openbioskill 0.1.1__tar.gz

openbioskill-0.1.1/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2026 Xiang
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

openbioskill-0.1.1/MANIFEST.in

@@ -0,0 +1,5 @@
+include README.md
+include LICENSE
+recursive-include skills *
+recursive-include openbioskill *.py
+global-exclude __pycache__ *.py[cod]

openbioskill-0.1.1/PKG-INFO

@@ -0,0 +1,151 @@
+Metadata-Version: 2.1
+Name: openbioskill
+Version: 0.1.1
+Summary: OpenBio CLI and skill bundles.
+Author: Xiang Li
+License: MIT License
+        
+        Copyright (c) 2026 Xiang
+        
+        Permission is hereby granted, free of charge, to any person obtaining a copy
+        of this software and associated documentation files (the "Software"), to deal
+        in the Software without restriction, including without limitation the rights
+        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+        copies of the Software, and to permit persons to whom the Software is
+        furnished to do so, subject to the following conditions:
+        
+        The above copyright notice and this permission notice shall be included in all
+        copies or substantial portions of the Software.
+        
+        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+        SOFTWARE.
+        
+Keywords: bioinformatics,cli,skills
+Classifier: Development Status :: 3 - Alpha
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.12
+Description-Content-Type: text/markdown
+License-File: LICENSE
+
+# BioDeepagents CLI
+
+[![PyPI](https://img.shields.io/pypi/v/openbioskill?label=openbioskill&logo=pypi&logoColor=white)](https://pypi.org/project/openbioskill/)
+
+## PyPI Package
+
+The `openbioskill` package ships the bioinformatics skill bundle so you can manage and distribute skills via PyPI.
+
+Install from PyPI:
+
+```bash
+python3 -m pip install openbioskill
+```
+
+The package includes:
+- Bundled bioinformatics skills under `skills/`
+- A console entry point: `openbio`
+
+Install the bundled skills to the default model path (`~/.claude/skills`):
+
+```bash
+openbio install
+```
+
+`openbio install` auto-detects these targets (in order) when no flags are passed:
+- Cursor: `~/.cursor/skills`
+- Claude Code: `~/.claude/skills`
+- Codex: `~/.codex/skills`
+- Gemini CLI: `~/.gemini/skills`
+- Deepagents CLI: `~/.deepagents/skills`
+
+If none are detected, it falls back to `~/.claude/skills`.
+
+Install to a different model path:
+
+```bash
+openbio install --model-name codex
+openbio install --model-name deepagents-cli
+```
+
+## Skills
+
+Upstream skill sources and datasets:
+- [claude-scientific-skills](https://github.com/K-Dense-AI/claude-scientific-skills)
+- [ClawBio](https://github.com/ClawBio/ClawBio)
+- [Indexd Skills Datasets](https://agent.indexd.org/skills-datasets)
+
+Skills are sourced from BioClaw. The following skills are sourced from claude-scientific-skills:
+- Bioinformatics & Genomics
+- Sequence Analysis: Process DNA/RNA/protein sequences with BioPython and pysam
+- Single-Cell Analysis: Analyze 10X Genomics data with Scanpy, identify cell types, infer GRNs with Arboreto
+- Variant Annotation: Annotate VCF files with Ensembl VEP, query ClinVar for pathogenicity
+- Variant Database Management: Build scalable VCF databases with TileDB-VCF for incremental sample addition, efficient population-scale queries, and compressed storage of genomic variant data
