Industrial cyber-physical systems (ICPSs) are widely regarded as the next generation industrial control systems and as one of the core technologies of the ongoing fourth industrial revolution. Despite its advantages, ICPSs are heavily dependent on the underlying physical process and their synthesis is a customized effort, demanding in terms of resources, which if not conducted carefully may impact the performance of the system. This work proposes a methodology to tackle ICPS synthesis in a systematic way, by using a set of industrial agents that take as input and standardized process description file and automatically deploy a modular ICPS from predesigned functional containers. Concrete examples on a tanks system and an industrial paste thickener are presented to illustrate the potential of the proposed methodology.