القائمة
Download files from the NCI Genomic Data Commons (GDC) using the GDC Data Transfer Tool and REST API, supporting both open-access and controlled-access data.
التثبيت باستخدام Codex أو Claude انسخ هذا Prompt والصقه في Codex أو Claude أو مساعد آخر ليراجع صفحة Skill ويثبّتها لك.
استنادا إلى تصنيف SOC المهني
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| name | download-gdc |
| description | Download files from the NCI Genomic Data Commons (GDC) using the GDC Data Transfer Tool and REST API, supporting both open-access and controlled-access data. |
id, filename, md5, size, state)TCGA-BRCA) and filters to query and build a manifest--token-file FILE — GDC user token for controlled-access data (required for dbGaP-protected files)--outdir DIR — output directory (default: gdc_downloads)--jobs N — number of parallel download streams (default: 1; max recommended: 8)--retries N — retry count on network errors (default: 3)--no-verify — skip MD5 verification after download--dry-run — print manifest and download commands without executing--data-type TYPE — filter for manifest generation (e.g., "Aligned Reads", "Masked Somatic Mutation")--workflow TYPE — workflow filter (e.g., "STAR 2-Pass", "MuTect2")--experimental-strategy — filter (e.g., "RNA-Seq", "WXS", "WGS")Obtain a manifest:
id, filename, md5, size, state).curl -o manifest.txt \
"https://api.gdc.cancer.gov/manifest?ids=$(echo "$UUIDS" | tr ' ' ',')"
curl -XPOST "https://api.gdc.cancer.gov/files" \
-H "Content-Type: application/json" \
-d '{"filters":{"op":"and","content":[
{"op":"=","content":{"field":"cases.project.project_id","value":"TCGA-BRCA"}},
{"op":"=","content":{"field":"data_type","value":"Aligned Reads"}},
{"op":"=","content":{"field":"access","value":"open"}}]},
"fields":"file_id,file_name,md5sum,file_size,state",
"size":"10000","format":"tsv"}'
Check access tier: inspect the access field in the API response.
open: no token needed.controlled: --token-file is required; warn the user if it is absent.Download with gdc-client:
gdc-client download \
-m manifest.txt \
[-t token.txt] \
-d "$OUTDIR" \
--n-processes "$JOBS" \
--retry-amount "$RETRIES"
Verify MD5 checksums:
while IFS=$'\t' read -r uuid filename md5 size state; do
[[ "$uuid" == "id" ]] && continue
actual=$(md5sum "$OUTDIR/$uuid/$filename" | awk '{print $1}')
if [[ "$actual" != "$md5" ]]; then
echo "CHECKSUM FAIL: $filename" >&2
fi
done < manifest.txt
Organize files (optional): flatten the <uuid>/<filename> layout into a user-specified directory structure by data type, project, or sample.
Write download_report.tsv with: uuid, filename, expected_md5, actual_md5, size_bytes, status.
<outdir>/<uuid>/<filename> (GDC default layout)manifest.txt used for the download (generated or provided)download_report.tsv with columns: uuid, filename, expected_md5, actual_md5, size_bytes, status (OK / CHECKSUM_FAIL / MISSING)failed_uuids.txt listing UUIDs that failed all retry attemptsgdc-client command issuedgdc-client) must be installed; download from https://gdc.cancer.gov/access-data/gdc-data-transfer-tool.--jobs > 1) may trigger GDC rate limiting; start with 3–4 jobs and increase cautiously.