Day 2: test use of cvmfs with Rstudio image

Sydney-Informatics-Hub / rnaseqOct23_Testing

This document is for addressing issues encountered when preparing for the Oct23 nf-core/rnaseq workshop

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Day 2: test use of cvmfs with Rstudio image #7

Closed georgiesamaha closed 11 months ago

georgiesamaha commented 1 year ago

Can we use count matrix hosted on CVMFS for day 2 or will we need to download it to VM?

nandan75 commented 11 months ago

I did a primary test to use the rstudio from cvmfs path and it works

mkdir -p /tmp/rstudio-server

PASSWORD='abc' singularity exec \ -B /tmp/rstudio-server:/var/lib/rstudio-server \ -B /tmp/rstudio-server:/var/run/rstudio-server \ -B /home/ubuntu/working_directory/Day-2:/home \ /cvmfs/data.biocommons.aarnet.edu.au/training_materials/SIH_training/IntroRNAseq_1023/rstudio_4.1.0.sif \ rserver --auth-none=0 --auth-pam-helper-path=pam-helper --server-user ubuntu

I will try the symlinks

georgiesamaha commented 11 months ago

Works without issue.