skill

bioos-navigen

A specialized, pluggable system prompts to enhance general AI agent as Bio-OS expert designed to operate on the Bio-OS platforms.

GBA-BI/bioos-navigencommunitylistedunreviewed

Use skill

Set up

Skills are installed by placing their folder where your agent loads skills.

Download ZIP from GitHub Open the repository

The download comes from github.com/GBA-BI/bioos-navigen itself, not from our server, so what you get is exactly what its author published.

Install instructions come from the README

Skills do not use an MCP config. Follow the steps in the README below.

README

synced Oct 26, 2026

Bio-OS Navigen Agent

Bio-OS Navigen is a skill-based agent instruction set for operating Bio-OS workflows through natural language. It separates scientific routing from execution details, so the same bioinformatics workflow knowledge can run through either MCP/plugin tools or the pybioos CLI.

Skill Layout

This repository maintains three complementary skill trees:

Directory	Use Case	Execution Surface
`skills-bioinformatics/`	Domain/business-layer skills for genomics, transcriptomics, single-cell analysis, microbiome, pathogen analysis, early warning, proteomics, and Bio-OS image catalogs.	Execution-neutral. These skills route scientific intent and refer to stable skill names such as `bioos_platform_operator`, without depending on whether the backend is MCP/plugin or CLI.
`skills/`	Platform-operation skills for agents connected to Bio-OS through tools exposed by `bioos-mcp-server` or the OpenClaw BioOS plugin.	Uses tool names such as `submit_workflow`, `upload_files_to_workspace`, `get_workflow_logs`, and `create_iesapp`.
`skills-cli/`	Platform-operation skills for agents that call pybioos directly from a shell.	Uses concrete CLI commands such as `bioos workflow submit ...` and `bioos file upload ...`. This tree includes `bioos_cli_locator` to verify CLI availability and authentication.

The intended pairing is:

MCP/plugin mode: install skills/ plus skills-bioinformatics/.
Direct CLI mode: install skills-cli/ plus skills-bioinformatics/.

Use only one platform-operation tree at a time: choose skills/ if the machine is wired to bioos-mcp-server or the OpenClaw plugin, and choose skills-cli/ if the machine only needs to call pybioos directly. You do not need to install both.

skills/ and skills-cli/ should stay behaviorally synchronized. skills-bioinformatics/ should remain neutral and should not mention either directory by name; that is the small trick that lets the same business-layer workflows work with both execution surfaces.

Installation

To load these skills into your developer assistant, you can use the automatic setup script or configure them manually. The installation is configured at the project level.

Quick Install (Project-Level)

To automatically install these skills into your project directory:

Clone or pull the bioos-navigen repository to your local machine:
```
git clone https://github.com/GBA-BI/bioos-navigen.git
```

Enter your project directory, copy the setup_skills.sh script, grant execution permissions, and run it by specifying the source repository path:

# Enter your project directory
cd /path/to/your/project

# Copy setup_skills.sh from the cloned repo
cp /path/to/bioos-navigen/setup_skills.sh .

# Grant execution permission
chmod +x setup_skills.sh

# Run setup and specify the source path of bioos-navigen
./setup_skills.sh --copy --source /path/to/bioos-navigen

This script will automatically detect and install the skills into the local config folders of the following developers' assistants in your project:

Antigravity (.agent/skills/)
Codex (.agents/skills/ and .codex/skills/)
Claude Code (.claude/skills/)

Manual Installation (Project-Level)

If you prefer to configure the skills manually, run the following commands from the repository root.

Copying Skills Physically (Deployment)

# Create local agent configuration directories
mkdir -p .agent/skills .agents/skills .codex/skills .claude/skills

# Copy skills (e.g. for Antigravity)
cp -R skills-cli/* .agent/skills/
cp -R skills-bioinformatics/* .agent/skills/

Linking Skills Relatively (Development)

To link custom skills without duplicating files, you can create relative symlinks:

# Create directories if not exists
mkdir -p .agent/skills

# Create relative symlinks
cd .agent/skills
ln -s ../../skills-cli/* .
ln -s ../../skills-bioinformatics/* .

Architecture

Bio-OS Navigen uses a three-tier capability model:

Tier	Layer	Examples
Tier 1	Atomic platform capabilities	`bioos_data_fetcher`, `bioos_docker_builder`, `bioos_wdl_scripter`, `bioos_workspace_parser`, `bioos_platform_operator`
Tier 2	Pipeline orchestration	`bioos_pipeline_developer`
Tier 3	End-to-end SOPs	`bioos_paper2workspace`, `bioos_workspace2paper`

The bioinformatics skills sit above this stack: they choose the right workflow and hand execution to the synchronized platform-operation skills.

Related Projects

pybioos: install with pip install pybioos; provides the root bioos CLI used by skills-cli/.
bioos-mcp-server: GBA-BI/bioos-mcp-server; exposes Bio-OS operations as MCP tools used by skills/.
bioos-claw: GBA-BI/BioOS-Claws; OpenClaw tools aligned with the MCP tool names.

Development Notes

Keep workflow-facing file-input behavior synchronized between skills/ and skills-cli/.
Keep business-layer guidance in skills-bioinformatics/ execution-neutral.
In CLI mode, use bioos_wdl_scripter for WDL generation, remote validation, and diagnosis of WDL-related run failures.
The legacy modular prompt files live under system_prompt/, and GEMINI.md is the compiled single-file prompt for agents that cannot load skills directly.

Contact

For feedback or issues during the trial phase, please contact the development team.