As whole genome sequencing becomes more accessible, genomic analysis is becoming an increasingly important component of undergraduate and graduate education in the biological sciences. The small size and high coding densities of phage genomes present an excellent tool for providing “hands-on” genomic research experiences to students, and since 2010 we have offered an intensive, semester-long course that utilizes phages as a foundation for learning genomics. Our initial genomic annotation pipeline required training students in the use of many different tools, shepherding them along the process of running them, and managing immense numbers of files by hand. We have vastly improved upon this model with the implementation of browser-based Galaxy and Apollo workflows. Galaxy provides a unified interface to disparate toolsets, and it allows instructors to noninvasively track student progress throughout the semester. The ability to chain tasks together into workflows in Galaxy obviates the issue of guiding students through multistep processes, and it allows administrators to define policies from the outset to handle result set management and curation. During the annotation portion of the course, Apollo has revolutionized the annotation process by allowing professors and biocurators to view and work with student annotations in real time. Additionally, Apollo has allowed us to visualize new depths of data by having a standardized format for evidence tracks (BLAST results, conserved domains, signal sequences, etc.) which are displayed alongside the genome. This standardized evidence and result display has greatly reduced the context switching imposed on students when attempting to collate evidence from multiple software programs, the outputs of which appear in different formats such as web pages, images, and various text formats. Through this radical change to our course, we have been able to set aside class time for instruction that had originally been consumed by troubleshooting or repetitive data transfer tasks.