Administration:Installing WormBase

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This document describes how to install WormBase locally on your own machine. Please note that as of August 2013, WormBase is almost entirely a distributed cloud-based application. Although possible to install and run on a single server (or cloud instance) the directions below may be slightly out-of-sync with how the principal WormBase architecture is built.



As of April 2012, the suggested minimum hardware requirements for a basic installation of WormBase are:

  • 500 GB disk space (1 TB preferable)
  • 8 GB RAM

Operating Systems

You should be able to install and run the site on any Unix-y OS, including Mac OS X. This document only describes installation on Debian and Debian-ish OSes like Amazon's Linux. Your actual mileage may vary on other operating systems.

Basic System Configuration

Users And Groups

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.

$ groupadd acedb

acedb user

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

$ 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.

$ groupadd wormbase

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

$ usermod -a -G acedb,wormbase [your_login_name]

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

Create Directories

Create a root directory for all WormBase-related files. Although this directory can reside anywhere on your filesystem, for consistency with WormBase proper, we recommend installing at /usr/local/wormbase. You'll need suitable privileges to install in this location.'

The root container for all things WormBase

  • /usr/local/wormbase, owner=root group=wormbase mode=drwxrwsr-x
$ cd /usr/local
$ sudo mkdir wormbase
$ sudo chown root:wormbase wormbase
$ sudo chmod 2775 wormbase

The AceDB directory contains acedb and associated databases:

  • /usr/local/wormbase/acedb, owner=acedb group=acedb,mode=drwxrwsr-x
$ mkdir /usr/local/wormbase/acedb
$ chmod 2775 /usr/local/wormbase/acedb
$ sudo chown acedb:acedb /usr/local/wormbase/acedb

The website/ directory contains one or many versions of the website:

  • /usr/local/wormbase/website, owner=[ANYONE] group=wormbase,mode=drwxrwsr-x
$ mkdir /usr/local/wormbase/website
$ chmod 2775 /usr/local/wormbase/website
$ sudo chgrp wormbase /usr/local/wormbase/website

The services/ directory contains optional services such as e-pcr, blast, and nginx:

  • /usr/local/wormbase/services, owner=[ANYONE] group=wormbase,mode=drwxrwsr-x
$ mkdir /usr/local/wormbase/services
$ chmod 2775 /usr/local/wormbase/services
$ sudo chgrp wormbase /usr/local/wormbase/services

The databases/ directory contains databases driving a number of features:

  • /usr/local/wormbase/databases, owner=[ANYONE] group=wormbase,mode=drwxrwsr-x
$ mkdir /usr/local/wormbase/databases
$ chmod 2775 /usr/local/wormbase/databases
$ sudo chgrp wormbase /usr/local/wormbase/databases

The logs/ directory contains WormBase-wide log and pid files

  • /usr/local/wormbase/logs, owner=[ANYONE] group=wormbase,mode=drwxrwwrwx
$ mkdir /usr/local/wormbase/logs
$ chmod 2775 /usr/local/wormbase/logs
$ sudo chgrp wormbase /usr/local/wormbase/logs

Installing Library Prerequisites

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.

     sharutils \
     gcc g++ \
     curl wget \
     bzip2 \
     mysql-client \
     mysql-server \
     libgd2-xpm \
     xinetd \
     libdbd-mysql \
     libdbd-mysql-perl \
     libapache2-mod-perl2 \
     libgtk2.0-0 \
     libgtk2.0-dev \
     emacs \
     git \
     byacc \
     libreadline-gplv2-dev \
     flex \
     libdb4.6 \
     libdb-dev \
     xml2 libxml2 libxml2-dev \
     libmysql++-dev \
     ncurses-bin \
     libxmu-dev \
     graphviz \
     libssl-dev \
     uuid \
     uuid-dev \
     libxslt1-dev \
     xsltproc \
     libgdbm3 \
     libgdbm3-dev \
     libstdc++ \

Build xapian (or install from package if available):

$ wget
$ tar xzf xapian-core*.tgz
$ cd xapian-core
$ ./configure
$ make
$ sudo make install

Install Search::Xapian

$ perl -MCPAN -e 'install Search::Xapian'

Install Perl 5.10.1 or greater

You'll need Perl version 5.10.1 or greater.

