Cloud-based automated deployment of applications and infrastructures to provide turnkey appliances for reusable bioinformatic applications
Creators: name: Perrin, Sandrine
name: Lorenzo, Jonathan
name: Brancotte, Bryan
name: Jean-François Gibrat
name: Blanchet, Christophe
Publisher: name: F1000Research
Year: 2017

description: <i>Introduction</i><br><br>The life sciences community has heterogeneous needs in terms of bioinformatics resources, software and services. There is a need of turnkey work environments, called appliances, and of an eased maintenance of such appliances. Those needs can be addressed by cloud technologies, and are tackled since 2012 at the French Institute of Bioinformatics (IFB) [1], which set up a cloud to fulfill the community needs. Users can access tools and data sets through appliances, which are referenced and described in a bioinformatic-oriented marketplace. The amount of services available rose quickly.<br><br><i>Methods &amp; Results</i><br><br>The appliance maintenance, i.e. installing or updating packages and their dependencies, can be achieved by several package managers like pip install, Debian package, Conda [2] or containers with Docker [3]. But then the maintenance has to be done in different environments<br>The bioinformatic community uses regularly these package managers and contributes to enrich softwares list in open repository. Developer can push a new recipe to install an application.<br>In a cloud context, we need a manager to easily and rapidly deploy a virtual machine and install tools and configurations from a pre-defined recipe. The IFB-Core uses Puppet [4], an open-source configuration management tool, to automatically deploy and configure virtual machine with a customizable list of services. Puppet installs and configures all required applications, and the virtual machine itself without user actions. Puppet comes with a graphical user interface called Foreman [5].<br><br>Appliances automated build provides a reproducible environment to help developer to build, test and validate their application and to help biologists to analyze their data in a perfectly controlled and traceable environment. The virtual machine can be created as many times as necessary, independently of user's data.<br><br>IFB is involved in CYCLONE [6], a H2020 European Project, aiming to implement automated solution to deploy complex infrastructure for bioinformatics use cases. Analysis of biological data can involve very large datasets, for example for NGS data analysis, and then require significant computing resources. Two use cases are supported by IFB-Core in the project CYCLONE to illustrate these needs (details on [7]):<br>    Cloud virtual pipeline for microbial genomes analysis: create a preconfigured cluster with Sun Grid Engine (SGE) scheduler to launch a complex genomes annotation platform;<br>    Live remote cloud processing of sequencing data: create a preconfigured cluster Docker Swarm to run mapping step on sequencing data.<br>    <br><i>References</i><br><br>1.    http://www.france-bioinformatique.fr/<br>2.    http://conda.pydata.org/docs/intro.html<br>3.    https://www.docker.com/<br>4.    https://puppet.com<br>5.    https://theforeman.org<br>6.    http://www.cyclone-project.eu<br>7.    https://cyclone.france-bioinformatique.fr/usecases