Customer Training

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Bioinformatic Analysis with Containers

24.1.2023 09:00 +02:00 EET - 25.1.2023 16:00 +02:00 EET

On-site

Bioinformatics tools often require installing different dependencies in a controlled environment. Containers allow you to logically package your application (e.g., a bioinformatics tool) together with libraries and other dependencies, providing isolated environments for running your software services. Containerized applications can be run in an isolated runtime environment independent of the actual environment (e.g., private data center, the public cloud, or even a developer’s personal laptop) in which the applications are running in. These are recently gaining popularity as a standard way to distribute, deploy, and run services by developers and system administrators. This course will introduce the basic concepts of containers and their deployment at CSC.

Expected learning in this course

Basic understanding of containers is necessary to work with containerized bio applications. This course will introduce the fundamentals of containers with a special focus on their deployment in an HPC environment.

In this course, you will learn:

- The essential concepts of HPC containers
- The basics of building and running containers
- Containerized applications in bioinformatics

Pre-requisites

One should be comfortable working with the command line environment in Linux, be able to use any common editors (e.g., vi, nano, or emacs, etc.) and have some familiarity with HPC environment.

So, ideal candidates for this course are:

- Bioinformaticians or computer scientists with some bio-background
- Biologists with Linux skills and/or basics of HPC environment

Expected way of learning

- Lectures
- Hands-on exercises

Practicalities (More information will be updated here)

e-Lena e-learning platform will be used in the course.

The is a two-day course, from 9 AM to 4 PM

Program
24th, January 2023

Brief Introduction on CSC HPC systems
CSC- specific containers (e.g., Tykky)
Introduction to singularity/apptainer
Building container images

25th, January 2023

Introduction to docker containers
Conversion of docker containers to singularity ones on CSC systems
Containerized bioapplications
Workflows at CSC

Lecturers

Laxman Yetukuri and Ari-Matti Saren

Event time

Starts:  

24.1.2023 09:00 +02:00 EET

Ends:  

25.1.2023 16:00 +02:00 EET

Event location

On-site


Organizer

CSC in collaboration with EuroCC