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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.
Download the latest source from http://ftp.gnu.org/non-gnu/cvs/source/stable/1.11.22/ (you may be able to download binaries from here instead if you prefer). At the time of writing this is version 1.11.22 and the file to download is cvs-1.11.22.tar.gz
Unpack the source in a working directory with:
gunzip < cvs-1.11.22.tar.gz | tar xvf - cd cvs-1.11.22You will probably already have Perl installed. You need Perl5, version 5.8.0 or higher to run the website. We run the site under Perl 5.8.7. To see if you have Perl installed, and/or to check it's version number, type:
perl -vIf you don't have Perl installed, or need to upgrade, go to http://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.
Download the appropriate standard binaries from http://dev.mysql.com/downloads/mysql. Get the current stable version - at the time of writing, this is 5.0.51.
Create a directory for MySQL to be installed into. A subdirectory of this will hold the databases, so choose somewhere that has sufficient space free - at least 600 GB for the complete set. We will use /data/ as an example. Again, when following these instructions, replace /data/ with whatever path you choose.
Move the binary tarball to /data/
Unpack the tarball with:
$ 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.
Download the Apache2 source tarball from http://httpd.apache.org/dist/httpd/. Get the current stable version (Please NOTE 2.2.9 is buggy don't use!) so at the time of writing, this is 2.2.8, and the file to download is httpd-2.2.8.tar.gz.
Download the mod_perl source from http://www.cpan.org/modules/by-module/Apache2/ . Again, get the latest version, currently this is 2.0.4 and the file to download is mod_perl-2.0.4.tar.gz.
Unpack all the sources in a working directory with:
tar zxf httpd-2.2.8.tar.gzThe httpd.conf files etc assume you install this in an apache2 subdirectory of your websites server root.
Build the perl makefile:
perl Makefile.PL PREFIX=Apache directory MP_APXS=Apache directory/bin/apxsRun the 'make' utility:
make...and install
make installThe 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 -The modules that are required are listed below, along with their URLs. The file part of the URL is current at the time of writing - you should install whatever is the latest version of the module.
The Ensembl website contains a page called DotterView which displays a graphical dotplot comparison of two sequences, using the application Dotter. If you wish to use this page on a local installation you will need a local Dotter binary:
Dotter is part of the AceDB package available at:
http://www.acedb.org/Software/Downloads/supported.shtml
Pre-built binaries are available for alpha/Tru64 unix and intel/linux. All other flavours will have to be built from sources.
The acedb code makes use of the GTK graphics and GNU readline packages. If you don't have these on your system you can either install them yourself or use the copies distributed with the acedb source.
To install them go to
www.gtk.orgfor the GTK package and
ftp://ftp.cwru.edu/pub/bash/readline-4.3.tar.gzfor readline.
Follow the GTK and GNU instructions for installing these packages.
If you want to use the versions distributed with the acedb source then follow the instructions for making them in the next section.
Next ungzip/untar the acedb package into an temporary directory:
mkdir acedbSet an environment variable to tell the build process what platform you are building on - one of:
ALPHA_4 ALPHA_4_GCC ALPHA_4_GCC_OPT ALPHA_4_LINUX ALPHA_4_OLDSTYLE ALPHA_4_OPT ALPHA_5 ALPHA_CHRONO_4For example (in csh):
setenv ACEDB_MACHINE SOLARIS_4Consult the AceDB documentation if you need more help.
If you wish to use the GTK/readline packages distributed with acedb you should build them before building any acedb code:
make gnulibsTo build the dotter binary issue the command:
make dotter(If you just run "make" you will build the whole of AceDB - which is unnecessary).
The build will place the executable at:
./bin.${ACEDB_MACHINE}/dotterCheck that the binary runs properly and then copy it to your Ensembl shared binaries directory. DotterView should now work.
Back to: ← Installing the code components
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