Oscar

Running the BIDS validator on Oscar

0. Summary of commands

version=v2.3.0
bids_directory=${HOME}/xnat-exports/bnc/study-demodat2/bids
simg=/oscar/data/bnc/simgs/brownbnc/xnat-tools-${version}.sif
apptainer exec \
  --no-home \
  -B ${bids_directory}:/bids:ro \
  -B /oscar/scratch/${USER}:/scratch \
  ${simg} \
  env DENO_DIR=/scratch/deno deno run -A -qr jsr:@bids/validator /bids

1. Log into oscar and start an interactive section

If you are using the Desktop app on Open OnDemand, then you are already inside an interactive session and you just need to open the terminal. Otherwise, you can start an interactive job of 1 hour with

interact -n 2 -t 01:00:00 -m 8g

2. Define variables

Specify the version of xnat-tools you want to use. Any version from v2.1.0 onward will automatically run the most recent version of the BIDS validator.

version=v2.3.0

You can run ls /oscar/data/bnc/simgs/brownbnc/xnat-tools* to print all available versions

Set up paths

Specify your bids directory. This is where dataset_description.json file lives

bids_directory=${HOME}/xnat-exports/bnc/study-demodat2/bids

Path to Apptainer/Singularity Image for xnat-tools, which contains the BIDS validator

simg=/oscar/data/bnc/simgs/brownbnc/xnat-tools-${version}.sif

3. Run the main executable via apptainer [formerly singularity]

The following command runs the BIDS validator (via our xnat-tools apptainer image) to test if a directory is BIDS compliant. The command tells apptainer to launch the xnat-tools-${version}.sif image and run the @bids/validator with a program called deno. The bids validator expects a directory as an input, which in this case corresponds to ${bids_directory}. The -B ${bids_directory}:/bids:ro makes the ${HOME}/xnat-exports/bnc/study-demodat2/bids directory available read-only inside the container at the path /bids.

apptainer exec \
  --no-home \
  -B ${bids_directory}:/bids:ro \
  -B /oscar/scratch/${USER}:/scratch \
  ${simg} \
  env DENO_DIR=/scratch/deno deno run -A -qr jsr:@bids/validator /bids