bio-batch-downloads SKILL.md skillA
bio-batch-downloads from fridrichmethod/awesome-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add fridrichmethod/awesome-skills/bio-batch-downloads@git:20260528.89ddef6Pins git:20260528.89ddef6 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- fridrichmethod/awesome-skills
- Path
skills/batch-downloads/SKILL.md- Versions recorded
- 2
- Latest version
- git:20260528.89ddef6, committed May 28, 2026
- First version recorded
- May 17, 2026
- Size
- 15,535 bytes
- Repository stars
- 15
- License
- a license file GitHub does not identify
Download large datasets from NCBI efficiently using EPost, history server, batching, rate limiting, and retry logic. Use when bulk-fetching tens of thousands of sequences, pulling all results of a large ESearch, designing reproducible pipelines, comparing E-utilities to NCBI Datasets v2 CLI, or implementing checksum-validated downloads. Encodes WebEnv TTL (~8h), EPost 200-ID limit, retmax caps, parallelization design, and integrity verification.
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
## Version Compatibility Reference examples tested with: BioPython 1.83+, NCBI Datasets CLI 16.0+, Entrez Direct 21.0+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show biopython` then `help(Bio.Entrez.efetch)` to check signatures - CLI: `datasets --version` and `efetch -version` If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Batch Downloads **"Download N thousand records from NCBI without getting blocked"** -> The right answer is rarely "parallelize requests". For >5000 records the answer is the **history server**: search once, fetch in chunks server-side. For >100,000 records or whole genomes, the modern answer is **NCBI Datasets v2 CLI** -- the E-utilities are not optimized for bulk genome/gene data anymore. This skill encodes (a) when to use each retrieval strategy, (b) the precise rate-limit math, (c) WebEnv lifecycle for long-running jobs, (d) how to design retry/resume, and (e) when to defect to Datasets CLI instead. - Python: `Entrez.esearch(usehistory='y')` + chunked `Entrez.efetch()` (BioPython) …
Read the whole file at its exact version.
How to install
mdr add fridrichmethod/awesome-skills/bio-batch-downloads@sha256:a881cf05825df0a3The line at the top of this page pins the label git:20260528.89ddef6, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_mckof6t7gl3jai4t)
3 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 2 versions of this file, between May 17, 2026 and May 28, 2026, about one every 11 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260528.89ddef6 latest | 2026-05-28 | 89ddef6 | 15,535 B | A | view · diff |
| git:20260517.81511a7 | 2026-05-17 | 81511a7 | 12,235 B | A | view |
Audit of the latest version
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (15535 bytes)
- pass: No zero-width or bidi control characters
- pass: No instruction hidden inside an HTML comment
- pass: No link to an exfiltration or paste host
- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
- pass: No text hidden with inline styles
- pass: No prompt-injection phrasing
- pass: No curl or wget piped into a shell
- pass: No recursive delete of root, home or parent
- pass: No instruction to read or print local credentials
- pass: No base64 blob over 200 characters
- pass: No link to a raw IP address
- pass: No script tag
Source
fridrichmethod/awesome-skills · 15 stars · license a license file GitHub does not identify · pushed 2026-11-02 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_mckof6t7gl3jai4t GET https://markdownregistry.com/api/v1/resolve?ref=fridrichmethod/awesome-skills/bio-batch-downloads GET https://markdownregistry.com/api/v1/blob/a881cf05825df0a35bf77c3fc16939d5dd2a8a84d1d3acc5cb03738242001e5c
Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.
Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.
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