The Ensembl Compara API (Application Programme Interface) serves as a middle layer between the underlying MySQL database and the user's script. It aims to encapsulate the database layout by providing high level access to the database.
Find more information (including the installation guide and a tutorial) on the Ensembl website: http://www.ensembl.org/info/docs/api/compara/
See the main Ensembl repository for the guidelines on user contributions
If working with HAL files, additional setup is required. First, install progressiveCactus:
git clone git://github.com/glennhickey/progressiveCactus.git
cd progressiveCactus
git pull
git submodule update --init
cd submodules/hal/
git checkout master
git pull
cd ../../
make
export PROGRESSIVE_CACTUS_DIR=$PWD
Now, we need to set up the Compara API:
cd ensembl-compara/xs/HALXS
perl Makefile.PL
make
Please email comments or questions to the public Ensembl developers list at http://lists.ensembl.org/mailman/listinfo/dev
Questions may also be sent to the Ensembl help desk at http://www.ensembl.org/Help/Contact
