kemal
b63852e775
Phase 0 deliverables: full technical specification and roadmap (SIMURGARRAY_MASTER_PLAN.md), bootstrap script for reference open-source repos and tiered dataset fetch script with checksums.
25 lines
973 B
Bash
Executable File
25 lines
973 B
Bash
Executable File
#!/usr/bin/env bash
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# Shallow-clone reference open-source repositories into refs/ (git-ignored).
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# GPL repos are for use as external oracles only — do not copy their code into SimurgArray.
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set -euo pipefail
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cd "$(dirname "$0")/.."
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mkdir -p refs
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repos=(
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"Illumina/BeadArrayFiles" # BSD-2
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"Illumina/GTCtoVCF" # Apache-2.0
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"freeseek/gtc2vcf" # MIT
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"freeseek/mocha" # MIT
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"broadinstitute/picard" # MIT (see src/main/java/picard/arrays)
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"WGLab/PennCNV" # Unlicense
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"sbslee/pypgx" # MIT
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"PharmGKB/PharmCAT" # MPL-2.0 (oracle)
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"HenrikBengtsson/illuminaio" # GPL-2 (oracle only)
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"gjun/verifyIDintensity" # GPL-3 (oracle only)
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)
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for r in "${repos[@]}"; do
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d="refs/${r#*/}"
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if [[ -d "$d/.git" ]]; then echo "skip $d"; continue; fi
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git clone --depth 1 "https://github.com/$r.git" "$d"
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done
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echo "done: $(ls refs | wc -l) repos in refs/"
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