLS
Storable
SVG
SVG::Graph
Test::Pod
Text::Shellwords
Time::Format
WeakRef
XML::SAX
XML::Parser
XML::DOM
XML::Writer
XML::Twig
XML::Simple
Flickr::API
Flickr::API::Simple (private)
Log::Log4perl
Bio::Graphics
Data::Stag
Class::Base

YAML LWP ExtUtils::MakeMaker Bundle::CPAN Cache::Cache Cache::FileCache CGI CGI::Session CGI::Cache CGI::Toggle Date::Calc Date::Manip DB_File DBI Digest::MD5 GD  GD::SVG GD::Graph GD::Graph::pie HTML::TokeParser IO::Scalar IO::String Image::GD::Thumbnail MIME::Lite Net::FTP Proc::Simple readline Search::Indexer SOAP::Lite Statistics::OLS Storable SVG SVG::Graph Test::Pod Text::Shellwords Time::Format WeakRef XML::SAX XML::Parser XML::DOM XML::Writer XML::Twig XML::Simple Flickr::API Log::Log4perl Bio::Graphics Data::Stag Class::Base

Note that even with INSTALL_BASE and install_base set for EUMM/MB, installation of some modules into local non-privileged paths will FAIL. This is almost always due to an attempt to install man pages in system paths not using one of the INSTALL* paths. The only solution with these modules is to install them by hand...

Ace.pm (for the Classic WormBase site)

Ace.pm provides programmatic access to Acedb. You can install it via CPAN:

 cpan> install Ace

During configuration, choose option (3), then set the remaining variables as follows:

 Site-specific configuration files:  /usr/local/wormbase/website-classic/conf
                           CGI path:  /usr/local/wormbase/website-classic/cgi-bin
                          HTML path:  /usr/local/wormbase/website-classic/html

BioPerl

Check out bioperl-live from my developer account:

 $ cd /usr/local/wormbase/build
 $ svn co svn+ssh://USERNAME@dev.open-bio.org/home/svn-repositories/bioperl/bioperl-live/trunk bioperl-live
 $ mv bioperl-live bioperl-live-tharris
 $ cd bioperl-live-tharris
 $ perl ./Build.PL install_base /usr/local/wormbase/extlib
 $ ./Build test
 $ ./Build install

Installing additional Perl modules

To install Perl modules that are not included on this list (or are new dependencies):

1. Your CPAN is configured to install to /usr/local/wormbase/extlib

You can set this in ~/.cpan/CPAN/MyConfig.pm

'makepl_arg' => q[INSTALL_BASE=/usr/local/wormbase/extlib],

OR

2. If building by hand, you call Makefile.PL as:

  perl Make.PL INSTALL_BASE=/usr/local/wormbase/extlib

Generic Genome Browser

GBrowse 2.x

$ cd /usr/local/wormbase/build
$ cvs -d:pserver:anonymous@gmod.cvs.sourceforge.net:/cvsroot/gmod login
$ cvs -d:pserver:anonymous@gmod.cvs.sourceforge.net:/cvsroot/gmod co Generic-Genome-Browser

$ mv Generic-Genome-Browser Generic-Genome-Browser-head-anonymous
$ ln -s Generic-Genome-Browser-head-anonymous development-Generic-Genome-Browser
$ perl ./Build.PL --install_base /usr/local/wormbase/extlib

$ ./Build reconfig
NOTE: Run ./Build reconfig to change existing configuration.
Reuse previous configuration as defaults? [y ]

**Beginning interactive configuration**
Directory for GBrowse's config and support files? [/usr/local/wormbase/website-classic/conf/gb2]

   // DO NOT CHANGE: CGI::Toggle has hard-coded paths
Directory for GBrowse's static images & HTML files? [/usr/local/wormbase/website-classic/html/gbrowse2] 
Directory for GBrowse's temporary data [/usr/local/wormbase/tmp/gbrowse2] 
Directory for GBrowse's example databases [/usr/local/wormbase/website-classic/html/gbrowse2] 
Apache CGI scripts directory? [/usr/local/wormbase/website-classic/cgi-perl/seq]    // Will automatically create a gb2/ subdirectory
Internet port to run demo web site on (for demo)? [8000] 
Apache loadable module directory (for demo)? [/usr/lib/apache2/modules] 
User account under which Apache daemon runs? [www-data] 
Automatically update Apache config files to run GBrowse? [y] n

This will install all the GBrowse libraries into my shared library path. This might not be optimal...

