RNAseq workshop 2023 testing

October 4, 2023 ยท View on GitHub

A short description of what this repository is for, which project it is linked to.

How to use this repository

Provide instructions on how to use the repository for your project. For example:

  • Place all code/notebooks/scripts in the Scripts directory
  • If needing to break up content, delete Scripts directory and create a subdirectory for each objective or workshop session
  • Use .gitignore to manage files and directories that should not be committed
  • Each subdirectory should contain a descriptive README.md
  • Include any useful files and scripts in the relevant subdirectories
  • Explanation of test dataset(s) if required

Environment set up

We are using Nimbus bioimage for the workshop. Using the following tools and versions:

  • nf-core/2.9
  • singularity/3.8.7
  • nextflow/23.04.2.5870

Compute environment

All testing for this workshop is being performed on Pawsey's Nimbus cloud. VMs are 2c.8r with 40Gb of disk. To create an instance:

  • Open Nimbus dashboard
  • Navigate to rnaseq-workshop project in the top menu drop down
  • Add the 8787 network port for Rstudio (this was done for whole project)
    • In side menu go to Network > Security Group
    • Follow instructions here
  • Create an instance
    • In side menu go to Compute > Instances > Launch Instance
    • Provide a name for the instance
    • Source: Pawsey Bio - Ubuntu 22.04 - 2023-06
    • Flavour: n3.2c8r
    • Networks: Public external
    • Security Groups: port 8787, rnaseq-workshop-SSH-ICMP
    • Keypair: either specify existing or make a new one and save to your local machine
    • Launch instance

Test data

Testing with 2022 rnaseq workshop material on CVMFS. To access from the Nimbus CLI:

ls /cvmfs/data.biocommons.aarnet.edu.au/training_materials/SIH_training/IntroRNAseq_0922/
ls /cvmfs/data.biocommons.aarnet.edu.au/training_materials/SIH_training/UnlockNfcore_0523/
  • You will need to cache with (ls) before trying to use the files
  • You cannot cd into CVMFS, it is read-only

External resources