Description

Installs 412 bioinformatics skills covering sequence analysis, RNA-seq, single-cell, variant calling, metagenomics, structural biology, and 54 more categorie...

README (SKILL.md)

bioSkills Installer

Name: BioSkills
Author: djemec

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 scripts/install-bioskills.sh

Or install only specific categories:

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

What Gets Installed

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

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

Related Skills

After installation, 425 individual skills become available across these categories: sequence-io, sequence-manipulation, database-access, alignment, alignment-files, variant-calling, phylogenetics, differential-expression, structural-biology, single-cell, pathway-analysis, restriction-analysis, methylation-analysis, chip-seq, metagenomics, long-read-sequencing, read-qc, read-alignment, rna-quantification, genome-assembly, genome-intervals, data-visualization, expression-matrix, copy-number, proteomics, flow-cytometry, population-genetics, multi-omics-integration, spatial-transcriptomics, machine-learning, workflow-management, microbiome, metabolomics, phasing-imputation, primer-design, hi-c-analysis, imaging-mass-cytometry, atac-seq, crispr-screens, reporting, experimental-design, clinical-databases, tcr-bcr-analysis, small-rna-seq, epitranscriptomics, clip-seq, ribo-seq, genome-engineering, systems-biology, epidemiological-genomics, immunoinformatics, comparative-genomics, alternative-splicing, chemoinformatics, liquid-biopsy, genome-annotation, gene-regulatory-networks, causal-genomics, rna-structure, temporal-genomics, ecological-genomics, workflows

Usage Guidance

This skill appears coherent for installing many bioinformatics helper skills: it needs git and will clone a GitHub repo and run an installer script from that repo. Before installing, review and trust the remote repository and the specific commit hash the installer expects. Because the installer executes install-openclaw.sh from the cloned repo (not included in the package), that remote script could perform any actions on your user account. Safer steps: inspect the repository and the install-openclaw.sh content on GitHub, run the installer on a disposable/isolated environment or container, back up any important OpenClaw data (~/.openclaw), and consider using the --categories option to limit what is installed. If you cannot review the remote script, do not run the installer on sensitive systems.

Capability Analysis

Type: OpenClaw Skill Name: bioskills Version: 3.0.0 The skill bundle is an installer for bioinformatics tools. The `SKILL.md` provides clear, benign instructions without any prompt injection attempts. The `scripts/install-bioskills.sh` script clones a remote GitHub repository (`https://github.com/GPTomics/bioSkills.git`) and executes an installer script (`install-openclaw.sh`) from within it. Crucially, the script includes a strong integrity check by verifying the cloned repository's commit hash against a hardcoded `EXPECTED_COMMIT` (`fae219d8cacb7be84b96b3a99122556c1a42a47b`). This significantly mitigates supply chain risks by ensuring only a specific, verified version of the remote code is executed. All file system and network operations are consistent with the stated purpose of installing software, and there is no evidence of data exfiltration, persistence mechanisms, or other malicious intent.

Capability Assessment

✓ Purpose & Capability

The name/description claim to install a large collection of bioinformatics skills and the provided installer script implements that: it clones a GitHub repository and runs an OpenClaw installer from it. Required binaries (git and either python3 or Rscript) match the stated bioinformatics purpose and there are no unrelated environment variables or credentials requested.

ℹ Instruction Scope

SKILL.md tells the agent/user to run scripts/install-bioskills.sh (included). That script clones the declared GitHub repo, verifies a specific commit hash, and then executes install-openclaw.sh from the cloned repo. The instructions do not request unrelated files/credentials, but they do cause execution of a remote script (install-openclaw.sh) whose contents are not present in the package — that grants the remote repository the ability to perform arbitrary install-time actions on the user’s machine.

✓ Install Mechanism

No binary package downloads from untrusted hosts. The installer uses git to clone a GitHub repository (a well-known host) and enforces a single expected commit hash for integrity checks, which mitigates supply-chain risk. The script does not extract arbitrary archives from unknown servers.

✓ Credentials

No credentials or privileged environment variables are requested. The script writes to user-local paths ($HOME/.openclaw/...), which is appropriate for a user-level installer. Required binaries are proportional to the task.

✓ Persistence & Privilege

The skill is not always-enabled and does not request elevated platform privileges in its metadata. The installer creates and modifies files in the user's home directory (~/.openclaw) and can remove those files via --uninstall. Note: the executed install-openclaw.sh (from the cloned repo) could alter other parts of the environment — that script was not provided for review.

Version History

v3.0.0

- Added git as a required dependency for installation (now requires "git" alongside "python3" or "Rscript"). - Pinned to v3.0 of BioSkills

v2.0.0

- Increased the total number of skills from 412 to 425. - Expanded category coverage from 60 to 62 categories, adding "temporal-genomics" and "ecological-genomics". - The Workflows category now installs 40 skills (previously 38). - Updated documentation to reflect new categories and skill counts throughout. - Reworded skills to self-heal

v1.0.0

Initial release of the bioSkills installer meta-skill. - Installs all 412 bioinformatics skills across 60 categories. - Supports both full installation and selective installation by category. - Covers key areas such as sequence analysis, RNA-seq, single-cell, variant calling, metagenomics, structural biology, and more. - After installation, skills are automatically triggered as needed for various bioinformatics tasks.

Metadata

Slug bioskills

Version 3.0.0

License —

All-time Installs 1

Active Installs 1

Total Versions 3

Frequently Asked Questions

What is BioSkills?

Installs 412 bioinformatics skills covering sequence analysis, RNA-seq, single-cell, variant calling, metagenomics, structural biology, and 54 more categorie... It is an AI Agent Skill for Claude Code / OpenClaw, with 1133 downloads so far.

How do I install BioSkills?

Run "/install bioskills" in the OpenClaw or Claude Code chat to install it in one step — no extra setup required.

Is BioSkills free?

Yes, BioSkills is completely free (open-source). You can download, install and use it at no cost.

Which platforms does BioSkills support?

BioSkills is cross-platform and runs anywhere OpenClaw / Claude Code is available (darwin, linux).

Who created BioSkills?

It is built and maintained by djemec (@djemec); the current version is v3.0.0.

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