Ashbya Genome Database .



All data sets in the Ensembl system are stored in relational databases. For each of the Ensembl databases the project provides a specific Perl API. This document aims to explain the installation procedure for Ensembl Perl APIs. As Ensembl takes also advantage of code provided by the Bioperl project, installation of the Bioperl package is part of this description.

Ensembl uses the Concurrent Versions System (CVS) for storing the source codes. You will need CVS installed if you want to download Ensembl code through anonymous cvs access. There is also a web-based CVS repository. This system will help you keeping up to date with developments and bug fixes.

Installation Procedure

  1. Create an installation directory

    mkdir src
    cd src
  2. Connect to the Bioperl CVS server

    cvs -d login

    When prompted the password is 'cvs'.

  3. Install Bioperl (version 1.2)

    cvs -d checkout -r branch-1-2 bioperl-live
  4. Connect to the Ensembl CVS server

    cvs -d login
    cvs -d  login 

    When prompted the password is 'CVSUSER'.

  5. Install the Ensembl Core Perl API for version 40

    cvs -d checkout -r branch-ensembl-40 ensembl
  6. Install the Ensembl Variation Perl API for version 40

    cvs -d checkout -r branch-ensembl-40 ensembl-variation
  7. Install the Ensembl Compara Perl API for verion 40

    cvs -d checkout -r branch-ensembl-40 ensembl-compara

    NB: You can install as many Ensembl APIs as you need in this way.

  8. Set up your environment

    You have to tell Perl where to find the modules you just installed. You can use the "use lib" clause in your script but if you want to make these modules available for all your scripts, the best way is to add them into the PERL5LIB environment variable.

    • Under bash:

      export PERL5LIB
    • Under csh or tcsh:

      setenv PERL5LIB ${PERL5LIB}:${HOME}/src/bioperl-live
      setenv PERL5LIB ${PERL5LIB}:${HOME}/src/ensembl/modules
      setenv PERL5LIB ${PERL5LIB}:${HOME}/src/ensembl-compara/modules

    NB: If you installed extra Ensembl APIs, don't forget to add their path to the PERL5LIB environment variable.


© 2024 University of Basel. This product includes software developed by Ensembl.

AGD version 3 based on Ensembl release 40 - Aug 2006