Galaxy is a workflow manager adopted in many life science research environments in order to facilitate the interaction with bioinformatics tools and the handling of large quantities of biological data. Through a coherent work environment and an user-friendly web interface it organizes data, tools and workflows providing reproducibility, transparency and data sharing functionalities to users.
Currently, Galaxy instances can be deployed in three ways, each one with pros and cons: public servers, local servers and commercial cloud solutions. In particular, the demand for cloud solutions is rapidly growing (over 2400 Galaxy cloud servers launched in 2015), since they allow the creation of a ready-to-use galaxy production environment avoiding initial configuration issues, requiring less technical expertise and outsourcing the hardware needs. Nevertheless relying on commercial cloud providers is quite costly and can pose ethical and legal drawbacks in terms of data privacy.
ELIXIR-IIB in the framework of the INDIGO-DataCloud project is developing a cloud Galaxy instance provider, allowing to fully customize each virtual instance through a user-friendly web interface, overcoming the limitations of others galaxy deployment solutions. In particular, our goal is to develop a PaaS architecture to automate the creation of Galaxy-based virtualized environments exploiting the software catalogue provided by the INDIGO-DataCloud community (www.indigo-datacloud.eu/service-component).
Once deployed each Galaxy instance will be fully customizable with tools and reference data and running in an insulated environment, thus providing a suitable platform for research, training and even clinical scenarios involving sensible data. Sensitive data requires the development and adoption of technologies and policies for data access, including e.g. a robust user authentication platform.
The system allows to setup and launch a virtual machines configured with the Operative System (CentOS 7 or Ubuntu 14.04/16.04) and the auxiliary applications needed to support a Galaxy production environment such as PostgreSQL, Nginx, uWSGI and Proftpd and to deploy the Galaxy platform itself. It is possible to choose between different tools preset, or flavors: basic Galaxy or Galaxy configured with a selection of tools for NGS analyses already installed and configured (e.g. SAMtools, BamTools, Bowtie, MACS, RSEM, etc…) together with reference data for many organisms.