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Notes for running new deno validator on HPC using singularity #2129

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yarikoptic opened this issue Sep 9, 2024 · 0 comments
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Notes for running new deno validator on HPC using singularity #2129

yarikoptic opened this issue Sep 9, 2024 · 0 comments

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@yarikoptic
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Based on info from

for @jungheejung and others who might need it (until it is made easier, see e.g. #1963)

  • get deno singularity container: singularity pull docker://denoland/deno (in my demo case under /tmp)
  • prepare a folder for deno cache: mkdir -p ~/.var/deno-dir
  • cd to folder with your dataset and run validation: singularity exec -B ~/.var/deno-dir:/deno-dir /tmp/deno_latest.sif deno run --allow-read --allow-env --reload -A https://github.com/bids-standard/bids-validator/raw/deno-build/bids-validator.js $PWD

NB I assume that it is working since it didn't crash yet ;-)

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