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# Download ICGC public release in a semi-automated manner |
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# |
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# Usage: ./download_icgc.sh |
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# |
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# Be sure to check the original link to contain all summary files |
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# https://dcc.icgc.org/releases/release_23/Summary |
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# and list all files you want from the cohorts in contents(). |
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# |
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# There may be different contents in the project folders. Check a couple, e.g.: |
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# https://dcc.icgc.org/releases/release_23/Projects/CLLE-ES |
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# https://dcc.icgc.org/releases/release_23/Projects/BRCA-US |
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# https://dcc.icgc.org/releases/release_23/Projects/PBCA-DE |
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set -x |
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URL=https://dcc.icgc.org/api/v1/download?fn= |
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RELEASE=23 |
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summary=( |
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donor.all_projects.tsv.gz |
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donor_biomarker.all_projects.tsv.gz |
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donor_exposure.all_projects.tsv.gz |
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donor_family.all_projects.tsv.gz |
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donor_surgery.all_projects.tsv.gz |
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donor_therapy.all_projects.tsv.gz |
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sample.all_projects.tsv.gz |
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simple_somatic_mutation.aggregated.vcf.gz |
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specimen.all_projects.tsv.gz |
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) |
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# comment out datasets you don't want |
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contents=( |
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copy_number_somatic_mutation.%.tsv.gz |
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donor.%.tsv.gz |
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donor_biomarker.%.tsv.gz |
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donor_exposure.%.tsv.gz |
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donor_family.%.tsv.gz |
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donor_therapy.%.tsv.gz |
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exp_array.%.tsv.gz |
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exp_seq.%.tsv.gz |
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meth_array.%.tsv.gz |
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meth_seq.%.tsv.gz |
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mirna_seq.%.tsv.gz |
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protein_expression.%.tsv.gz |
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sample.%.tsv.gz |
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simple_somatic_mutation.open.%.tsv.gz |
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specimen.%.tsv.gz |
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structural_somatic_mutation.%.tsv.gz |
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) |
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download_file() { |
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mkdir -p release_$RELEASE/$(dirname $1) |
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[ ! -f release_$RELEASE/$1 ] && |
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wget -q --show-progress $URL/release_$RELEASE/$1 -O release_$RELEASE/$1 |
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} |
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download_file Projects/README.txt |
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STUDIES=$(egrep -o "[A-Z]+-[A-Z]+" release_$RELEASE/Projects/README.txt) |
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for SUM in "${summary[@]}"; do |
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download_file Summary/$SUM |
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done |
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for STUDY in $STUDIES; do |
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for CONTENT in "${contents[@]}"; do |
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download_file Projects/$STUDY/$(sed "s/%/$STUDY/" <<< $CONTENT) |
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done |
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done |
