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.

Note about BioMart

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 a public git repo.

You can download our mart databases from our FTP site for local access, with the following caveat; we are using biomart version 0.7, so you will need to install this legacy version from as a standalone service. We are unable to support this installation as it is provided by an external project.

Installation instructions

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 have moved development into git, and the old CVS server has now been shut down. Releases from 32 onwards are available on

  1. Go to the server-root directory: cd /usr/local/ensembl
  2. Install the Ensembl modules
    1. Clone Ensembl git tools from GitHub - this will make it fast and easy to clone Ensembl repositories

      $ git clone
      $ 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 public-web

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

  3. Install the core BioPerl modules - see API installation documentation.

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


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