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Clouds are rapidly becoming an important platform for scientific applications. In this paper we describe our experiences running a scientific workflow application in the cloud. The application was developed to process astronomy data released by the Kepler project, a NASA mission to search for Earth-like planets orbiting other stars. This workflow was deployed across multiple clouds using the Pegasus Workflow Management System. The clouds used include several sites within the FutureGrid, NERSC's Magellan cloud, and Amazon EC2. We describe how the application was deployed, evaluate its performance executing in different clouds (based on Nimbus, Eucalyptus, and EC2), and discuss the challenges of deploying and executing workflows in a cloud environment. We also demonstrate how Pegasus was able to support sky computing by executing a single workflow across multiple cloud infrastructures simultaneously.