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Workshops

Basic Docker and Singularity  
Oct 24, 2022 - Nov 4, 2022
Registration for this workshop is closed.


In this workshop, we will cover,

  1. How to install and run Linux software in Docker or Singularity containers;
  2. How to setup and run software in Conda through Docker containers; 

Containers are increasingly popular for running Linux software. Containerized software is easy to deploy, and more importantly, it ensures the reproducibility of software or pipelines ran in different hardware and system environments. A docker image with installed software can be built on your Mac or Windows laptop, and the image files can be uploaded to the BioHPC server to process your data files. During this workshop, you will learn through examples how to install Linux software in Docker or Singularity containers, how to build Docker or Singularity images of your data analysis pipeline,  and how to deploy the images on BioHPC servers.

Session1:  slides   exercises video

Session2:  slides   exercises video

Workshop Outline  
Session 1 Oct 24 2022 3:30PM - 5:00PM Zoom
Concept of Linux Containers; How to build Docker images and run software in Docker containers;  
Session 2 Oct 31 2022 3:30PM - 5:00PM Zoom
How to build and run Conda applications in Docker; Convert Docker image to Singularity; Run software in Singularity;
Session 3 Nov 1 2022 3:30PM - 5:00PM 624 Rhodes Hall
In person office hour.

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