Docker virtualization allows for software tools to be executed inan isolated and controlled environment referred to as acontainer. In Docker containers, dependencies are providedexactly as intended by the developer and, consequently, theysimplify the distribution of scientific software and fosterreproducible research. The Docker paradigm is that each containerencapsulates one particular software tool. However, to analyzecomplex biomedical data sets, it is often necessary to combineseveral software tools into elaborate workflows. To address thischallenge, several Docker containers need to be instantiated andproperly integrated, which complicates the software deploymentprocess unnecessarily. Here, we demonstrate how an extension toDocker, Docker compose, can be used to mitigate these problems byproviding a unified setup routine that deploys several tools inan integrated fashion. We demonstrate the power of this approachby example of a Docker compose setup for a drug target screeningplatform consisting of five integrated web applications andshared infrastructure, deployable in just two lines of codes.