Workshop: Singularity Containers for Bioinformatics


You’ll need a laptop with a web browser and a terminal. See also the Setup page.

You might want to brush up on the fundamentals of the Linux Shell for HPC.

Also, the tutorial Containers on HPC and Cloud with Singularity is the ideal starting point prior to going through this workshop.

Video Recordings: advanced excerpts from the workshop sessions and the entire panel discussions are now available on the Pawsey Centre Youtube channel, playlist here.


00:00 1. Prep 1: setup SSH connection with the cloud
00:15 2. Prep 2: refresher on the Linux shell (bash)
00:30 3. Session 1: containerising a pipeline
01:30 4. Session 2: setting up graphical applications
02:30 5. Session 3: building containers
03:30 Finish

The actual schedule may vary slightly depending on the topics and exercises chosen by the instructor.