Upgrading Perl via apt (recommended)

Let your operating system managing your version of Perl.

Configure your apt preferences

Add the following to /etc/apt/sources.list

deb stable main non-free contrib
deb testing main non-free contrib
deb unstable main non-free contrib

Configure your preferences in /etc/apt/preferences:

Package: *
Pin: release a=stable
Pin-Priority: 700
Package: *
Pin: release a=testing
Pin-Priority: 650
Package: *
Pin: release a=unstable
Pin-Priority: 600

Finally, install Perl

sudo apt-get update
sudo apt-get install perl/testing perl-base/testing perl-modules/testing libperl5.10/testing libperl-dev/testing

And confirm

$ perl -v
 This is perl, v5.10.1 (*) built for x86_64-linux-gnu-thread-multi
 (with 40 registered patches, see perl -V for more detail)

Installing Perl from source

We recommend installing a local version of Perl and required libraries. This makes management dramatically easier. We keep our Perl with the webapp itself.

If you have sufficient privileges, you may wish to use your pre-installed system Perl.

bash> mkdir ~/website/perl
bash> cd ~/src
bash> curl -O
bash> cd ~/build
bash> tar xzf ../src.perl-5.10.1.tar.gz
bash> cd perl-5.10.1
bash> ./Configure -des -Dprefix=$HOME/website/perl/5.10.1
bash> make
bash> make test
bash> make install

Be sure to set up your your system to preferentially use this newly installed Perl:

bash> export PATH=~/wormbase/perl/5.10.1/bin:${PATH}

Install the Webapp

Fetch the current production code from the git repository on github.

$ cd /usr/local/wormbase/website
$ git clone
$ mv website YOUR_NAME // name can be anything you want; useful for maintaining multiple versions

Install local:: lib

The preferred method uses the web app's Makefile.PL and Module::Install to build all dependencies. We maintain local copies of all libraries with each version of the webapp.

Build and install dependencies

$ mkdir /usr/local/wormabase/extlib
$ cd /usr/local/wormbase/website/YOUR_NAME
$ perl Makefile.PL
$ make installdeps

See the documentation on Managing Perl Libraries for additional details.

Required 3rd-party Applications

Starman: the lightweight http server

PSGI: specification for Perl superglue between frameworks and servers. Plack is an implementation of PSGI. Compare to Rack (Ruby) or Jack (Javascript).

Starman is a high performance pre-forking Perl PSGI server. We're using it in place of Apache+fastcgi.mod_perl.

Install Plack and Starman

cpanm Task::Plack
cpanm Starman


The PSGI glue resides at:


Starting Starman

starman script/wormbase.psgi
starman -MFindBin script/wormbase_production.psgi

Set up starman to launch automatically

Copy the stub init script from wormbase/conf/starman/starman.init:

 cp /usr/local/wormbase/admin/conf/starman/starman.init


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)
$ 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 ACeDB 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
 // ####  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
// 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-wormbase
        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:

$ sudo /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



Install mysql and various libraries via apt-get if you haven't already. You will need the unstable and testing repositories set up when upgrading Perl.

 $ sudo apt-get install libncurses5/testing
 $ sudo apt-get install mysql-common/testing libmysqlclient16 mysql-server-5.1/testing \
         mysql-client-5.1/testing libdbd-mysql/testing libdbd-mysql-perl/testing

With this installation, databases are located at /var/lib/mysql. We want to relocate this to /usr/local/mysql/data to be consistent with the WormBase. We also want to able to write to this directory from the command line, so:

$ sudo nano /etc/my.cnf
Set datadir to /usr/local/mysql/data
$ mkdir -p /usr/local/mysql/data
$ sudo chown -R mysql:mysql /usr/local/mysql
$ sudo chmod 2775 /usr/local/mysql/data 

Mysqld will automatically be setup to launch at server boot (rc3 and rc5).

