Software Ensembl Website Installation Configuring an Ensembl WebsiteThis section explains the configuration changes you have to make so that Ensembl will run on your local set-up.
The configuration for the website is split up into site-wide configuration and species configuration. The default configuration files can all be found in the "conf" subdirectory of your server-root.
The site-wide configuration (Apache config, global settings) is stored in conf/SiteDefs.pm.
The species configuration (database names, etc.) is kept in the conf/ini_files directory as a series of "ini" files.
To create a new species-specific ini file, copy an existing one and use that as a template. These lines will need to be edited by hand:
Elsewhere in the documentation you will read about how to extend Ensembl by writing your own plugins. A by product of this extensibility is that you can also use plugins to simply configure your server. For example, in your checked out copy of Ensembl there is a public-plugins with a mirror directory. The mirror/conf directory contains DEFAULTS.ini and SiteDefs.pm files which can be used to configure your copy of Ensembl.
If you have 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.
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 the mirror plugin mentioned above.
Now go into the public-plugins/mirror/conf directory and make the changes listed below to SiteDefs.pm and ini_files/DEFAULTS.ini:
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.
You should only change the values, that is the parts between single quotes.
$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';
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.
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.
Change the values of the following to have the details for your web_user database
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.
If you wish to use Ensembl 'as-is', with the full list of species found in the release you downloaded, you can skip to the next section.
If you wish to add or remove species, please see the species configuration page.
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:
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.
In the [general] section, change the values of ENSEMBL_DBUSER and ENSEMBL_DBPASS to the username and password you want MySQL to be accessed by. Set ENSEMBL_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:
[ENSEMBL_WEBSITE] USER=mysqluser2 PASS=helppass HOST=mysqlserver2 PORT=4444
In the [databases] section, change the values of ENSEMBL_DB, ENSEMBL_OTHERFEATURES, etc. to match the names of the core, OTHERFEATURES, etc. databases you created.
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
These are used to provide sample links for the top right-hand corner of dynamic pages, as well as for the links in the site maps. If you would like to include these in any added species, copy the [SEARCH_LINKS] section from another species, remove any views that do not apply to your species (e.g. species with no chromosomes have no link to MapView) and then edit the links to point to representative sequence locations, genes, etc.
If you extend Ensembl by adding new views, don't forget to add sample links to the ini files!
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 ENSEMBL_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: ENSEMBL_GO = your_go_database_name to the [databases] section along with ENSEMBL_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:
[ENSEMBL_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 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.
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
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. Unisearch does not do cross species queries (too time consuming for the Unisearch's MySQL queries).
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.
Please note that the suggested set-up for Apache, mod_perl, MySQL and all Ensembl modules is not intended to provide high-level security. We strongly recommend that you get your systems administrator to audit any system that you provide to others. In particular, note that the perl.startup file in the conf directory may be run as root, so be careful about permissions on this file.
We are not responsible for any damage or loss of data resulting or arising from running the Ensembl website on your own machines.
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