 $ ./Build test
 $ ./Build install

[tharris@wb-dev: GBrowse-1.988-2nGezp]> ./Build apache_conf
NOTE: Run ./Build reconfig to change existing configuration.

INSTRUCTIONS: Paste the following into your Apache configuration
file. You may wish to save it separately and include it using the
Apache "Include /path/to/file" directive. Then restart Apache and
point your browser to http://your.site/gb2/ to start browsing the
sample genomes.

>>>>>> cut here <<<<<
Alias        "/gb2/i/" "/var/tmp/gbrowse2/images/"
Alias        "/gb2"    "/usr/local/wormbase/website-classic/html/gb2"
ScriptAlias  "/gb2"      "/usr/local/wormbase/website-classic/cgi-perl/gb2/gb2"

<Directory "/usr/local/wormbase/website-classic/html/gb2">
  Options -Indexes -MultiViews +FollowSymLinks
</Directory>

<Directory "/usr/local/wormbase/website-classic/cgi-perl/gb2/gb2">
  SetEnv PERL5LIB "/usr/local/wormbase/extlib/lib:/usr/local/wormbase/extlib:/usr/local/wormbase/extlib/lib/perl5/x86_64-linux-gnu-thread-multi:/usr/local/wormbase/extlib/lib/perl5"
  SetEnv GBROWSE_CONF   "/usr/local/wormbase/website-classic/conf/gb2"
</Directory>


<IfModule mod_fastcgi.c>
  Alias /fgb2 "/usr/local/wormbase/website-classic/cgi-perl/gb2/gb2"
  <Location /fgb2>
    SetHandler   fastcgi-script
  </Location>
  FastCgiConfig -initial-env PERL5LIB=/usr/local/wormbase/extlib/lib:/usr/local/wormbase/extlib:/usr/local/wormbase/extlib/lib/perl5/x86_64-linux-gnu-thread-multi:/usr/local/wormbase/extlib/lib/perl5 -initial-env GBROWSE_CONF=/usr/local/wormbase/website-classic/conf/gb2
</IfModule>

<IfModule mod_perl.c>
   Alias /mgb2 "/usr/local/wormbase/website-classic/cgi-perl/gb2/gb2"
   PerlSwitches -I/usr/local/wormbase/extlib/lib -I/usr/local/wormbase/extlib -I/usr/local/wormbase/extlib/lib/perl5/x86_64-linux-gnu-thread-multi -I/usr/local/wormbase/extlib/lib/perl5
   <Location /mgb2>
     SetHandler perl-script
     PerlResponseHandler ModPerl::Registry
     PerlOptions +ParseHeaders
   </Location>
</IfModule>

GBrowse 1.x stable

 $ cd /usr/local/wormbase/build
 $ cvs -d :pserver:anonymous@gmod.cvs.sourceforge.net:/cvsroot/gmod login
 $ cvs -d :pserver:anonymous@gmod.cvs.sourceforge.net:/cvsroot/gmod co -r stable Generic-Genome-Browser
 $ ln -s Generic-Genome-Browser-stable-anonymous
 $ perl Makefile.PL INSTALL_BASE=/usr/local/wormbase/extlib
   Apache root directory (enter  for none)? 
   Apache conf directory? [/etc/apache2] /usr/local/wormbase/website-classic/conf
   Apache htdocs directory? [/var/www] /usr/local/wormbase/website-classic/html
   Apache cgibin directory? [/usr/lib/cgi-bin] /usr/local/wormbase/website-classic/cgi-perl/seq
   GBrowse root for static files? [gbrowse] gbrowse

AceDB

I always build acedb from source.

