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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.

  1. Go to the server-root directory: cd /usr/local/ensembl
  2. Install the Ensembl modules
    1. Log into the Sanger CVS server (using a password of "CVSUSER"):
      $ cvs -d :pserver:cvsuser@cvs.sanger.ac.uk:/cvsroot/ensembl  login
      Logging in to :pserver:cvsuser@cvs.sanger.ac.uk:2401/cvsroot/ensembl
      CVS password: CVSUSER 
      
    2. To check out the most recent stable version of the ensembl API and web code from CVS (i.e. to download the code from the Sanger CVS server onto your local machine) you need to use the latest branch of the code. Please note the code on the CVS HEAD is under development and unstable. Use the following command making sure you use the code that matches your databases:
      $ cvs -d :pserver:cvsuser@cvs.sanger.ac.uk:/cvsroot/ensembl co -r branch-ensembl-67 ensembl-api ensembl-website 
      

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

    apache2/
    conf/
    ensembl/
    ensembl-compara/
    ensembl-draw/
    ensembl-external/
    ensembl-funcgen/
    ensembl-variation/
    htdocs/
    modules/
    perl/
    public-plugins/
    utils/

    N.B. You can also view the Ensembl CVS 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 are aiming to resolve this issue in the not-too-distant future, by rewriting the Ensembl BLAST interface and parser.

    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:

    apache2/
    bioperl-live/
    conf/
    ensembl/
    ensembl-compara/
    ensembl-draw/
    ensembl-external/
    ensembl-variation/
    htdocs/
    modules/
    perl/
    public-plugins/
    utils/

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

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