Ensembl Compara API

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.

Installation

Perl modules

We use a number of Perl modules that are all available on CPAN. We recommend using cpanminus to install these. You will need both the Core API dependencies and ours.

API to access HAL alignments (progressive-Cactus)

If working with HAL files, additional setup is required. There are several ways of installing the dependencies.

Complete installation of progressive-Cactus

Follow this procedure if you intend to run the cactus aligner. If Cactus is already installed on your system, you can directly jump to the section about setting up the API. Otherwise, do this:

git clone https://github.com/glennhickey/progressiveCactus.git
cd progressiveCactus
# Make sure we use the latest version
git pull
# Download the dependencies
git submodule update --init

# We specifically need a more recent version of "hal"
cd submodules/hal/
git checkout master
git pull
cd ../..

cd submodules/sonLib
# edit include.mk and add " -fPIC" at the end of the cflags_opt line (line 44)
cd ../..

# Compile
make
# Check it passes the test-suite. You should see "Result: PASS"
make test
pwd  # Prints the installation path

Note that on some Ubuntu installations, you may have to do this as well:

    sudo apt-get install python-dev
    sudo ln -s /usr/lib/python2.7/plat-*/_sysconfigdata_nd.py /usr/lib/python2.7/

Now, we need to set up the Compara API:

cd ensembl-compara/src/perl/xs/HALXS
perl Makefile-progressiveCactus.PL path/to/cactus
make

If you have the PROGRESSIVE_CACTUS_DIR environment variable defined, you can skip path/to/cactus on the Makefile command-line, e.g.:

cd ensembl-compara/src/perl/xs/HALXS
perl Makefile-progressiveCactus.PL
make

On the EBI main cluster, do not load /nfs/software/ensembl/latest/envs/basic.sh in your .bashrc, and replace perl with /nfs/software/ensembl/latest/linuxbrew/bin/perl when invoking Makefile-progressiveCactus.PL.

Installation via Linuxbrew

If you have a Linuxbrew installation of Ensembl that includes HAL, do this instead:

cd ensembl-compara/src/perl/xs/HALXS
perl Makefile-Linuxbrew.PL path/to/linuxbrew_home
make

If you have the LINUXBREW_HOME environment variable defined, you can skip path/to/linuxbrew_home on the Makefile command-line.

Separate installation of all dependencies

On many OSes you may be able to install hdf5 system-wide via your software manager. This usually brings in regular security updates etc. Then, you need to install these two libraries:

• sonLib
• hal

You will have to patch sonLib/include.mk like in the progressiveCactus instructions above. Then run this makefile

cd ensembl-compara/src/perl/xs/HALXS
perl [email protected] path/to/sonLib path/to/hal
make

If you can't have hdf5 installed system-wide, install it manually from:

• hdf5

And run this makefile

cd ensembl-compara/src/perl/xs/HALXS
perl Makefile.PL path/to/hdf5 path/to/sonLib path/to/hal
make

Additional data files (e.g. HAL alignments)

Alignments using the method CACTUS_HAL or CACTUS_HAL_PW require extra files to be downloaded from ftp://ftp.ensembl.org/pub/data_files/multi/hal_files/ in order to be fetched with the API. The files must have the same name as on the FTP and must be placed under multi/hal_files/ within your directory of choice. Finally, you need to define the environment variable COMPARA_HAL_DIR to the latter.

Contact us

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