This page covers information on how to use the new 'Pawsey Bio - Ubuntu 20.04 - 2021-11' image for Nimbus. Instructions on how to choose this image when creating your instance can be found here. This Bio-image is created to cater to bioinformatics users who prefer to have their instances pre-installed with software commonly used in the bioinformatics domain. Some of the software are part of Pawsey's ongoing effort to improve the experience of bioinformatics users at Pawsey.
Pre-installed software
The list of pre-installed software is as follows:
Ansible - an automation platform that Pawsey uses to automate a number of software deployment
CernVM-FS - a read-only file system for accessing reference datasets
Docker - a popular container engine
Jupyter Notebook (container)
Lmod - a modules environment that we use at Pawsey for loading sotware
Nextflow - a popular workflow manager
Pip - a Python package installer
Python3
RStudio (contrainer)
Singularity - a popular container engine that can be used on HPC
We will cover instructions for how to use CernVM-FS, Jupyter Notebook, RStudio, Singularity-HPC on this page. For instructions for other packages, please see the software's original documentation page.