kemalandClaude Opus 5.5
ee4ebaaa1e
Phase 0 deliverables: full technical specification and roadmap (SIMURGARRAY_MASTER_PLAN.md), CLAUDE.md, bootstrap script for reference open-source repos and tiered dataset fetch script with checksums. Co-Authored-By: Claude Opus 5.5 <[email protected]> Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
66 lines
3.6 KiB
Bash
Executable File
66 lines
3.6 KiB
Bash
Executable File
#!/usr/bin/env bash
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# Download SimurgArray datasets into data/<tier>/ and record sha256 checksums.
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# Vendor files are for personal research use only; never commit them.
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# Usage: bash scripts/fetch_data.sh p0|p1|p2
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set -euo pipefail
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cd "$(dirname "$0")/.."
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tier="${1:?usage: fetch_data.sh p0|p1|p2}"
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mkdir -p "data/$tier"
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sums="data/CHECKSUMS.sha256"; touch "$sums"
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get() { # get <url> <dest-dir>
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local url="$1" dir="$2" f
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f="$dir/$(basename "${url%%\?*}")"
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if [[ -s "$f" ]]; then echo "have $f"; else
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if command -v aria2c >/dev/null; then aria2c -x8 -s8 -c -d "$dir" "$url"
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else wget -c -P "$dir" "$url"; fi
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fi
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grep -q " $f\$" "$sums" || sha256sum "$f" >> "$sums"
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}
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GDA=https://webdata.illumina.com/downloads/productfiles/global-diversity-array
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G1K=https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/supporting/hd_genotype_chip
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case "$tier" in
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p0)
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d=data/p0/gda_demo36; mkdir -p "$d"
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get "$GDA/infinium-global-diversity-array-8-v1-0-D1-demo-data-36.zip" "$d"
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get "https://support.illumina.com/content/dam/illumina-support/documents/downloads/productfiles/global-diversity-array/infinium-global-diversity-array-8-v1-0_D1_SampleSheet_Demo_36.csv" "$d"
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get "$GDA/infinium-global-diversity-array-8-v1-0-D1-manifest-file-bpm.zip" "$d"
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# CSV manifest and EGT: file names can change; if these fail, download manually from
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# https://support.illumina.com/array/array_kits/infinium-global-diversity-array/product-files.html
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get "$GDA/infinium-global-diversity-array-8-v1-0-D1-manifest-file-csv.zip" "$d" || echo "!! fetch CSV manifest manually"
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get "$GDA/infinium-global-diversity-array-8-v1-0-D1-cluster-file.zip" "$d" || echo "!! fetch EGT manually"
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if command -v Rscript >/dev/null; then
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Rscript -e 'if(!requireNamespace("BiocManager",quietly=TRUE)) install.packages("BiocManager",repos="https://cloud.r-project.org"); BiocManager::install(c("IlluminaDataTestFiles","hapmap370k"),ask=FALSE,update=FALSE)'
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Rscript -e 'cat(system.file("extdata",package="IlluminaDataTestFiles"),"\n")' > data/p0/bioc_fixture_path.txt
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else
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echo "!! R not found: install IlluminaDataTestFiles + hapmap370k from Bioconductor for parser fixtures"
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fi
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echo "NOTE: GSA v4 PGx demo (36 samples) + product files: download manually from"
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echo " https://support.illumina.com/downloads/infinium-gsa-v4-pgx-demo-data-set-iscan.html"
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echo " https://support.illumina.com/array/array_kits/infinium-global-screening-array-v4-pgx/product-files.html"
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;;
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p1)
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d=data/p1/1kg_omni_broad; mkdir -p "$d"
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for f in HumanOmni2.5-4v1-Multi_B.bpm HumanOmni2.5-4v1_B.csv; do get "$G1K/broad_intensities/$f" "$d" || true; done
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echo "Listing broad_intensities/ (pick EGT + the 107 GB Omni25_idats_gtcs_2141_samples.tgz):"
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curl -s "$G1K/broad_intensities/" | grep -o 'href="[^"]*"' | cut -d'"' -f2 | grep -v '^?' || true
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echo "Then: bash scripts/fetch_data.sh p1-big (downloads the 107 GB archive)"
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d=data/p1/1kg_omni_sanger; mkdir -p "$d"
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echo "Sanger set index:"; curl -s "$G1K/sanger_intensities/" | grep -o 'href="[^"]*"' | cut -d'"' -f2 | grep -v '^?' || true
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d=data/p1/gse165845; mkdir -p "$d"
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get "https://ftp.ncbi.nlm.nih.gov/geo/series/GSE165nnn/GSE165845/suppl/GSE165845_RAW.tar" "$d"
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;;
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p1-big)
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get "$G1K/broad_intensities/Omni25_idats_gtcs_2141_samples.tgz" data/p1/1kg_omni_broad
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;;
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p2)
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d=data/p2; mkdir -p "$d/gse96909" "$d/gda_pgx480"
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get "https://ftp.ncbi.nlm.nih.gov/geo/series/GSE96nnn/GSE96909/suppl/GSE96909_RAW.tar" "$d/gse96909"
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get "https://s3.amazonaws.com/webdata.illumina.com/downloads/productfiles/global-diversity-array-pgx/GDAPGx_Demo_idats.zip" "$d/gda_pgx480"
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;;
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*) echo "unknown tier $tier"; exit 2;;
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esac
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echo "checksums in $sums"
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