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Agent skill

bioSkills Installer

by GPTomics in GPTomics/bioSkills

Installs the bioSkills collection of 425 bioinformatics skills in one step, or only chosen categories, so sequencing, RNA-seq, single-cell and variant tasks get specialized help.

MITAuto-check passedResearch & Science

Install bioSkills Installer

skills CLI
$ npx skills add GPTomics/bioSkills --skill clawhub-installer -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI
$ gh skill install GPTomics/bioSkills clawhub-installer --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy
$ git clone --depth 1 https://github.com/GPTomics/bioSkills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/clawhub-installer .claude/skills/clawhub-installer && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Facts

Skill name
clawhub-installer
GitHub stars
1.2k
Used in
1 other repo
Token cost
~789 tokens
SKILL.md length
229 words
Files
2 (incl. scripts)
Skills in repo
559
Repo updated
First seen
Licence
MIT

At a glance

Installs the bioSkills collection of 425 bioinformatics skills in one step, or only chosen categories, so sequencing, RNA-seq, single-cell and variant tasks get specialized help.

  • Setting up bioinformatics skills on a new machine
  • SKILL.md covers Installation, What Gets Installed, After Installation and Source
  • Runs Shell scripts from its folder; calls bash
  • Installing only the single-cell or variant-calling skill groups

What it does

This meta-skill installs the whole bioSkills collection, described as 425 skills across 62 categories, by running the bundled scripts/install-bioskills.sh. The script downloads and installs everything by default. Passing a categories option with a comma-separated list, such as single-cell, variant-calling and differential-expression, installs only those groups.

The collection groups its skills into areas such as sequence and alignment, read processing, RNA-seq and expression, single-cell and spatial, variant analysis, epigenomics, metagenomics, genome assembly, proteomics and metabolomics, phylogenetics, structural biology, CRISPR screens and flow cytometry, pathway and multi-omics integration, and end-to-end workflows from FASTQ to results. Once installed, the skills trigger on the task at hand, for example finding differentially expressed genes from RNA-seq counts or calling variants from a whole genome sequencing BAM file.

When your agent uses it

  • Setting up bioinformatics skills on a new machine
  • Installing only the single-cell or variant-calling skill groups
  • A bioinformatics task needs a specialized skill that is not installed yet

Example prompts

  • “Install the bioSkills collection so I can analyze RNA-seq data.”
  • “Install only the single-cell, variant-calling and differential-expression categories of bioSkills.”
  • “I need to call variants from a whole genome BAM file, so set up whichever bioinformatics skills are missing.”

Requirements

  • Bash to run scripts/install-bioskills.sh
  • Network access to download the skills

What it can do on your machine

Read from SKILL.md and the folder at commit d91ed3d. It shows what the files ask for, not the result of running them.

  • Tool permissions

    Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.

    From allowed-tools in the SKILL.md frontmatter.

  • Runs code

    Ships 1 file in scripts/ (Shell), which the agent can run.

    Shell commands in SKILL.md call:

    • bash

    From the folder's file list and the shell code blocks in SKILL.md.

  • Network

    No URLs in SKILL.md.

    From URLs in SKILL.md, links to its own repository left out.

  • Credentials

    Names no API keys, tokens, secrets or passwords.

    From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

bioSkills Installer loads about 789 tokens when it runs. Until then it costs about 76 tokens; SKILL.md has 229 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~76
When it runs · the whole SKILL.md, loaded when a task matches
~789

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check passed

The automated check found no risky patterns in SKILL.md.

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); the scripts in this folder are not scanned.

SKILL.md

The full file from GPTomics/bioSkills at commit d91ed3d, republished under its MIT licence (© GPTomics). 229 words, ~789 tokens.

Download SKILL.mdSave it as .claude/skills/clawhub-installer/SKILL.md (or your agent's skills folder). This skill also uses 1 other file; get the full folder from GitHub.
name
clawhub-installer
description
Installs 425 bioinformatics skills covering sequence analysis, RNA-seq, single-cell, variant calling, metagenomics, structural biology, and 56 more categories. Use when setting up bioinformatics capabilities or when a bioinformatics task requires specialized skills not yet installed.

bioSkills Installer

Meta-skill that installs the full bioSkills collection (425 skills across 62 categories) for bioinformatics analysis.

Installation

Run the bundled install script to download and install all bioSkills:

bash
bash scripts/install-bioskills.sh

Or install only specific categories:

bash
bash scripts/install-bioskills.sh --categories "single-cell,variant-calling,differential-expression"

What Gets Installed

425 skills across 62 categories covering:

  • Sequence & Alignment (40): sequence-io, sequence-manipulation, alignment, alignment-files, database-access
  • Read Processing (11): read-qc, read-alignment
  • RNA-seq & Expression (14): differential-expression, rna-quantification, expression-matrix
  • Single-Cell & Spatial (25): single-cell, spatial-transcriptomics
  • Variant Analysis (21): variant-calling, copy-number, phasing-imputation
  • Epigenomics (25): chip-seq, atac-seq, methylation-analysis, hi-c-analysis
  • Metagenomics & Microbiome (13): metagenomics, microbiome
  • Genomics & Assembly (29): genome-assembly, genome-annotation, genome-intervals, genome-engineering, primer-design
  • Regulatory & Causal (13): gene-regulatory-networks, causal-genomics, rna-structure
  • Temporal & Ecological (11): temporal-genomics, ecological-genomics
  • Immunology & Clinical (25): immunoinformatics, clinical-databases, tcr-bcr-analysis, epidemiological-genomics
  • Specialized Omics (36): proteomics, metabolomics, alternative-splicing, chemoinformatics, liquid-biopsy
  • RNA Biology (20): small-rna-seq, epitranscriptomics, clip-seq, ribo-seq
  • Phylogenetics & Evolution (16): phylogenetics, population-genetics, comparative-genomics
  • Structural & Systems (11): structural-biology, systems-biology
  • Screens & Cytometry (22): crispr-screens, flow-cytometry, imaging-mass-cytometry
  • Pathway & Integration (14): pathway-analysis, multi-omics-integration, restriction-analysis
  • Infrastructure (39): data-visualization, machine-learning, workflow-management, reporting, experimental-design, long-read-sequencing
  • Workflows (40): end-to-end pipelines (FASTQ to results)

