Mareuil F, Doppelt-Azeroual O and Ménager H. A public Galaxy platform at Pasteur used as an execution engine for web services [version 1; not peer reviewed]. F1000Research 2017, 6:1030 (poster) (doi: 10.7490/f1000research.1114334.1)
Galaxy (Afgan et al. 2016) is an open, web-based platform for accessible, reproducible, and transparent computational biomedical research.
Since 2013, scientists from the Institut Pasteur have access to a galaxy instance where they can ask to use any tool available on the Institute cluster. Today, Galaxy@Pasteur instance is public; more than 280 tools are available and usable with approximately 3000 jobs per month for the 695 registered users as well as 1500 jobs per month launched by anonymous users.
However, in some cases, the complexity and specificities of the required applications call for the development of custom web interface.
For the last 4 years, to answer this problematic, several web services were created around this Galaxy instance:
- MetaGenSense (Correia et al. 2015) (https://metagensense.web.pasteur.fr), an online LIMS which launches workflows to analyse metagenomic data.
- NGphylogeny.fr an updated of the well known phylogeny.fr website (GCC17 Talk by Damien Correia: Performing Next Generation Phylogenetic Analyses with NGPhylogeny.fr)
- Booster, (http://booster.c3bi.pasteur.fr/)
- Shaman, (Quereda et al. 2016) a SHiny application for Metagenomic ANalysis (http://shaman.c3bi.pasteur.fr/, in progress)
For these web services, Galaxy is used as an execution engine to launch a tool or a workflow on the Institut Pasteur cluster. Web services communicate with Galaxy using directly the Galaxy API or via the Bioblend library (Sloggett et al. 2013).
This approach allows to manage only one server opened to external users; giving an access to the Pasteur ressources (storage and cluster power). Moreover use Galaxy as an execution engine decreases the development effort for web services.