$ tar xzf ACEDB-source*    // CAUTION: Tarbomb.
// Requires installation of a whole bunch of things first: libgtk2.0-0 libgtk2.0-dev libglib, byacc, etc, etc
// Modify the makefile: create a target for server programs (xace tace saceserver sgifacerver)
// This is all I care about:
   SERVERS = xace tace saceserver sgifaceserver saceclient
   servers: $(SERVERS)
$ export ACEDB_MACHINE=LINUX_4
$ make servers
$ cd ~acedb
$ ln -s bin-VERSION bin 
$ cp tace xace sgifaceserver saceserver saceclient ~acedb/bin/.
$ sudo chown root:root ~acedb/bin/*

Testing the Installation

At this point, you can test whether the socket server runs correctly. Provided that you have added yourself to the acedb group, you can run the following command:

 % ~acedb/bin/sgifaceserver ~acedb/wormbase
 // Database directory: /usr/local/wormbase/acedb/wormbase
 // Shared files: /usr/local/acedb
 // #### Server started at 2001-07-23_16:42:31
 // #### host=mondseer.cshl.org  listening port=23100
 // #### Database dir=/usr/local/acedb/elegans
 // ####  Working dir=/usr/local/acedb/elegans
 // #### clientTimeout=600 serverTimeout=600 maxKbytes=0 autoSaveInterval=600

 // Server listening socket 28 created

The line "listening port=23100" indicates that the server is listening to port 23100. Open a new terminal window and use saceclient to confirm that you can communicate with the server:

% ~acedb/bin/saceclient localhost -port 23100
Please enter userid: anonymous
Please enter passwd:
acedb@localhost> find Sequence
// Response: 65 bytes.

// Found 236493 objects in this class
// 236493 Active Objects
acedb@localhost> quit
// Closing connection to server.
// Client sent termination signal by server.
// Response: 13 bytes.
// A bientot
// Please report problems to acedb@sanger.ac.uk
// Bye

Configuring Acedb to start automatically under xinetd

Install xinetd (not standard in Debian) if you didn't already:

  $ sudo apt-get install xinetd

Create a configuration file for acedb:

 $ sudo emacs /etc/xinetd.d/acedb-wormbase 

 # file: /etc/xinetd.d/acedb-wormbase
 # default: on
 # description: wormbase acedb database
 service acedb
 {
        protocol                = tcp
        socket_type             = stream
        port                    = 2005
        flags                   = REUSE
        wait                    = yes
        user                    = acedb
        group                   = acedb
        log_on_success          += USERID DURATION
        log_on_failure          += USERID HOST
        server                  = /usr/local/wormbase/acedb/bin/sgifaceserver
        server_args             = /usr/local/wormbase/acedb/wormbase 1200:1200:0
 }

Edit /etc/services. Although xinetd is not supposed to use /etc/services, the following line must be added:

acedb-wormbase           2005/tcp

Restart xinetd with the following command:

# /etc/init.d/xinetd reload (or restart)

You should now be able to talk to the database using saceclient:

% ~acedb/bin/saceclient localhost -port 2005

MySQL

Installation

Install mysql and various libraries via apt-get if you haven't already:

 $ sudo apt-get install mysql-server-5.0 mysql-server libdbd-mysql libdbd-mysql-perl

If it fails, then disable innodb by default. edit /etc/mysql/my.cnf file (uncomment the line):

 #skip-innodb
 $ sudo apt-get purge   mysql-server-5.0 mysql-server  
 $ sudo apt-get install mysql-server-5.0 mysql-server

With this installation, databases are located at /var/lib/mysql. We want to able to write to this directory from the command line, so:

 $ sudo chmod 2775 /var/lib/mysql

Mysqld will automatically be setup to launch at server boot (rc3 and rc5) -- no need to mess with init scripts.

