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Nimbus for Bioinformatics

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Summary

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
  • Singularity-HPC - a container modules installer
  • Spack - a package management tool

Instructions

We will cover instructions for how to use CernVM-FS, Jupyter Notebook, RStudio, Singularity-HPC on this page. For instructions for other software listed above, please see the software's original documentation page.

CernVM-FS

CernVM-FS is a read-only file system that was developed by another supercomputing centre (Cern). It allows files such as reference datasets that are commonly used by many researchers to be accessed, added to, and updated in the one location. At Pawsey, we currently mirror the datasets that are on Galaxy Project's repository. Please note that the datasets may not be comprehensive, and this service is not meant to replace your current methods for accessing public datasets.

On Nimbus instances created with the bio image, you can simple refer to and use the path to the datasets as follows:

ls /cvmfs/data.galaxyproject.org

Note: It may take a minute or two to load the folders. When you have done it once, it will not take as long to show again.

Jupyter Notebook 


RStudio


Singularity-HPC


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