+- Gene Discovery: Query NCBI Gene, UniProt, and Ensembl for comprehensive gene information
+- Network Analysis: Identify protein-protein interactions via STRING, map to pathways (KEGG, Reactome)
+
+| Skill | Description |
+| --- | --- |
+| [bio-orchestrator](skills/bio-orchestrator/SKILL.md) | Meta-agent that routes bioinformatics requests to specialised sub-skills. Handles file type detection, analysis planning, report generation, and reproducibility export. |
+...
+| [vcf-annotator](skills/vcf-annotator/SKILL.md) | Annotate VCF variants with VEP, ClinVar, gnomAD frequencies, and ancestry-aware context. Generates prioritised variant reports. |
+
+This project is basing on [deepagents](https://github.com/langchain-ai/deepagents) CLI, an open source coding assistant that runs in your terminal, similar to Claude Code.
+
+## Verified K-Dense Skills (146 total)
+- `iso-13485-certification` (author: K-Dense Inc.) – comprehensive ISO 13485:2016 QMS guidance with gap analysis tooling, clause-by-clause references, and templates for Quality Manuals, procedures, and Medical Device Files so teams can assess readiness and build compliant documentation.
+
+| Skills Source | Verified # | Total # | Verification Methods |
+| --- | --- | --- | --- |
+| `claude-scientific-skills` (K-Dense Inc.) | 146 | 147 (total skills in `skills/`) | Metadata-driven audit: only `SKILL.md` files with `skill-author: K-Dense Inc.` are promoted from `skills_unverified/claude-scientific-skills/` into `skills/`, ensuring each verified skill is explicitly claimed by the author. |
+
+*Key Features:**
+- **Built-in Tools**: File operations (read, write, edit, glob, grep), shell commands, web search, and subagent delegation
+- **Customizable Skills**: Add domain-specific capabilities through a progressive disclosure skill system
+- **Persistent Memory**: Agent remembers your preferences, coding style, and project context across sessions
+- **Project-Aware**: Automatically detects project roots and loads project-specific configurations 
+
+<img src="cli-banner.jpg" alt="deep agent" width="100%"/>
+
+
+## 🐳 Docker
+
+Build the CLI image from the repository root so both the CLI sources and the shared `deepagents` package are available to Docker:
+
+This project is a docker-compose hosted a deepagents-cli, and inside container some other agents(e.g. dsl) were also hosted. 
+
+```bash
+docker compose run --rm --service-ports --build flask-app
+```
+
+Copy the sample configuration into place and edit the credentials or tracing toggles you need:
+
+
+```bash
+docker run --rm -it -P \
+  -v "$(pwd)/workspace/:/workspace/project" \
+  --env-file ./.env \
+  deepagents-cli
+```
+Type naturally as you would in a chat interface. The agent will use its built-in tools, skills, and memory to help you with tasks.
+
+> [!WARNING]
+> **Human-in-the-Loop (HITL) Approval Required**
+>
+> Potentially destructive operations require user approval before execution:
+> - **File operations**: `write_file`, `edit_file`
+> - **Command execution**: `shell`, `execute`
+> - **External requests**: `web_search`, `fetch_url`
+> - **Delegation**: `task` (subagents)
+>
+> Each operation will prompt for approval showing the action details. Use `--auto-approve` to skip prompts:
+> ```bash
+> deepagents --auto-approve
+> ``` 

