Ensembl

Introduction

Ensembl produces a range of utilities and tools, most especially, an API.

It is mostly a perl endeavour, though a RESTful API is alsof available, although this newer and quite possibly not as powerful as the historical perl installation.

Components

ensembl-git-tools

Seemingly just a tool set to enable downloading (i.e not even installation) of the other tools. Merely amount to beign able to execute the following

git ensembl --clone api

This will clone the following:

• ensembl
• ensembl-compara
• ensembl-fncgen
• ensembl-io
• ensembl-variation

The ensembl-tools is not retrieved.

ensembl

This poorly named component can be referred to as core.

It has a useful collection of scripts inside its misc_scripts subdirectory, most especially "ping_ensembl.pl". Using this (after loading the ensembl-api module of course) will give a good idea if the API is working or not.

ensembl-tools

Unlike the other components, this does not contain a modules subdirectory. However, all its components are hidden inside a scripts subdirectory.

This component contains:

• assembly-converter
• id_history_converter
• region_reporter
• variant_effect_predictor

Variant Effect Predictor

Essentially this is a workspace organizer, as one of its chief aims is to enable a cache (a local storage) of species data in order to circumvent having to download or access remote databases.