Ashbya Genome Database .

Information Software Perl API Installation

Introduction

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

   cd
   mkdir src
   cd src
   

2. Connect to the Bioperl CVS server

   cvs -d :pserver:cvs@cvs.bioperl.org:/home/repository/bioperl login
   

   When prompted the password is 'cvs'.

3. Install Bioperl (version 1.2)

   cvs -d :pserver:cvs@cvs.bioperl.org:/home/repository/bioperl checkout -r branch-1-2 bioperl-live
   

4. Connect to the Ensembl CVS server

   cvs -d :pserver:cvsuser@cvs.sanger.ac.uk:/cvsroot/ensembl login
   

   cvs -d :pserver:cvsuser@cvsro.sanger.ac.uk:/cvsroot/CVSmaster  login 
   

   When prompted the password is 'CVSUSER'.

5. Install the Ensembl Core Perl API for version 40

   cvs -d :pserver:cvsuser@cvs.sanger.ac.uk:/cvsroot/ensembl checkout -r branch-ensembl-40 ensembl
   

6. Install the Ensembl Variation Perl API for version 40

   cvs -d :pserver:cvsuser@cvs.sanger.ac.uk:/cvsroot/ensembl checkout -r branch-ensembl-40 ensembl-variation
   

7. Install the Ensembl Compara Perl API for verion 40

   cvs -d :pserver:cvsuser@cvs.sanger.ac.uk:/cvsroot/ensembl 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:

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

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