Set up mysql permissions

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

Repeat for:

  • autocomplete
  • b_malayi
  • c_briggsae
  • c_elegans
  • c_elegans_gmap
  • c_elegans_pmap
  • c_japonica
  • c_remanei
  • c_brenneri
  • h_bacteriophora
  • p_pacificus
  • ps1010

Generic Genome Browser

See GBrowse Administration for details on how to install GBrowse.

Optional 3rd-party Applications


We use nginx as a lightweight proxy server and load balancing server. You can skip this step and simply connect directly to the Starman http server. Otherwise, see the production environment documentation on installing and configuring nginx.


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 A typical choice of WU-BLAST for Linux is blast2.linux26-i686.tar.gz.

You can skip this step if you don't want to provide BLAST services at your site.

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

$ ls -l /usr/local/wormbase/services/wublast
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/


A modified version of the epcr source can be found in the checked out website code in src/. See the enclosed README describing changes made to the original e-PCR distribution. The binary should be placed in /usr/local/wormbase/services.

   $ cd /usr/local/wormbase/website/production/src
   $ make
   $ install e-PCR /usr/local/wormbase/services/epcr


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/wormbase/services/blat/bin
 $ cd /usr/local/wormbase/services/blat/bin
 $ wget  (for Intel Linux)
 $ unzip
 $ rm 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 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

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

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

Installing Databases NOT DONE

Primary database (AceDB)

GFF Sequence feature database (MySQL)

Support Databases

Support databases are automatically synced to the nodes that require them by wormbase-admin/update/production/ This is run from wb-dev.

0 1 * * * /home/tharris/projects/wormbase/wormbase-admin/update/production/

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

Starting The Webapp

Set up environment:

$ cd /your/checked/out/source
$ cp wormbase.env.template wormbase.env  // Edit as necessary.
$ source wormbase.env

Start the built in development server:

$ script/wormbase_server -p 9999 -r -d   // choose a suitable port.

Start up a starman server via plack:

$ cd /your/checked/out/source
$ source wormbase.env
$ starman -- port 9999 wormbase.psgi // choose a suitable port.

At this point, you should now be able to connect to WormBase at:


If you are running your site on one of the ports matching the nginx reverse proxy configuration as described above, you should be able to:

To run your site using the init script:

source wormbase.env
./script/ start


Checking out the Administration module

Fetch the administration code repository (privileged users only, for now)

todd> mkdir -p ~/projects/wormbase
todd> cd ~/projects/wormbase
todd> hg clone ssh://  // Assuming you have already set up your ssh keys at bitbucket

Updating the web application

Updating databases

Backing up your system


Set up the following cronjobs:

Log Rotation (root cron)

# Rotate WormBase logs
10 1 * * * /home/todd/projects/wormbase/admin/maintenance/

Or via logrotate:

00 00 * * * /usr/sbin/logrotate -s /var/tmp/logrotate.status /usr/local/wormbase/admin/crons/wormbase-logrotate.conf

The contents of this file look like this:

/usr/local/wormbase/logs/*_log {
        rotate 3650  # keep 10 years worth of logs
        mail   # when a log file expires, email it to me.
                /usr/local/apache2/bin/apachectl graceful

For nodes running acedb, add the following entry which deals with its massive log files:

# Purge epic ACEDB logs
35 * * * * /home/todd/projects/wormbase/admin/maintenance/

Watch for runaway httpd processes:

  • /5 * * * * /usr/local/wormbase/admin/monitoring/

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

Installing MySQL and BLAT monitoring scripts NOT DONE


   $ 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/
   0 * * * * /usr/local/wormbase/util/admin/

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 \

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/
0 * * * * /usr/local/wormbase/util/admin/

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/ You will need both.

# Rotate httpd logs
 10 1 * * * /usr/local/wormbase/bin/
 # 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.

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: /


Appendix 1: Mac OS 10.6 (Snow Leopard) Prequisites

XCode > 3.21

You will need this for building C libraries as well as fixing the broken Perl that shipping with 10.6.

