Configuring an Ensembl Website

This section explains the configuration changes you have to make so that Ensembl will run on your local set-up.

N.B. If you installed Ensembl prior to release 31 you will have edited files in the conf directory. From version 32 there is a new approach to configure the site using plugins.

Setting up the "Mirror Plugin"

In the main conf directory you will find a file called Plugins.pm-dist. Copy this file and name it Plugins.pm (i.e. without the -dist extension). This file sets up any plugins required by the website, including the mirror plugin mentioned above.

$SiteDefs::ENSEMBL_PLUGINS = [
  'EnsEMBL::Mirror'    => $SiteDefs::ENSEMBL_SERVERROOT.'/public-plugins/mirror',
  'EnsEMBL::Ensembl'   => $SiteDefs::ENSEMBL_SERVERROOT.'/public-plugins/ensembl'
];

As you can see, the default mirror setup uses two plugins:

• public-plugins/ensembl, which contains all the species configuration files, species home pages and public documentation
• public-plugins/mirror, which contains only the files needed to configure your mirror

Note that the array of plugins is in order of precedence, so that in the default setup, the mirror plugin overrides the base Ensembl one. DO NOT edit the files in public-plugins/ensembl, as your changes may be overwritten when you update to the next release.

Now go into the public-plugins/mirror/conf directory and make the changes listed below to SiteDefs.pm and ini_files/DEFAULTS.ini:

public-plugins/mirror/conf/SiteDefs.pm

First copy SiteDefs.pm-dist to SiteDefs.pm in this directory. If you open this file in a text editor, such as vi, you will see it is a Perl module with a single method "update_conf" which contains the changes needed to configure your copy of the website. The "update_conf" method consists of a list of variables (of the form $SiteDefs::ENSEMBL_whatever),

Below are the variables you will need to change to match your installation. If you wish, you can change any variables that are defined in the main SiteDefs.pm file.

Note: You should only change the values, that is the parts between single quotes.

General configuration

$SiteDefs::ENSEMBL_SERVERROOT sets the filesystem location of the web server root directory. By default, this is determined dynamically based on the location of the SiteDefs.pm file. You can, however, hard-code this value if you wish. For example, if you installed the Ensembl site in /usr/local/ensembl, then you could change this line of SiteDefs to read:

  $SiteDefs::ENSEMBL_SERVERROOT = '/usr/local/ensembl';

Configuration of the Apache web server

Change $SiteDefs::ENSEMBL_SERVERNAME to the web name of the server - e.g. "www.yoursite.org". This value is dynamically set to the server hostname by default.

Change $SiteDefs::ENSEMBL_USER and $SiteDefs::ENSEMBL_GROUP to the system user and group you want the Apache web server to run as. Usually, for security, this is a special user (such as "nobody") who has very few permissions.

Mail configuration - error messages

If you want errors to be automatically emailed to you, change $SiteDefs::ENSEMBL_MAIL_ERRORS to the value 1, and change $SiteDefs::ENSEMBL_ERRORS_TO to your email address. If you don't want errors mailed, set $SiteDefs::ENSEMBL_MAIL_ERRORS to 0.

User database - Database and cookie configuration

Change the values of the following to have the details for your web_user database

  $SiteDefs::ENSEMBL_USERDB_NAME
  $SiteDefs::ENSEMBL_USERDB_HOST
  $SiteDefs::ENSEMBL_USERDB_USER
  $SiteDefs::ENSEMBL_USERDB_PASS

Remember this database needs a user with update/insert/delete privileges. Additionally if you wish to change the encryption keys used to "protect" the cookies, $SiteDefs::ENSEMBL_ENCRYPT_0 should be a six digit hex-number and $SiteDefs::ENSEMBL_ENCRYPT_1, _2 and _3 should each contain two alphanumeric characters. Unless you are particularly concerned about people changing cookies, the default values will probably do.

Temporary Files

There are three temporary file locations that can be configured:

  $SiteDefs::ENSEMBL_TMP_DIR       General storage for temporary files
  $SiteDefs::ENSEMBL_TMP_DIR_IMG   Storage for image files
  $SiteDefs::ENSEMBL_TMP_DIR_BLAST Storage for blast files

The values for these should be set to an appropriate filesystem path.

Some temporary files need to be referenced by URL from web pages. The first two tmp directories above therefore have URL aliases, also configured within SiteDefs.pm. You should not need to edit these.

  $SiteDefs::ENSEMBL_TMP_URL       URL alias for $ENSEMBL_TMP_DIR
  $SiteDefs::ENSEMBL_TMP_URL_IMG   URL alias for $ENSEMBL_TMP_DIR_IMG

There are two further temporary file configuration options available:

• $SiteDefs::ENSEMBL_TMP_CREATE If set, then at apache startup the server will attempt to create any temporary directories that have been configured, but which don't already exist. It also changes their ownership to $SiteDefs::ENSEMBL_USER.$SiteDefs::ENSEMBL_GROUP
• $SiteDefs::ENSEMBL_TMP_DELETE If set, then at apache startup the server will attempt to delete the contents of $ENSEMBL_TMP_DIR and $SiteDefs::ENSEMBL_TMP_DIR_IMG.

public-plugins/mirror/conf/ini-files/DEFAULTS.ini
and public-plugins/mirror/conf/ini-files/[Species_name].ini

Again the first thing to do is make a copy of the DEFAULTS.ini-dist file as DEFAULTS.ini, then you will need to go in and edit the appropriate lines of the DEFAULTS.ini.