Set up mysql permissions

# mysql -u root -pPASSWORD
 mysql> grant select on elegans.* to nobody@localhost;

Repeat for:

c_briggsae
c_japonica
c_remanei
c_brenneri
p_pacificus
b_malayi
c_elegans_gmap
c_elegans_pmap
autocomplete
h_bacteriophora

Apache2 and mod_perl

Installation

sudo apt-get install apache2
sudo apt-get install libapache2-mod-perl2

Configuration

We will set up WormBase to be a virtual host running on the default port 80. Add the following configuration directives to /etc/apache2/sites-enabled/000-default:

<VirtualHost *:80>
   Include /usr/local/wormbase/website-classic/conf/httpd.conf
   // ServerName dev.wormbase.org
   // UseCanonicalName on
</VirtualHost>

Be certain to remove or comment out the default configuration.

Modify /usr/local/wormbase/website-classic/conf/httpd.conf to match the new directory layout.

TODO: I NEED TO ACCOUNT FOR OTHER VIRUTAL SERVERS RUNNING ON THE DEVELOPMENT SITE

Important Fix for mod_perl2/mod_dir incompatibility (the index.html problem)

mod_perl2 intercepts Apache requests before any other modules. This means that for locations/directories configured with PerlHandlers that requests for dir or dir/ will NOT automatically redirect to the value of DirectoryIndex. To fix this problem, the lib/Apache/AddWormBaseBanner.pm needs to be modified:

Insert the following:

# We need two additional modules:
use Apache2::Const -compile => qw(DIR_MAGIC_TYPE OK DECLINED);
use Apache2::SubRequest;

sub handler {
   my $r = shift;
 # --> Copy and paste starting here...
 # A directory request has content-type = httpd/unix directory                                                             
 # we check that the uri ends in a slash, since only in that case                                            
 # do we want to redirect, and finally to avoid redirect loops                                                                                      
 # we only do this on the initial request.                                                                                                
 # You must load Apache2::SubRequest in order to run internal_redirect                                                                                                        
 if ($r->content_type eq 'httpd/unix-directory'
     && $r->uri =~ '/$' && $r->is_initial_req ) {
     #        print STDERR "Accepting Directory Request\n";                                                                                                          
      # warn "internal request";                                                                                                                                                                                
       $r->internal_redirect($r->uri . 'index.html');
       return OK;
   }

Build ePCR NOT DONE

e-PCR (modified version, required for e-PCR search page)

This is located in the directory /usr/local/wormbase/e-PCR, which will come into existence after the WormBase site update program wb_update_wormbase.pl has been successfully run (see below for details). Once the directory has been generated, run:

   $ cd /usr/local/wormbase/e-PCR
   # Edit 'makefile' to run install rather than ginstall, which doesn't exist on Fedora Linux
   $ make
   $ make install   # or just run 'install e-PCR /usr/local/bin'

The file /usr/local/wormbase/e-PCR/README-Wormbase describes the changes that were made to the original e-PCR distribution.

Installing BLAT

Jim Kent's BLAT (blast-like alignment tool) is a fast nucleotide aligner used by the blast search page. If you do not plan to support blast searches, you may safely skip this step.

# mkdir -p /usr/local/blat/bin¬†; cd /usr/local/blat/bin
 % wget http://www.soe.ucsc.edu/~kent/exe/linux/blatSuite.33.zip  (for Intel Linux)
% unzip blatSuite.33.zip
% rm blatSuite.33.zip version.doc 11.ooc

Note that this choice gives precompiled binaries for an Intel-based Linux distribution as of March 2006. It would probably be worth checking http://www.soe.ucsc.edu/~kent/exe/linux to see if there is a more up-to-date version than 33. Also, other operating systems will need other binaries. E.g., for Mac OS X, instead run:

 % wget http://www.soe.ucsc.edu/~kent/exe/osX/blatSuite.33.zip

For other types of operating systems (e.g., Linux on Opteron-based machines), see http://www.soe.ucsc.edu/~kent/exe/ for the available choices.

