A short description of what this repository is for, which project it is linked to.
Provide instructions on how to use the repository for your project. For example:
- Place all code/notebooks/scripts in the
Scriptsdirectory - If needing to break up content, delete
Scriptsdirectory and create a subdirectory for each objective or workshop session - Use
.gitignoreto 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
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
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
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