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.
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
- Singularity-HPC - a container modules installer
- Spack - a package management tool
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.
/cvmfs/data.galaxyproject.org