Course website
Teachers
Authors
Attribution
This course is partly inspired by the Carpentries Docker course, the official Snakemake tutorial and the Introduction to Snakemake workshop from SIB-Days 2022.
Material
- This website
- Google doc (through mail)
Learning outcomes
General learning outcomes
After this course, you will be able to:
- Understand the basic concepts and terminology associated with virtualization with containers
- Customise, store, manage and share containerised environments with Docker
- Use Apptainer to run containers on a shared computer environment (e.g. a HPC cluster)
- Understand the basic concepts and terminology associated with workflow management systems
- Create a computational workflow that uses containers and package managers with Snakemake
Learning outcomes explained
To reach the general learning outcomes above, we have set a number of smaller learning outcomes. Each chapter (found at Course material) starts with these smaller learning outcomes. Use these at the start of a chapter to get an idea what you will learn. Use them also at the end of a chapter to evaluate whether you have learned what you were expected to learn.
Learning experiences
To reach the learning outcomes we will use lectures, exercises, polls and group work. During exercises, you are free to discuss with other participants. During lectures, focus on the lecture only.
Exercises
Each block has practical work involved. Some more than others. The practicals are subdivided into chapters, and we’ll have a (short) discussion after each chapter. All answers to the practicals are incorporated, but they are hidden. Do the exercise first by yourself, before checking out the answer. If your answer is different from the answer in the practicals, try to figure out why they are different.
Asking questions (online only)
During lectures, you are encouraged to raise your hand if you have questions.
If the course is online, a main source of communication will be our slack channel. Ask background questions that interest you personally at #background. During the exercises, e.g. if you are stuck or don’t understand what is going on, use the slack channel #q-and-a. This channel is not only meant for asking questions but also for answering questions of other participants. If you are replying to a question, use the “reply in thread” option:
The teachers will review the answers, and add/modify if necessary. If you are really stuck and need specific tutor support, write the teachers or helpers personally.
To summarise:
- During lectures: raise hand
- Personal interest questions: #background on slack
- During exercises: raise hand/#q-and-a on slack