This is some code I have developed during my PhD thesis to download genomes and orthologues from Ensembl in Java, using the ensj API.
The repository has been reconstructed from regular backups I had, but this means there are no useful commit messages. It is there for historical purposes, as a legacy. It worked at the time, but I quickly decided to use BioMart instead.
It is very likely that the code won't work on recent versions of Ensembl !
You will need to add two JAR files in your CLASSPATH:
ensj-39.2.jarmysql-connector-java-3.1.8-bin.jar
This code may be freely distributed and modified under the terms of the GNU General Public License version 3 (GPL v3) and the CeCILL licence version 2 of the CNRS. These licences are contained in the files:
- LICENSE-GPL.txt (or (http://www.gnu.org/licenses/gpl-3.0-standalone.html))
- LICENCE-CeCILL.txt (or [http://www.cecill.info/licences/Licence_CeCILL_V2-en.html])
Copyright for this code is held jointly by the Dyogen (DYnamic and Organisation of GENomes) team of the Institut de Biologie de l'Ecole Normale Supérieure (IBENS) 46 rue d'Ulm Paris, and the individual authors (Matthieu Muffato).