35 lines
1.5 KiB
Bash
35 lines
1.5 KiB
Bash
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#!/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=$(git rev-parse --show-toplevel)
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# Define absolute directory path
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DIR="$REPO_ROOT/resources_test/visium"
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# from https://www.10xgenomics.com/resources/datasets/human-ovarian-cancer-1-standard
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mkdir -p "$DIR"
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# Input Files - download to the specific directory
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curl -o "$DIR/Visium_FFPE_Human_Ovarian_Cancer_fastqs.tar" https://cf.10xgenomics.com/samples/spatial-exp/1.3.0/Visium_FFPE_Human_Ovarian_Cancer/Visium_FFPE_Human_Ovarian_Cancer_fastqs.tar
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curl -o "$DIR/Visium_FFPE_Human_Ovarian_Cancer_image.jpg" https://cf.10xgenomics.com/samples/spatial-exp/1.3.0/Visium_FFPE_Human_Ovarian_Cancer/Visium_FFPE_Human_Ovarian_Cancer_image.jpg
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curl -o "$DIR/Visium_FFPE_Human_Ovarian_Cancer_probe_set.csv" https://cf.10xgenomics.com/samples/spatial-exp/1.3.0/Visium_FFPE_Human_Ovarian_Cancer/Visium_FFPE_Human_Ovarian_Cancer_probe_set.csv
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# Extract in the specific directory
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tar xvf "$DIR/Visium_FFPE_Human_Ovarian_Cancer_fastqs.tar" -C "$DIR"
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# Create subsampled dataset with ImageMagick
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# https://imagemagick.org/index.php
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mkdir -p "$DIR/subsampled"
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convert "$DIR/Visium_FFPE_Human_Ovarian_Cancer_image.jpg" -resize 2000x2000 "$DIR/subsampled/Visium_FFPE_Human_Ovarian_Cancer_image.jpg"
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for f in "$DIR"/Visium_FFPE_Human_Ovarian_Cancer_fastqs/*L001*R*; do
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gzip -cdf "$f" | head -n 40000 | gzip -c > "$DIR/subsampled/$(basename "$f")";
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done
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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/visium \
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--delete \
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--dryrun
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