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Perl API Installation with Git

Introduction

Ensembl uses Git and GitHub for storing the source code and keeping track of source code revisions. This system will help you keeping up to date with developments and bug fixes. You will need Git installed if you want to download Ensembl code. A list of graphical Git clients can be found here.

There is also an Ensembl Virtual Machine available for download which comes with the latest API pre-installed. You may download this and get started immediately with the API without having to go through the steps below. Full instructions are available here

Installation Procedure

  1. Create an installation directory

    $ cd
    $ mkdir src
    $ cd src
    
  2. Take a clone of BioPerl from GitHub

    $ git clone https://github.com/bioperl/bioperl-live.git
    Cloning into 'bioperl-live'...
    remote: Counting objects: 99558, done.
    remote: Compressing objects: 100% (23306/23306), done.
    remote: Total 99558 (delta 76021), reused 99097 (delta 75628)
    Receiving objects: 100% (99558/99558), 140.34 MiB | 5.66 MiB/s, done.
    Resolving deltas: 100% (76021/76021), done.
    
  3. Install the Ensembl git tools to allow easy management of the Ensembl repos.

    $ git clone https://github.com/Ensembl/ensembl-git-tools.git
    $ export PATH=$PWD/ensembl-git-tools/bin:$PATH
    
  4. Install the APIs that you need. You can install all the APIs using the git ensembl command:

    $ git ensembl --clone api
    

    Or you can install APIs individually as needed:

    $ git clone https://github.com/Ensembl/ensembl.git
    $ git clone https://github.com/Ensembl/ensembl-variation.git
    $ git clone https://github.com/Ensembl/ensembl-funcgen.git
    $ git clone https://github.com/Ensembl/ensembl-compara.git
    

    APIs installed this way will automatically be on the release/78 branch.

  5. Set up your environment as described in the basic installation instructions.

In case you want to update the Perl APIs to a more recent version, keep in mind that the API and database versions must be identical; you can use a simple Git command to achieve this.

  1. Change the working directory to the directory into which you originally installed the APIs.

    $ cd
    $ cd src
    
  2. Use the git ensembl command to change branches:

    $ git ensembl --checkout --branch release/78 api
    

    Or update each repo individually:

    $ cd ensembl
    $ git checkout release/78
    $ cd ..
    

    Git will automatically add, modify or delete files so that your working directory will resemble the branch you selected.

Debugging an Installation

Sometimes installations can go wrong. You should follow our debugging installation guide to help diagnose and resolve installation issues.