Systems, methods, and apparatus are provided for operating a cluster tool including receiving recipe time data; receiving transfer time data; receiving process programs and associated substrate lots wherein the process programs include a plurality of sequences; determining cluster tool chambers associated with sequences that are bottleneck sequences; setting equipment constant values for components of the cluster tool to implement transfer priorities wherein the chambers associated with bottleneck sequences are given highest priority; executing a next sequence based on the transfer priorities; and repeating the determining, setting and executing for each remaining sequence. Numerous additional aspects are disclosed.