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* update chunking strategy - smaller 3d chunks for bigstitcher - moves rechunking from zarr2bdv to apply_flatfield_corr * make logging visible for bigstitcher (for coiled debugging)
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Original file line number | Diff line number | Diff line change |
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#!/bin/bash | ||
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if ! command -v singularity >/dev/null 2>&1; then | ||
echo "Error: 'singularity' is not installed or not in the PATH." >&2 | ||
exit 1 | ||
fi | ||
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container='docker://khanlab/spimprep-deps:main' | ||
unset SNAKEMAKE_PROFILE | ||
singularity exec ${container} snakemake --config --set-resources bigstitcher:mem_mb=30000 fuse_dataset:mem_mb=30000 -pr $@ | ||
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