openbioskill-0.1.1/README.md

@@ -0,0 +1,114 @@
+# BioDeepagents CLI
+
+[![PyPI](https://img.shields.io/pypi/v/openbioskill?label=openbioskill&logo=pypi&logoColor=white)](https://pypi.org/project/openbioskill/)
+
+## PyPI Package
+
+The `openbioskill` package ships the bioinformatics skill bundle so you can manage and distribute skills via PyPI.
+
+Install from PyPI:
+
+```bash
+python3 -m pip install openbioskill
+```
+
+The package includes:
+- Bundled bioinformatics skills under `skills/`
+- A console entry point: `openbio`
+
+Install the bundled skills to the default model path (`~/.claude/skills`):
+
+```bash
+openbio install
+```
+
+`openbio install` auto-detects these targets (in order) when no flags are passed:
+- Cursor: `~/.cursor/skills`
+- Claude Code: `~/.claude/skills`
+- Codex: `~/.codex/skills`
+- Gemini CLI: `~/.gemini/skills`
+- Deepagents CLI: `~/.deepagents/skills`
+
+If none are detected, it falls back to `~/.claude/skills`.
+
+Install to a different model path:
+
+```bash
+openbio install --model-name codex
+openbio install --model-name deepagents-cli
+```
+
+## Skills
+
+Upstream skill sources and datasets:
+- [claude-scientific-skills](https://github.com/K-Dense-AI/claude-scientific-skills)
+- [ClawBio](https://github.com/ClawBio/ClawBio)
+- [Indexd Skills Datasets](https://agent.indexd.org/skills-datasets)
+
+Skills are sourced from BioClaw. The following skills are sourced from claude-scientific-skills:
+- Bioinformatics & Genomics
+- Sequence Analysis: Process DNA/RNA/protein sequences with BioPython and pysam
+- Single-Cell Analysis: Analyze 10X Genomics data with Scanpy, identify cell types, infer GRNs with Arboreto
+- Variant Annotation: Annotate VCF files with Ensembl VEP, query ClinVar for pathogenicity
+- Variant Database Management: Build scalable VCF databases with TileDB-VCF for incremental sample addition, efficient population-scale queries, and compressed storage of genomic variant data
+- Gene Discovery: Query NCBI Gene, UniProt, and Ensembl for comprehensive gene information
+- Network Analysis: Identify protein-protein interactions via STRING, map to pathways (KEGG, Reactome)
+
+| Skill | Description |
+| --- | --- |
+| [bio-orchestrator](skills/bio-orchestrator/SKILL.md) | Meta-agent that routes bioinformatics requests to specialised sub-skills. Handles file type detection, analysis planning, report generation, and reproducibility export. |
+...
+| [vcf-annotator](skills/vcf-annotator/SKILL.md) | Annotate VCF variants with VEP, ClinVar, gnomAD frequencies, and ancestry-aware context. Generates prioritised variant reports. |
+
+This project is basing on [deepagents](https://github.com/langchain-ai/deepagents) CLI, an open source coding assistant that runs in your terminal, similar to Claude Code.
+
+## Verified K-Dense Skills (146 total)
+- `iso-13485-certification` (author: K-Dense Inc.) – comprehensive ISO 13485:2016 QMS guidance with gap analysis tooling, clause-by-clause references, and templates for Quality Manuals, procedures, and Medical Device Files so teams can assess readiness and build compliant documentation.
+
+| Skills Source | Verified # | Total # | Verification Methods |
+| --- | --- | --- | --- |
+| `claude-scientific-skills` (K-Dense Inc.) | 146 | 147 (total skills in `skills/`) | Metadata-driven audit: only `SKILL.md` files with `skill-author: K-Dense Inc.` are promoted from `skills_unverified/claude-scientific-skills/` into `skills/`, ensuring each verified skill is explicitly claimed by the author. |
+
+*Key Features:**
+- **Built-in Tools**: File operations (read, write, edit, glob, grep), shell commands, web search, and subagent delegation
+- **Customizable Skills**: Add domain-specific capabilities through a progressive disclosure skill system
+- **Persistent Memory**: Agent remembers your preferences, coding style, and project context across sessions
+- **Project-Aware**: Automatically detects project roots and loads project-specific configurations 
+
+<img src="cli-banner.jpg" alt="deep agent" width="100%"/>
+
+
+## 🐳 Docker
+
+Build the CLI image from the repository root so both the CLI sources and the shared `deepagents` package are available to Docker:
+
+This project is a docker-compose hosted a deepagents-cli, and inside container some other agents(e.g. dsl) were also hosted. 
+
+```bash
+docker compose run --rm --service-ports --build flask-app
+```
+
+Copy the sample configuration into place and edit the credentials or tracing toggles you need:
+
+
+```bash
+docker run --rm -it -P \
+  -v "$(pwd)/workspace/:/workspace/project" \
+  --env-file ./.env \
+  deepagents-cli
+```
+Type naturally as you would in a chat interface. The agent will use its built-in tools, skills, and memory to help you with tasks.
+
+> [!WARNING]
+> **Human-in-the-Loop (HITL) Approval Required**
+>
+> Potentially destructive operations require user approval before execution:
+> - **File operations**: `write_file`, `edit_file`
+> - **Command execution**: `shell`, `execute`
+> - **External requests**: `web_search`, `fetch_url`
+> - **Delegation**: `task` (subagents)
+>
+> Each operation will prompt for approval showing the action details. Use `--auto-approve` to skip prompts:
+> ```bash
+> deepagents --auto-approve
+> ``` 

