March 3, 2017

Ensembl 60 top tip #1

Ensembl 60 came out yesterday. For those of you who are technical developers like us who do in-depth hacking of the source code, there's two things that have changed which you need to be aware of:

(this information is shamelessly cribbed from the ensembl-dev mailing list - if you need more details, email the Ensembl team - or you could also email us at Eagle...)

MVC structure

Changes have been made to the low-level code in order to more closely adhere to the MVC design pattern. This does not affect higher-level customisations such as those based on EnsEMBL::Web::Component, but may affect developers who hack the underlying modules. More information can be found in the online documentation:


The modules used to create the page template have been moved from EnsEMBL::Web::Document::HTML to EnsEMBL::Web::Document::Element. If you modify the Ensembl page template in your plugin, you will need to move your files to this new namespace, change each 'render' method to 'content' and alter it to return an HTML string instead of calling the print method.

Modules that create dynamic content within a static page (e.g. news, ftp tables) remain in the old namespace.

Topics: Big data technology, Bioinformatics, eaglensembl, Ensembl, genome browser, genome content management, Open source, problems