We study the problem of compilation of quantum algorithms into optimized physical-level circuits executable in a quantum information processing (QIP) experiment based on trapped atomic ions. We report a complete strategy: starting with an algorithm in the form of a quantum computer program, we compile it into a high-level logical circuit that goes through multiple stages of decomposition into progressively lower-level circuits until we reach the physical execution-level specification. We skip the fault-tolerance layer, as it is not necessary in this work. The different stages are structured so as to best assist with the overall optimization while taking into account numerous optimization criteria, including minimizing the number of expensive two-qubit gates, minimizing the number of less expensive single-qubit gates, optimizing the runtime, minimizing the overall circuit error, and optimizing classical control sequences. Our approach allows a trade-off between circuit runtime and quantum error, as well as to accommodate future changes in the optimization criteria that may likely arise as a result of the anticipated improvements in the physical-level control of the experiment.