MySQL >= 5.1

MySQL is not expressly required, but you do need it for building DBD::mysql.

bash> cd src
bash> curl -O
bash> tar xzf mysql-5.1.41.tar.gz
bash> cd mysql-5.1.41
bash> ./configure --prefix=/usr/local/mysql \
                  --with-extra-charsets=complex \
                  --enable-thread-safe-client \
                  --enable-local-infile \
                  --enable-shared \
bash> make
bash> sudo make install
bash> cd /usr/local/mysql
bash> sudo ./bin/mysql_install_db --user=mysql
bash> sudo chown -R mysql ./var


bash> curl -O
bash> tar xzf libpng-*
bash> ccd libpng*
bash> ./configure
bash> make
bash> sudo make install


bash> curl -O
bash> tar xzf gd*
bash> cd gd*
bash> ./configure
bash> make
bash> sudo make install

Appendix 2: mod_perl and Apache installation

WormBase no longer runs off apache and mod_perl, although it is entirely possible to do so. Here's how to install these components.

I prefer to build httpd and mod_perl from source; it seems easier than waiting for package repositories to be updated. Besides, I really despise Debian's apache layout. It's horrid.


Assuming you have already fetched the source into ~/src:

# Build httpd 2.2.11
cd ~/src
tar xzf httpd-2.2.11.tar.gz
cd httpd-2.2.11
./configure --enable-mods-shared=all --enable-proxy
sudo make install
# Build mod_perl2-0.4
cd ~/src
cd mod_perl-2.0.4
perl -I/usr/local/wormbase/website-classic/extlib Makefile.PL INSTALL_BASE=/usr/local/wormbase/website-classic/extlib
// When prompted for the apxs path, enter: /usr/local/apache2/bin/apxs
sudo make install


We typically set up services as individual virtual servers. Here's an example. See "Special Services" below for additional details.

Modify the primary httpd.conf file (/usr/local/apache2/conf/httpd.conf) as follows:

#User daemon
User nobody

Set up a virtual host on your port. Adjust PerlSwitches as appropriate for your architecture, and the Listen directive of the primary apaache httpd.conf file as appropriate.

<VirtualHost *:80>
  Include /usr/local/wormbase/website-classic/conf/httpd.conf
  PerlOptions +Parent
  PerlSwitches -Mlib=/usr/local/wormbase/website-classic/extlib/lib/perl5 \
  #   PerlInterpStart 2                                                                                                
   #   PerlInterpMax 2                                                                                              
  <Directory "/usr/local/wormbase/website-classic/html">
       DirectoryIndex index.html
       #       Order deny,allow         
       #       Deny from all                                                                                            
  # Redirect requests for the old movable type atom feeds to feedburner
  RewriteEngine ON
  #   RewriteRule ^/rss/wormbase-live-atom\.xml$ [R=301,L]
  RewriteRule ^/rss/wormbase-live-atom\.xml$ [R=301,L]
  RewriteRule ^/news\.xml$ [R=301,L]
  RewriteRule ^/rss/wormbase-live\.xml$ [R=301,L]

Enable virtual hosts in httpd.conf by uncommenting the following line:

# Include conf/extra/httpd-hosts.conf

Set up httpd to run under inet.d

cd /etc/init.d
sudo ln -s /usr/local/apache2/bin/apachectl httpd

Edit apachectl to make it "LSB" compliant (ie Debian compliant). Add the following after the she-bang:

### BEGIN INIT INFO                                                             
# Provides:          httpd                                                      
# Required-Start:    $all                                                       
# Required-Stop:     $remote_fs $syslog                                         
# Default-Start:     3 5                                                    
# Default-Stop:      0 1 2 4 6                                                      
# Short-Description: Start daemon at boot time                                  
# Description:       Enable service provided by daemon.                         
cd /etc/rc3.d
sudo ln -s ../init.d/apache2 S99apache2
cd ../rc5.d
sudo ln -s ../init.d/apache2 S99apache2

Or via update-rc.d

sudo update-rc.d apache2 start 99 3 5 . stop 0 1 2 4 6 .


cd ~/src
tar xzf php-5.2.4.tar.gz 
./configure --with-apxs2=/usr/local/apache2/bin/apxs --with-mysql
sudo make install


Todd Harris (