Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx skills add ammawla/encode-toolkit --skill bioinformatics-installergit clone --depth 1 https://github.com/ammawla/encode-toolkitWrote 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/ammawla/encode-toolkit/bioinformatics-installer)<a href="https://agentmods.dev/skills/ammawla/encode-toolkit/bioinformatics-installer"><img src="https://agentmods.dev/badge/skills/ammawla/encode-toolkit/bioinformatics-installer/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/ammawla/encode-toolkit/bioinformatics-installer"><img src="https://agentmods.dev/badge/skills/ammawla/encode-toolkit/bioinformatics-installer.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 | $0.00140 | $0.09943 |
| Opus 5.5 | $0.00056 | $0.03977 |
| Sonnet 5.5 | $0.00028 | $0.01989 |
| Haiku 4.5 | $0.00014 | $0.00994 |
Grade B, and why
bioinformatics-installer scanned grade B with 2 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-get update Makes network callslowCapability
Not a fault in itself. Listed so you know the mod talks to something, and to what.
wget http://homer.ucsd.edu/homer/configureHomer.pl The source is not reproduced here
Licensed AGPL-3.0
The repository is licensed AGPL-3.0, which this catalogue does not treat as permission to reproduce the file. Read it at the source.
What ships with it
13 files 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.
- environments/atacseq-env.yml 974 B
- environments/chipseq-env.yml 996 B
- environments/cutandrun-env.yml 979 B
- environments/dnaseseq-env.yml 1.1 KB
- environments/hic-env.yml 856 B
- environments/rnaseq-env.yml 808 B
- environments/wgbs-env.yml 917 B
- references/literature.md 8.8 KB
- scripts/constraints.txt 23 KB
- scripts/install-nextflow.sh 7.0 KB runs code
- scripts/install-python-packages.sh 3.2 KB runs code
- scripts/install-r-packages.R 5.2 KB
- scripts/requirements.in 512 B
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 Changed · +48 lines scan D → B 676b7cc5d5d1
- 1mo ago First seen · 722 lines · 140 tokens per session scan D 2150c3875b82
bioinformatics-installer is a skill published in the GitHub repository ammawla/encode-toolkit (21 stars, last pushed 26d ago), licensed AGPL-3.0. It adds 140 tokens to every session and 9,943 once invoked, about $0.0006 per session on Opus 5.5. A static security scan graded it B with 2 findings (asks for root, makes network calls). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.
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