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. Containerised 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 focus on the deployment of containerised applications in HPC environment. The course will also introduce a modern workflows manager (i.e., nextflow ) to perform complex analysis in bioinformatics.
Expected learning in this course
In this basic course, you will be introduced to the fundamentals of container technology in addition to the selected examples of containerised bioinformatics applications. This basic understanding of containers is necessary to be able to work with bio applications in a containerised environment with different options and requirements.
More specifically, you will learn:
- Basic concepts of CSC supercomputing environment (Puhti)
- The essential concepts of using containers
- The containerised applications in bioinformatics
- The basics of running Singularity containers in HPC environment
- Basic introduction to Nextflow
After this course, one will be able to launch and work with containerised applications in HPC environment
One should be comfortable working with the command line environment in Linux and able to use any common editors (e.g., vi, nano, or emacs, etc.) in order to get the maximum benefit from this course.
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
- Hands-on exercises
Practicalities (More information will be updated here)
e-Lena e-learning platform will be used in the course.
Program, 23rd, November
Introduction to CSC HPC environment
Fundamentals of containers
Program, 24th, November
Using container images in HPC environment
Containerised bio applications
Program, 25th, November
Converting docker images to singularity images
Building singularity container images
Program, 26th, November
Introduction to nextflow
Using singularity containers in nextflow
Running nextfflow at CSC
Laxman Yetukuri and Ari-Matti Saren