Cancer Genomics Tutorial of Delly
Delly is a structural variant calling algorithm that can be used to discover, genotype and visualize somatic & germline rearrangements. The Delly tutorial gitbook is written in markdown language and the content is tracked in the Delly tutorial github repository, please open an issue there if you notice any errors. The only dependency of this tutorial is Docker because the entire course data and tools are packaged in a single Docker Delly tutorial image.
docker pull trausch/tutorial-delly
To start the tutorial you then just need to open an interactive shell in the docker container.
docker run -it tutorial-delly /bin/bash
Some parts of the tutorial require a graphical user interface (GUI). The simplest way to enable GUIs in the docker container is to share your host's X-Server for the container's ID. This runTutorial shell script pulls the docker image, starts the docker container and adds the docker container ID as a client to your X-Server so that you can run applications with a graphical user interface. To ensure that everything is working you can start for instance xclock inside the container. A final exit closes the docker container.
./runTutorial.sh xclock exit