DKTK Snakemake Tutorial 2024
Learn how to do modern reproducible data science with Snakemake.
| Organizer | David Lähnemann, bioinformatician DKTK Essen/Düsseldorf & Johannes Köster, lead developer Snakemake, founder Bioconda. |
|---|---|
| Dates | 2024, Mar 05 - Mar 07 (you can register for days individually) |
| Audience | Primarily members of DKTK, but remaining places for any other members of the University of Duisburg-Essen and the University Medicine Essen. |
| Location | Audimax-Gebäude, Universitätsklinikum Essen, Kurssaal Audimax |
The Snakemake workflow management system is a tool to create reproducible and scalable data analyses. Workflows are described via a human readable, Python based language. They can be seamlessly scaled to server, cluster, grid and cloud environments, without the need to modify the workflow definition. Snakemake workflows can entail a description of required software, which will be automatically deployed to any execution environment. Finally, Snakemake can be used to automatically generate rich interactive visual reports that contain results together data provenance information. These reports can be easily shared with collaborators (e.g. via email) and only require a web browser for viewing.
With over 800k downloads on Bioconda and on average more than 10 new citations per week in 2022, Snakemake is a widely used and accepted standard for reproducible data science that has powered numerous high impact publications.
Program
Lunch breaks are planned for noon to 1pm. Coffee breaks will be scheduled flexibly during the course, as most parts are self-paced.
| Tue, Mar 05, 9:00 am - 04:00 pm | Introduction to the linux command line (everybody) and setup of DKFZ compute cluster access (DKTK members). |
|---|---|
| Wed, Mar 06, 09:00 am - 05:00 pm | Snakemake tutorial (basic usage in the morning, advanced usage in the afternoon) |
| Thu, Mar 07, 09:00 am - 04:00 pm | Snakemake hackathon: use or create Snakemake analysis workflows |
Requirements
- Basic programming or scripting experience (any language).
- A laptop with any operating system (Windows, MacOS or Linux):
- The linux command line introduction on Tuesday comes with installation instructions for the Unix shell.
- The Snakemake tutorial on Wednesday can be conducted entirely in a web browser.
- A working Eduroam connection (we also expect the Stiftungs-Wifi to work).
Further optional setup
- For everybody: To use the web-browser based version of the snakemake tutorial, you will need to have or create a GitHub Account.
- For DKTK members: Get your DKFZ account activated for the compute cluster, see step 2 of the DKTK-internal getting started guide. With this, we can get you sorted to do the command line introduction and the tutorial directly on the servers.
Course materials
- Software Carpentry course: "shell novice"
- Software Carpentry course: "shell extras"
- For DKTK members: Get set up on the cluster DKFZ cluster
- Snakemake Tutorial