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Ensembl is built on the following applications:
These applications are not version-specific for Ensembl; that is, if you upgrade your Ensembl installation to a newer version when one becomes available, you probably won't need to install new versions of these applications.
All of this software, like all of Ensembl, is Open Source software and can be downloaded and used free of charge. You should, however, check the documentation for each application to see what license it has been released under, particularly if you are installing Ensembl in a commercial environment.
The following instructions assume you have root access to the installation machine. If you do not, get your systems administrator to install this software for you.
You may have some or all of this software installed already. If you have any problems getting the site running with pre-installed software (in particular Apache with mod_perl installed from RPMs), we recommend simply installing the latest version using the following instructions.
CVS is a software version control system that we use for storing the source code to Ensembl. You will need CVS installed if you want to download the Ensembl source code. It will also help you keep up to date with any bug fixes. We also have a Web-based CVS repository.
gunzip < cvs-1.11.23.tar.gz | tar xvf - cd cvs-1.11.23 ./configure make make install
If you are on a Unix-based OS such as Mac OS X or Linux, you will already have Perl installed. You need Perl5, version 5.8.0 or higher, to run the website - we recommend avoiding 5.10.0 as it contains major bugs.
To see if you have Perl installed, and/or to check its version number, type:
perl -v
If you don't have Perl installed, or need to upgrade, go to www.cpan.org/ and choose the 'source code' install. Follow the installation instructions on the web site.
MySQL is a very popular Open Source relational database system. The easiest way to install MySQL is to use the pre-compiled binaries from http://dev.mysql.com. You can also get source from http://dev.mysql.com if you wish to compile MySQL yourself.
$ gunzip < mysql-WHATEVER.tar.gz | tar xvf -Follow the straightforward setup instructions in the INSTALL-BINARY file that comes with MySQL. It should be located in the "mysql-WHATEVER" directory you just unpacked.
Apache is the web server that the Ensembl site runs on. mod_perl is a module for Apache that enables it to compile perl scripts once rather than each time they are requested, and so makes everything run a lot faster.
Please follow these instructions precisely as often the default version of Apache or mod-perl does not work correctly for Ensembl.
tar zxf httpd-2.2.4.tar.gz tar zxf mod_perl-2.0.3.tar.gz | tar xvf - cd httpd-2.2.4 ./configure --enable-deflate --prefix=Apache directory cd ../mod_perl-2.0.3The httpd.conf files etc assume you install this in an apache2 subdirectory of your website's server root.
perl Makefile.PL PREFIX=Apache directory MP_APXS=Apache directory/bin/apxs
make
make install
The Ensembl website needs quite a few Perl modules to be installed in order for it to run. These modules can all be downloaded from www.cpan.org, and are all installed in much the same way: Download the module tarball, unpack in a working directory, and install the module:
gunzip < module.tar.gz | tar xvf - cd module perl Makefile.PL make make test make install
The modules that are required are listed below, along with their URLs. The listed version is either one we have tested on our own servers (Debian Lenny with Perl 5.10), or the closest available on CPAN. If you have tested a more up-to-date version successfully, please let us know!
These modules are mandatory for any website based on EnsEMBL::Web code.
Database abstraction layer, used to access non-genomic databases such as ensembl_website
Used by both web code and BioMart
Used to handle uploaded bz2 files
Used by the registry (core module in Perl 5.10)
Creates a unique ID
A common database interface for Perl
The MySQL drivers for the DBI interface
A Graphics library
Note: may require additional modules. Please read install docs.
Used to merge data from multiple configuration files
Used for getting size of images
Used for sequence handling
Used to handle uploaded bz2 files (bundled with recent versions of IO::Compress)
http://search.cpan.org/~pmqs/IO-Compress-2.024/lib/IO/Uncompress/Bunzip2.pm
Used by the variation API to pipe output directly into another file handle
used by DAS to communicate with DAS sources
Note: may require additional modules. Please read install docs.
Used by web forms to send email
Used by drawing code
Used to automatically identify the correct mime type of static files
Used for exporting Excel spreadsheets
used by Image exporter for exporting as PDF
used by DAS to communicate with DAS sources
Note: may require additional modules. Please read install docs.
used for exporting Excel spreadsheets
http://search.cpan.org/~jmcnamara/Spreadsheet-WriteExcel-2.22/
Used by website startup process
Used for code profiling (core module in Perl 5.10)
Required by Class::Std (core module in Perl 5.10)
used by DAS to parse DAS sources
Note: module is a wrapper around the expat library, which should be installed first:
Download the expat source from http://sourceforge.net/projects/expat/. Get the latest version (currently expat-1.95.8.tar.gz). Run the following commands:
gunzip < expat-1.95.8.tar.gz | tar xvf - cd expat-1.95.8 ./configure make make install
Atom feed parser, used to embed Ensembl blog entries on home page
The following are only needed for a local install of blastview within Ensembl:
Used by BlastView
The following are only needed if installing BioMart.
A Perl-specific system for writing Asynchronous web applications
Persistent session data in CGI applications
Automated accessor generator
Inheritable, overridable class and instance data accessor creation
Low-level interface to zlib compression library.
Stack trace and stack trace frame objects
Module that allows you to declare real exception classes in Perl
Perl modules for working with XML
Addition list functions not found in List::Util
A Perl port of the widely popular log4j logging package.
Perl module to format numbers for display
Used by BioMart
Used by BioMart
Used by BioMart
Used by BioMart
Used by BioMart
Used by BioMart
used by Mart to parse configuration
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