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From encode-toolkit
Downloads ENCODE data files (BED, FASTQ, BAM, bigWig) to a local directory with MD5 verification. Supports batch preview via dry-run and specific file accessions.
How this command is triggered — by the user, by Claude, or both
Slash command
/encode-toolkit:download-encodeThe summary Claude sees in its command listing — used to decide when to auto-load this command
Download ENCODE data files to a local directory. Use `encode_batch_download` with `dry_run=True` first to preview files. Then set `dry_run=False` to download. For specific files, use `encode_download_files` with file accessions. Always verify MD5 checksums. Refer to the download-encode skill for detailed guidance.
Download ENCODE data files to a local directory.
Use encode_batch_download with dry_run=True first to preview files. Then set dry_run=False to download. For specific files, use encode_download_files with file accessions. Always verify MD5 checksums.
Refer to the download-encode skill for detailed guidance.
npx claudepluginhub lansynergy/encode-toolkit3plugins reuse this command
First indexed May 8, 2026
/download-encodeDownloads ENCODE data files (BED, FASTQ, BAM, bigWig) to a local directory with MD5 verification. Supports batch preview via dry-run and specific file accessions.
/ingestImports data files into the project, generating metadata and provenance documentation, and updating the data manifest.
/claude-md-validateValidates CLAUDE.md files across directory tree for references, structure, consistency, content quality, integration, and deployment readiness, generating JSON reports and markdown summaries.
/verification-guideProvides verification checklist for Stage 0 fingerprint analysis YAML output before saving to .sourceatlas/overview.yaml, with bash scripts to check file paths, counts, configs, and git branch.
/checkFact-check content against the Midnight ecosystem. Extracts claims, classifies by domain, verifies each via midnight-verify, and produces a report.