After Installation

Once installed, skills are automatically triggered based on the task at hand. Example requests:

  • "I have RNA-seq counts from treated vs control samples - find the differentially expressed genes"
  • "Call variants from this whole genome sequencing BAM file"
  • "Cluster my single-cell RNA-seq data and find marker genes"
  • "Predict the structure of this protein sequence"
  • "Run a metagenomics classification on these shotgun reads"

Source

GitHub: https://github.com/GPTomics/bioSkills

© GPTomics, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

SKILL.md and 1 other file (scripts) in clawhub-installer of GPTomics/bioSkills.

  • SKILL.md
  • scripts/install-bioskills.sh

Open the folder on GitHubat commit d91ed3d

Used in 1 other repository

We found 1 copy of this SKILL.md (exact, near-identical or edited) in other folders, from 1 other GitHub owner. This page covers the copy in GPTomics/bioSkills, which our catalogue first saw on October 7, 2026.

Compare with similar skills

bioSkills Installer next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.

bioSkills Installer compared with similar skills
SkillStarsUsed inTokensAuto-checkLicenceRepo updated
bioSkills Installer this skillGPTomics/bioSkills1.2k1 repos~789Automated safety check: PassMIT
Tbtoolsxuzhougeng/wispterm442—~2.3kAutomated safety check: PassMIT
Pride FetchClawBio/ClawBio1.2k—~4.2kAutomated safety check: PassMIT
Alphagenome Single Variant Analysisgoogle-deepmind/science-skills3.2k2 repos~3kAutomated safety check: NotesApache-2.0
Chembl Databasegoogle-deepmind/science-skills3.2k2 repos~2.9kAutomated safety check: PassApache-2.0
13C Metabolic Flux AnalysisK-Dense-AI/scientific-agent-skills48k1 repos~3.2kAutomated safety check: PassMIT

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More from GPTomics/bioSkills

All 559 skills in this repo

  • Bio Alignment Io

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  • Amplicon Primer Clipping

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  • Alignment Filtering with samtools and pysam

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  • Bio Alignment Indexing

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Works with

Categories

Questions about bioSkills Installer

What does bioSkills Installer do?

Installs the bioSkills collection of 425 bioinformatics skills in one step, or only chosen categories, so sequencing, RNA-seq, single-cell and variant tasks get specialized help. sh. The script downloads and installs everything by default.

When should I use bioSkills Installer?

bioSkills Installer fits situations like: setting up bioinformatics skills on a new machine; installing only the single-cell or variant-calling skill groups; A bioinformatics task needs a specialized skill that is not installed yet.

How do I install bioSkills Installer in Claude Code?

Run `npx skills add GPTomics/bioSkills --skill clawhub-installer -a claude-code`. Or copy the skill folder (clawhub-installer in GPTomics/bioSkills) into .claude/skills/clawhub-installer in your project. Claude Code loads it when a task matches its description.

How do I install bioSkills Installer in Codex?

Run `npx skills add GPTomics/bioSkills --skill clawhub-installer -a codex`. Or copy the skill folder (clawhub-installer in GPTomics/bioSkills) into .agents/skills/clawhub-installer in your project. Codex loads it when a task matches its description.

Can I use bioSkills Installer in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add GPTomics/bioSkills --skill clawhub-installer -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/clawhub-installer, .gemini/skills/clawhub-installer, .github/skills/clawhub-installer and .opencode/skills/clawhub-installer in your project.

What does bioSkills Installer need to run?

Going by SKILL.md and its folder, bioSkills Installer needs a shell for the scripts in its folder and the command-line tools its instructions call (bash). Our summary lists: Bash to run scripts/install-bioskills.sh; Network access to download the skills.

Does bioSkills Installer access the network?

SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.

Is bioSkills Installer safe to install?

Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. The check reads SKILL.md only: the scripts in the folder are not scanned, so read them before running anything.

What licence does bioSkills Installer use?

bioSkills Installer is published under the MIT licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does bioSkills Installer use?

About 789 tokens (SKILL.md is roughly 3.2k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.

What are the alternatives to bioSkills Installer?

Skills that share tags, products or a category with bioSkills Installer: Tbtools (xuzhougeng/wispterm, 442 stars), Pride Fetch (ClawBio/ClawBio, 1.2k stars), Alphagenome Single Variant Analysis (google-deepmind/science-skills, 3.2k stars) and Chembl Database (google-deepmind/science-skills, 3.2k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains bioSkills Installer?

GPTomics (a GitHub organization) maintains it in GPTomics/bioSkills, which has 1,218 GitHub stars. The repository holds 559 skills in this directory. The repository was last updated on August 15, 2026.

Source: GPTomics/bioSkills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.