Download ENCODE genomics files
download-encodeskillsetup L2★35
ammawla/encode-toolkit ↗What it does
Download ENCODE data files in batch with MD5 verification
Best for
Bulk download and organization of ENCODE files when local infrastructure needed; starts with dry_run preview to confirm scope before committing.
Inputs
- · file accessions (ENCFF...)
- · search criteria (experiment, assay, format)
- · download directory path
Outputs
- · downloaded files (BED, BAM, bigWig, FASTQ)
- · MD5 verification checksums
- · organization by experiment/format/flat
Requires
- · ENCODE portal API
- · MD5 checksum verification
Preconditions
ENCODE accessions valid; download directory writable; restricted files need WorkOS credentials via encode_manage_credentials
Failure modes
- · dry_run=False without user confirmation → downloads unintended files
- · restricted file missing credentials → download fails silently
- · large batch (>50 files) may exceed API quota
Trust signals
- · MD5 verification included by default
- · Idempotent (skips already-downloaded files)
- · File organization options (experiment, format, nested)