From version 33 onwards you should be able to re-use the same Plugins.pm, SiteDefs.pm and DEFAULTS.ini file to configure your new Ensembl.

The format of the species-specific .ini files are similar to a standard windows ini file, i.e. split into sections identified by a header in square brackets, which contain key = value entries. When the Apache server is started, these files are parsed and stored in a file called config.packed in the conf directory. This config.packed file is regenerated whenever the server is restarted.

Database configuration

In the [general] section, change the values of DATABASE_DBUSER and DATABASE_DBPASS to the username and password you want MySQL to be accessed by. Set DATABASE_HOST and ENSEMBL_HOST_PORT to be the database server and port that MySQL is running on.

These are default settings - you can override them by adding a section for a particular database. For example, adding a section like the following into the mirror plugin would override the defaults in public-plugin for the ENSEMBL_WEBSITE database:

[DATABASE_WEBSITE]
USER=mysqluser2
PASS=helppass
HOST=mysqlserver2
PORT=4444

DAS Proxy

If you wish to display external DAS sources on your ensembl installation, and are behind a firewall, then you will need to set a value for ENSEMBL_DAS_PROXY. This should probably be set in DEFAULTS.ini, as the proxy is likely to be the same for all species. The value should be your usual web proxy setting, e.g.

ENSEMBL_DAS_PROXY = http://webproxy.mycompany.com:80

Fonts

For the past few releases Ensembl uses TrueType fonts in some of the images, These need to be configured in the '[ENSEMBL_STYLE]' section of the DEFAULTS.ini file.

[ENSEMBL_STYLE]
GRAPHIC_FONT         = arial                           ; Arial file is arial.ttf
GRAPHIC_FONT_FIXED   = cour                            ; Courier file is cour.ttf
GRAPHIC_TTF_PATH     = /usr/local/share/fonts/ttfonts/ ; remember the trailing slash
GRAPHIC_FONTSIZE     = 8                               ; Default font-size for graphic text...

You will likely need to change the path to where your local copy of these files is stored. Please note that Mac TTF files are a slightly different format and do not reliably work.

public-plugins/mirror/conf/ini-files/MULTI.ini

Create this file to configure the multi species databases. Configure the [general] section for connection to the MySQL server, as for the species-specific ini files. In the [databases] section, change the values of DATABASE_COMPARA and the various _MART entries to match the name of the ensembl_compara and ensembl_mart databases that you created.

In addition, if you chose to install a local GO database you can configure it here by adding an entry:

DATABASE_GO = your_go_database_name

to the [databases] section along with DATABASE_COMPARA and the BioMart datbases.

As in the other species.ini files, you can override the database connection settings for a particular database by adding a section similar to the following:

[DATBASE_MART_ENSEMBL]
USER=mysqluser2
PASS=dbpass
HOST=mysqlserver2
PORT=4444

The Mart configuration automatically creates a simplified BioMart configuration file martRegistry.xml in the conf directory at server start up. Read the BioMart install document how to edit this to create a more functional BioMart registry which leverages BioMart's advanced features such as federated searches.

BLAST

BLAST is not installed by default. You have to configure blast for a local installation. See documentation describing how to configure BLAST.

All relevant fasta files are on ftp://ftp.ensembl.org/pub.

SSAHA

SSAHA2 is not installed by default as it requires a large amount of memory to put the look up tables in memory. (Ensembl currently uses 10 4G machines for our SSAHA servers).

All relevant fasta files are on ftp://ftp.ensembl.org/pub. These need processing to produce the appropriate files. SSAHA2 servers can be configured for any DNA based data.

SSAHA2 software is at: http://www.sanger.ac.uk/Software/analysis/SSAHA2/.

Each species ini file (public-plugins/mirror/conf/ini-files/<Genus_species.ini>) needs the following:

[SSAHA2_DATASOURCES]
DATASOURCE_TYPE = dna
LATESTGP        = host:port        ; for unmased dna
CDNA_ALL        = host:port        ; for cDNA data 

Note on Ensembl Web Site Search

The Ensembl web site uses the Exalead search engine (http://www.exalead.com). Previously it used AltaVista (http://www.altavista.com/). This software requires a user license and cannot be distributed as part of the Ensembl web code.

By default, local installations of Ensembl use a simple search page called Unisearch that just does SQL searches against the database. This method is rather slow and crude, however. Also, Unisearch does not do cross species queries (too time consuming for the Unisearch's MySQL queries).

Site Preparation

cd into your server root and run the following commands:

  mkdir logs
  chown -R $ENSEMBL_USER:$ENSEMBL_GROUP .

where $ENSEMBL_USER and $ENSEMBL_GROUP are the web server user & group you configured in SiteDefs.

Your Ensembl site should now be ready to start up.

Next: Running the Site →