Perl API Installation with Git
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
Create an installation directory
$ cd $ mkdir src $ cd src
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.
Switch to BioPerl version 1.2.3. Do not worry about warnings from Git about being in a detatched HEAD state.
$ cd bioperl-live $ git checkout bioperl-release-1-2-3 $ cd ..
Important note: you must install version 1.2.3, not a more recent version. Starting with 1.2.4, major changes were made to the BioPerl API which have made it incompatible with Ensembl.
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
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/75 branch.
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.
Change the working directory to the directory into which you originally installed the APIs.
$ cd $ cd src
Use the git ensembl command to change branches:
$ git ensembl --checkout --branch release/75 api
Or update each repo individually:
$ cd ensembl $ git checkout release/75 $ 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.