Getting it into your agent
It runs from inside its repository, so the clone comes first — what it calls does not travel with the file alone.
git clone --depth 1 https://github.com/thesecondfox/skillnpx agentmods add skills/thesecondfox/skill/bio-database-access-sra-dataWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/thesecondfox/skill/bio-database-access-sra-data)<a href="https://agentmods.dev/skills/thesecondfox/skill/bio-database-access-sra-data"><img src="https://agentmods.dev/badge/skills/thesecondfox/skill/bio-database-access-sra-data/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/thesecondfox/skill/bio-database-access-sra-data"><img src="https://agentmods.dev/badge/skills/thesecondfox/skill/bio-database-access-sra-data.svg" alt="Reviewed on agentmods" width="80" height="20"></a>What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00044 | $0.02662 |
| Opus 5.5 | $0.00018 | $0.01065 |
| Sonnet 5.5 | $0.00009 | $0.00532 |
| Haiku 4.5 | $0.00004 | $0.00266 |
Grade D, and why
bio-sra-data scanned grade D with 3 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 1mo ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Asks for rootmediumPrivilege escalation
A mod that escalates privileges can change anything on the machine, not only the project.
sudo apt install sra-toolkit Recursive force deletehighDestructive command
rm -rf with a variable or a broad path is one typo away from removing the wrong tree.
rm -rf ${OUTDIR}/${SRR} Runs shell commandslowCapability
Expected in a hook, worth knowing in a rule or an instructions file.
- Python: `subprocess.run(['fasterq-dump', accession])` or `Entrez.efetch()` for metadata How it starts
The opening of the file, as written. The whole thing — 367 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Version Compatibility
Reference examples tested with: BioPython 1.83+, Entrez Direct 21.0+, SRA Toolkit 3.0+
Before using code patterns, verify installed versions match. If versions differ:
- Python:
pip show <package>thenhelp(module.function)to check signatures - CLI:
<tool> --versionthen<tool> --helpto confirm flags
If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.
SRA Data
Download raw sequencing data from the Sequence Read Archive using the SRA toolkit.
"Download FASTQ from SRA" → Fetch raw sequencing reads from an SRA accession as FASTQ files.
- CLI:
fasterq-dump SRR_ACCESSION(SRA Toolkit) - Python:
subprocess.run(['fasterq-dump', accession])orEntrez.efetch()for metadata
Installation
# macOS
brew install sratoolkit
# Ubuntu/Debian
sudo apt install sra-toolkit
# conda (recommended)
conda install -c bioconda sra-tools
# Verify installation
fasterq-dump --version
Core Commands
fasterq-dump - Download FASTQ (Recommended)
Fast, multithreaded FASTQ extraction. Preferred over fastq-dump.
# Download single SRA run as FASTQ
fasterq-dump SRR12345678
# Output: SRR12345678.fastq (single-end)
# Or: SRR12345678_1.fastq, SRR12345678_2.fastq (paired-end)
Key Options:
| Option | Description | Example |
|---|---|---|
-O / --outdir |
Output directory | -O ./fastq/ |
-o / --outfile |
Output filename | -o sample.fastq |
-e / --threads |
Number of threads | -e 8 |
-p / --progress |
Show progress bar | -p |
-S / --split-files |
Split paired reads (default) | -S |
-3 / --split-3 |
Also output unpaired reads | -3 |
--skip-technical |
Skip technical reads | --skip-technical |
-t / --temp |
Temp directory | -t /tmp |
-f / --force |
Overwrite existing | -f |
# Common usage with options
fasterq-dump SRR12345678 -O ./data/ -e 8 -p --skip-technical
# Force split files (paired-end)
fasterq-dump SRR12345678 -S -O ./data/
What ships with it
1 file beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 1mo ago First seen · 367 lines · 44 tokens per session scan D 64eaa2379631
bio-sra-data is a skill published in the GitHub repository thesecondfox/skill (3 stars, last pushed 6mo ago), licensed MIT. It adds 44 tokens to every session and 2,662 once invoked, about $0.0002 per session on Opus 5.5. A static security scan graded it D with 3 findings (asks for root, recursive force delete, runs shell commands). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-31.
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