EnsemblEnsembl Home

Installing the Ensembl and BioPerl modules

If you review the Site Structure part of this document, you will recall that the site is based around a single server-root directory. The Ensembl and BioPerl modules are all installed into this directory.

Please note: we no longer recommend installing BioMart as part of your Ensembl site. We have had to hack the code to integrate it, and our hacks are not in public CVS. If you would like to use BioMart, we suggest either linking to a public BioMart or, for your own data, setting up a BioMart instance using the new standalone Tomcat-based interface, available from biomart.org (currently version 0.8, rc6).

Choose a suitable location, and create your server-root directory. For the purposes of illustration, we will use /usr/local/ensembl. When following these instructions, replace /usr/local/ensembl with your chosen server-root.

Important notice: As of Release 75 we will be moving development into git. For the next several releases, the new branch will still be made available via CVS at release time, but there will be no further work on the CVS HEAD. Please see our blog for announcements about access to the new git repositories.

  1. Go to the server-root directory: cd /usr/local/ensembl
  2. Install the Ensembl modules
    1. Clone Ensembl git tools from GitHub

      $ git clone https://github.com/Ensembl/ensembl-git-tools.git
      $ export PATH=$PWD/ensembl-git-tools/bin:$PATH
      
    2. To check out the most recent stable version of the ensembl API and web code from GitHub you need to use the latest branch of the code. This will be set as the default branch in GitHub.

      $ git ensembl --clone web
      

    N.B. You can also view the Ensembl GitHub repository in your web browser.

  3. Install the BioPerl modules

    Important note: Recent versions of BioPerl are compatible with the Ensembl API but not with the current, rather old, blastview code.

    If you wish to install BLAST/BLAT on your mirror site, you will need to find a copy of BioPerl version 1.2.3 (unfortunately no longer available through the BioPerl CVS repository), not a more recent version. Starting with 1.2.4, major changes were made to the BioPerl API which make it incompatible with Ensembl blastview.

    We will be launching a new Ensembl BLAST interface and parser in early 2014 which will remove this problem.

    1. Log into the BioPerl CVS server (using a password of: cvs):

      cvs -d :pserver:cvs@cvs.open-bio.org:/home/repository/bioperl login
    2. Check-out the BioPerl code:

      cvs -d :pserver:cvs@cvs.open-bio.org:/home/repository/bioperl \
        co bioperl-live

    A listing of your server-root should now look something like:

    ensembl
    ensembl-compara
    ensembl-funcgen
    ensembl-git-tools
    ensembl-orm
    ensembl-tools
    ensembl-variation
    ensembl-webcode
    public-plugins

You should now have all the Ensembl website code and data installed and ready to configure.