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home / skills / gptomics / bioskills / bioskills-installer

bioskills-installer skill

/bioskills-installer

This skill installs the full bioSkills collection to enable comprehensive bioinformatics analysis across 425 skills.

This is most likely a fork of the bioskills skill from openclaw
npx playbooks add skill gptomics/bioskills --skill bioskills-installer

Review the files below or copy the command above to add this skill to your agents.

Files (2)
SKILL.md
4.3 KB
---
name: bioskills
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."
metadata: {"openclaw":{"requires":{"bins":["git"],"anyBins":["python3","Rscript"]},"os":["darwin","linux"],"emoji":"🧬"}}
---

# 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

| 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

Overview

This skill installs the complete bioinformatics skill set (425 skills across 62 categories) so an AI agent can perform a wide range of bioinformatics tasks. It bundles category-level installers and optional category filters so you can install everything or only the modules you need. Use it to provision a fully capable bioinformatics agent quickly and consistently.

How this skill works

The installer runs a script that downloads and registers individual skills grouped by category (sequence analysis, RNA-seq, single-cell, variant calling, metagenomics, structural biology, and many more). You can run the full install or pass a comma-separated list of categories to install a subset. After installation, skills are automatically selected by the agent based on the task context and inputs.

When to use it

  • Setting up a new bioinformatics AI agent or environment
  • Onboarding a team that needs consistent, reproducible bioinformatics capabilities
  • Preparing an agent to handle a broad project that spans multiple domains (e.g., RNA-seq + variant calling)
  • Installing specific domain modules when you only need targeted functionality
  • Provisioning offline or controlled environments where internet installs must be scripted

Best practices

  • Install the full collection on a dedicated analysis server to avoid dependency conflicts
  • Use category filters to reduce footprint when you only require a subset of skills
  • Keep the installer script and skill versions under version control for reproducibility
  • Run post-install validation by executing a few canonical workflows (e.g., FASTQ to differential expression) to confirm functionality
  • Document which categories you installed alongside project metadata for future audits

Example use cases

  • Install all skills for an internal bioinformatics platform used by multiple teams
  • Install only single-cell, spatial-transcriptomics, and differential-expression categories for a scRNA-seq project
  • Provision variant-calling, copy-number, and phasing-imputation skills for a clinical WGS pipeline
  • Add metagenomics and microbiome skills to analyze environmental shotgun sequencing
  • Set up a training instance with common workflows (FASTQ to results) for workshops

FAQ

Can I install only a few categories instead of everything?

Yes. The installer accepts a --categories argument with a comma-separated list to install selected categories only.

How will the agent choose the right skill after installation?

Skills are tagged by category and triggered automatically based on the task description and input types; no manual routing is required once installed.