The Cherenkov Telescope Array (CTA) is currently building the next generation, ground-based, very high-energy gamma-ray instrumentation. CTA is expected to collect very large datasets (in the order of petabytes) which will have to be stored, managed and processed. This paper presents a graphical user interface built inside a science gateway aiming at providing CTA-users with a common working framework. The gateway is WS-PGRADE/gUSE workflow-oriented and is equipped with a flexible SSO (based on SAML) to control user access for authentication and authorization. An interactive desktop environment is provided, called Astronomical & Physics Cloud Interactive Desktop (ACID). Users are able to exploit the graphical interface as provided natively by the tools included in ACID. A cloud data service shares and synchronizes data files and output results between the user desktop and the science gateway. Our solution is a first attempt towards an ecosystem of new technologies with a high level of flexibility to suit present and future requirements of the CTA community.