The blat server will be started automatically by the update script. For reference, the blat server is launched using the following command.

% /usr/local/blat/bin/gfServer start localhost 2003 \
     /usr/local/wormbase/blat/*.nib & > /dev/null 2>&1

Installing BLAST

The Blast page requires WU-BLAST. This is a closed-source derivative of NCBI's BLAST. However, WU-BLAST is free to academic users (with licensing) and is thought to have performance advantages over NCBI-BLAST; it can be downloaded from http://blast.wustl.edu/. A typical choice of WU-BLAST for Linux is blast2.linux26-i686.tar.gz.

Conversely, the Blast page can be deactivated if you don't want to provide BLAST searches at your site.

By default, WormBase expects WU-BLAST to be installed in /usr/local/wublast. This is the directory structure used by WormBase:

% ls -l /usr/local/wublast
ls -l /usr/local/wublast
total 72
lrwxrwxrwx  1 root  root     18 May  7 12:26  BLOSUM62 -> matrix/aa/BLOSUM62
-rw-r--r--  1 root  root  46789 Feb  5  1998  HISTORY
-rw-r--r--  1 root  root   6648 Mar  4  1997  README
drwxr-xr-x  2 root  root   4096 May  7  12:46 bin/
lrwxrwxrwx  1 root  root     25 Jul 24  08:20 databases -> /usr/local/wormbase/blast/
drwxr-xr-x  2 root  root   4096 Jan 27  2000  filter/
drwxr-xr-x  4 root  root   4096 Oct  4  1998  matrix/

which can be set up in this manner (adapt to your system):

$ cd /usr/local/wublast
$ zcat /usr/local/TGZ/blast2.linux26-i686.tar.gz | tar xf -
$ chown -R root:root *
$ mkdir bin
$ mv *fasta tblast* blast* *db xd* memfile pam wu-blastall bin
$ ln -s /usr/local/wormbase/blast databases

The important thing to note is that the databases directory is a symbolic link to /usr/local/wormbase/blast. This is where the update_wormbase.pl script (described in the next section) dumps its BLAST databases.

The WormBase Software

Check out the WormBase software from CVS:

 $ cd /usr/local/wormbase
 $ cvs -d formaggio.cshl.org:/usr/local/cvs_repository co wormbase-website
 $ mv wormbase-website website-classic

Configure localsdef.pm

$HOST

This is the name of the host where the socket server runs. It is set to "localhost" by default.

$PORT

This is the port on which the socket server runs, 2005 by default.

$ACEPASS, $USERNAME, $PASSWORD

These three items define the acedb username and password.

$MYSQL_HOST, $MYSQL_USER, $MYSQL_PASS

These three items define the mysql host, username, and password.

$MASTER

This is used only for the WormBase master site. Should be set to 0.

$MIRROR

Whether or not the site is a mirror. Should be set to the name of the mirror.

$DEVELOPMENT

Whether or not the site is a development site. Internally, this controls the nature of caching on the site. Should be set to 0.

$BLAST2WORMBASE, $WORMBASE2BLAST

These two options control where the blast script directs queries, and where those queries are returned. This is provided in the event that a second standalone blast server is provided. If not, these two options should point to:

$WORMBASE2BLAST=http://your.hostname.org/

Configuring Servers To Start Automatically

The final step is to arrange for Acedb to start automatically and for MySQL to restart if necessary.

