CI
13b9f1b077
Build pipeline: openpipelines-bio.openpipeline-spatial.update-mudata-pssvw
Source commit: 2f7991091d
Source message: linting
53 lines
1.4 KiB
Bash
Executable File
53 lines
1.4 KiB
Bash
Executable File
#!/bin/bash
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set -eo pipefail
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# get the root of the directory
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REPO_ROOT=$(git rev-parse --show-toplevel)
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# ensure that the command below is run from the root of the repository
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cd "$REPO_ROOT"
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DIR="resources_test/cosmx"
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ID="Lung5_Rep2"
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OUT="$DIR/$ID/"
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# create tempdir
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MY_TEMP="${VIASH_TEMP:-/tmp}"
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TMPDIR=$(mktemp -d "$MY_TEMP/$ID-XXXXXX")
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function clean_up {
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[[ -d "$TMPDIR" ]] && rm -r "$TMPDIR"
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}
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trap clean_up EXIT
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if [ ! -d "$OUT" ]; then
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flat_dataset="https://nanostring-public-share.s3.us-west-2.amazonaws.com/SMI-Compressed/Lung5_Rep2/Lung5_Rep2+SMI+Flat+data.tar.gz"
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wget "$flat_dataset" -O "$TMPDIR/Lung5_Rep2.tar.gz"
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mkdir -p "$TMPDIR/Lung5_Rep2"
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tar -xzf "$TMPDIR/Lung5_Rep2.tar.gz" -C "$TMPDIR/Lung5_Rep2"
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mkdir -p "$OUT"
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mv "$TMPDIR/Lung5_Rep2/Lung5_Rep2/Lung5_Rep2-Flat_files_and_images/"* "$OUT/"
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fi
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viash run src/filter/subset_cosmx/config.vsh.yaml -- \
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--input "$OUT" \
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--num_fovs 3 \
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--subset_transcripts_file True \
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--subset_polygons_file False \
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--output "${DIR}/${ID}_tiny"
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viash run src/convert/from_cosmx_to_h5mu/config.vsh.yaml -- \
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--input ${DIR}/${ID}_tiny \
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--output "$DIR/${ID}_tiny.h5mu" \
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--output_compression "gzip"
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rm -rf "$OUT"
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# Sync to S3
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aws s3 sync \
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--profile di \
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"$DIR" \
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s3://openpipelines-bio/openpipeline_spatial/resources_test/cosmx \
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--delete \
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--dryrun
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