Introduction to Container Computing with Singularity

Toby Hodges   2019-02-27   Comments Off on Introduction to Container Computing with Singularity

Date(s) - 2019-02-27
09:30 CET - 17:00 CET


Michael Hall (Iqbal Group, EMBL-EBI)
Josep Moscardó (IT Services Group, EMBL Heidelberg)


Anyone who has ever tried to reproduce an analysis performed by someone else knows the pain of managing dependencies and differences in computing environments. How often have you come across a tool or pipeline that “works on their machine” but takes hours to install and debug before you can run it on yours?

Containers are becoming increasingly popular for scientists needing to perform computational analyses: by packaging dependencies along with tools themselves, they allow analysis tasks and pipelines to be easily shared, scaled, and transferred between systems. One system that can be used to deploy containers is Singularity, which has recently become available for use on the EMBL compute cluster. Using Singularity, EMBL scientists can create containers that will allow them to easily run and test analyses locally before deploying these analyses at larger scale on the cluster and beyond, in “cloud” environments where necessary.

In this workshop, participants will be provided with an overview of containers and the problem that they are designed to solve then given an opportunity to gain practical experience of creating and running containers for their own analyses. Like all Bio-IT courses, the workshop will place an emphasis on hands-on training and practical examples.

Course Synopsis

  • What is a container?
  • What is Singularity?
  • How do I run a container on the EMBL cluster?
  • How do I create my own containers?
  • How do I access containers written by other people and/or share my own?
  • How do I access data from a container?


Participants will need to bring their own laptop with SSH access to the EMBL cluster. Familiarity with the Linux command line interface is required, as well as some experience with scripting e.g. in Bash and with the Slurm job scheduler system running on the cluster.

Live Streaming

Video of this workshop will be streamed to allow members at EMBL stations other than Heidelberg to join. For connection information, email Toby Hodges (link below). We will use the EMBL Chat system to communicate during the workshop, so that those joining remotely can ask questions.


Email Toby Hodges for more information.


Bookings are closed for this event.