encode_download_files
Download ENCODE files by accession to a local directory with MD5 verification, concurrent downloads, and flexible organization options.
Instructions
Download specific ENCODE files by accession to a local directory.
Downloads files from ENCODE to your local machine. Supports MD5 verification, concurrent downloads, and skip-if-already-downloaded.
WHEN TO USE: Use for downloading specific files by accession. For bulk downloads, prefer encode_batch_download. RELATED TOOLS: encode_batch_download, encode_search_files, encode_log_derived_file
Args: file_accessions: List of file accessions to download (e.g., ["ENCFF635JIA", "ENCFF388RZD"]) download_dir: Local directory path to save files (e.g., "/Users/you/data/encode") organize_by: How to organize downloaded files: - "flat": All files in download_dir (default) - "experiment": download_dir/ENCSR.../filename - "format": download_dir/bed/filename - "experiment_format": download_dir/ENCSR.../bed/filename verify_md5: Verify file integrity with MD5 checksum (default True)
Returns: JSON with download results for each file (path, size, success/error, MD5 status).
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| file_accessions | Yes | ||
| download_dir | Yes | ||
| organize_by | No | flat | |
| verify_md5 | No |