Installing MySQL and BLAT monitoring scripts

Run:

   $ cp -i /usr/local/wormbase/util/admin/blat_server.initd /etc/rc.d/init.d/blat_server

Then run:

   $ crontab -u root -e

to add the following entries to root's crontab:

   0 * * * * /usr/local/wormbase/util/admin/restart_mysqld.pl
   0 * * * * /usr/local/wormbase/util/admin/restart_blat.pl

Acedb log rotation

Acedb generates massive log files. To keep these from growing too large, add the following entry to root's crontab (or that of another privileged user):

   10 1 * * * /usr/local/wormbase/bin/rotatelogs.pl

Installing scripts to verify that the servers are running

Two scripts in the WormBase directory can be used to ensure that the mysql and blat servers are running. To install, them:

% sudo cp /usr/localwormbase/util/admin/blat_server.initd \
          /etc/rc.d/init.d/blat_server

Place the restart scripts under cron control of a privileged user. These commands will check every hour to see that the servers are running.

 % sudo crontab -u root -e

0 * * * * /usr/local/wormbase/util/admin/restart_mysqld.pl
0 * * * * /usr/local/wormbase/util/admin/restart_blat.pl

At the same time, you might also wish to automate the rotatation of logs to prevent them from growing to an unwieldy size. You'll find an appropriate log rotation configuration stanza in util/rotate_wormbase_logs and a log rotate script in /usr/local/wormbase/bin/rotatelogs.pl. You will need both.

# Rotate httpd logs
 10 1 * * * /usr/local/wormbase/bin/rotatelogs.pl
 # Rotate acedb logs
 10 1 * * * logrotate /usr/local/wormbase/util/rotate_wormbase_logs

This stanza will check that the acedb server logs do not grow larger than 100 MB.

Testing The Site

At this point, all components of a WormBase installation have been installed. You can test your installation by restarting the various server components of WormBase.

Restarting AceDB

# Via xinetd:
 $ /etc/init.d/xinetd reload (or restart)

# ...or using saceclient
 % saceclient localhost -port 2005
 acedb> password:
 acedb> shutdown now

Restarting MySQL

# Via mysqladmin...
 % mysqladmin -uroot -pPASSWORD shutdown
 
 # or using init.d
 $ /etc/init.d/mysql restart

Restarting Apache

When the configuration files have been checked and adjusted, restart Apache with the following command:

 $ /etc/init.d/apache restart

Check /usr/local/wormbase/logs/classic-error_log for WormBase-specific errors and /var/log/apache2/error_log for general errors.

BLAT

% /usr/local/blat/bin/gfServer start localhost 2003 \
     /usr/local/wormbase/blat/*.nib & > /dev/null 2>&1

Blocking robots

It can be useful to block search engines (such as Google) from crawling over one's mirror. To do this, go to /usr/local/wormbase/html, and make a file called "robots.txt" with the following contents:

   User-agent: *
   Disallow: /

Updating Production Nodes to match this reality

1. Create /usr/local/wormbase/website-classic

2. Move all website files into website-classic

3. Move database to /usr/local/wormbase

4. Create /usr/local/wormbase/logs

5. Install Perl Modules as described above

6. Install GBrowse as described above

7. Update admin module for pushing software to production (and for maintaining staging module)

AUTHOR

Todd Harris

OICR-Configuring the development machine

Contents

Address

Hardware

Server Configuration

Installing Libraries

Preparing directories and users

User and group accounts

Directories

Configure the FTP/Mirroring directory THIS IS NOT DONE YET

Perl modules

CPAN / Environment configuration

Basic required modules

Ace.pm (for the Classic WormBase site)

BioPerl

Installing additional Perl modules

Generic Genome Browser

AceDB

Testing the Installation

Configuring Acedb to start automatically under xinetd

MySQL

Installation

Set up mysql permissions

Apache2 and mod_perl

Installation

Configuration

Important Fix for mod_perl2/mod_dir incompatibility (the index.html problem)

Build ePCR NOT DONE

Installing BLAT

Installing BLAST

The WormBase Software

Configure localsdef.pm

Configuring Servers To Start Automatically

Installing MySQL and BLAT monitoring scripts

Acedb log rotation

Installing scripts to verify that the servers are running

Testing The Site

Restarting AceDB

Restarting MySQL

Restarting Apache

BLAT

Blocking robots

Updating Production Nodes to match this reality

AUTHOR

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