Excerpt: We will learn the basics of SnakeMake, how to translate a basic workflow, which is partly trivially parallelizable and in parts not, into SnakeMake, and how to utilize HPC resources in conjunction with SnakeMake. We will take a look at a generic workflow, consisting of a set of tasks, with varying interdependencies; we will learn how to identify these interdependencies between our tasks and how to design a workflow diagram around them.
Description: We will learn the basics of SnakeMake, which is an open-source tool that allows users to describe complex workflows with a hybrid of Python and shell scripting. By transferring our workflow diagram into a SnakeMake we will learn how to automate our workflow. Initial development of our workflow in SnakeMake will be in a terminal setup, as we do generically in our day-to-day lives, however we will then learn how to scale up and perform these tasks on a local supercomputing cluster.
Difficulty: Basic
Language: English
Prerequisite knowledge: Basic knowledge of Linux, the Terminal and Python
Target audience: The workshop is intended for beginners and more experienced people interested in optimizing and automating their workflows and ultimately transferring them to High-Performance Computing machines.
Skills to be gained:
- Workflow design, identification of interdependencies
- Basics of SnakeMake
- Transfering a generic workflow into SnakeMake
- Testing our SnakeMake in an interactive environment, and upscaling it for use on a supercomputing cluster
Workflow: The training is live, in the afternoon. Part of the training will be in the form of a lecture and part will be a practical session, where we will make use of the NSC Cluster at the Jožef Stefan Institute (as an educational member of SLING).
Virtual location: ZOOM (only registered participants will see ZOOM link)
Organizer:
Lecturer:
| Name: | Luka Leskovec |
| Description: | Scientist and educationalist involved in theoretical physics and supercomputing |
| E-mail: | luka.leskovec@fmf.uni-lj.si |
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