openbioskill-0.1.1/openbioskill/__init__.py

@@ -0,0 +1,2 @@
+"""OpenBio skill bundle installer package."""
+

openbioskill-0.1.1/openbioskill/cli.py

@@ -0,0 +1,74 @@
+from __future__ import annotations
+
+import argparse
+from pathlib import Path
+
+from openbioskill.installer import (
+    MODEL_DIRS,
+    detect_target_dir,
+    install_skills,
+)
+
+
+def _build_parser() -> argparse.ArgumentParser:
+    parser = argparse.ArgumentParser(
+        prog="openbio",
+        description="OpenBio CLI for managing bundled skills.",
+    )
+    subparsers = parser.add_subparsers(dest="command", required=True)
+
+    install_parser = subparsers.add_parser(
+        "install", help="Install bundled skills to ~/.{model_name}/skills."
+    )
+    install_parser.add_argument(
+        "--model-name",
+        choices=sorted(MODEL_DIRS),
+        help="Target model folder name. If omitted, auto-detect is used.",
+    )
+    install_parser.add_argument(
+        "--target-dir",
+        type=Path,
+        help="Explicit destination path. Overrides --model-name when set.",
+    )
+    install_parser.add_argument(
+        "--force",
+        action="store_true",
+        help="Overwrite existing files in the destination.",
+    )
+    install_parser.add_argument(
+        "--dry-run",
+        action="store_true",
+        help="Print actions without writing files.",
+    )
+
+    return parser
+
+
+def main() -> int:
+    args = _build_parser().parse_args()
+    if args.command != "install":
+        raise SystemExit(2)
+
+    if args.target_dir:
+        target_dir = args.target_dir
+        selected_model = "custom"
+        auto_detected = False
+    else:
+        selected_model, target_dir, auto_detected = detect_target_dir(args.model_name)
+
+    copied, skipped = install_skills(
+        target_dir=target_dir,
+        force=args.force,
+        dry_run=args.dry_run,
+    )
+    mode = "dry-run" if args.dry_run else "installed"
+    detect_note = "auto-detected" if auto_detected else "selected"
+    print(
+        f"{mode}: copied={copied} skipped={skipped} "
+        f"model={selected_model} ({detect_note}) target={target_dir}"
+    )
+    return 0
+
+
+if __name__ == "__main__":
+    raise SystemExit(main())

openbioskill-0.1.1/openbioskill/installer.py

@@ -0,0 +1,136 @@
+from __future__ import annotations
+
+import argparse
+import shutil
+from importlib import resources
+from pathlib import Path
+
+DEFAULT_MODEL_NAME = "claude"
+MODEL_DIRS = {
+    "cursor": ".cursor",
+    "claude": ".claude",
+    "codex": ".codex",
+    "gemini": ".gemini",
+    "deepagents": ".deepagents",
+    "deepagents-cli": ".deepagents",
+}
+AUTO_DETECT_ORDER = ("cursor", "claude", "codex", "gemini", "deepagents")
+
+
+def _parse_args() -> argparse.Namespace:
+    parser = argparse.ArgumentParser(
+        description="Install bundled OpenBio skills into ~/.{model_name}/skills."
+    )
+    parser.add_argument(
+        "--model-name",
+        choices=sorted(MODEL_DIRS),
+        help="Target model folder name. If omitted, auto-detect is used.",
+    )
+    parser.add_argument(
+        "--target-dir",
+        type=Path,
+        help="Explicit destination path. Overrides --model-name when set.",
+    )
+    parser.add_argument(
+        "--force",
+        action="store_true",
+        help="Overwrite existing files in the destination.",
+    )
+    parser.add_argument(
+        "--dry-run",
+        action="store_true",
+        help="Print actions without writing files.",
+    )
+    return parser.parse_args()
+
+
+def model_name_to_target_dir(model_name: str, home: Path | None = None) -> Path:
+    base = home or Path.home()
+    model_root = MODEL_DIRS.get(model_name, f".{model_name}")
+    return base / model_root / "skills"
+
+
+def detect_target_dir(
+    model_name: str | None = None, *, home: Path | None = None
+) -> tuple[str, Path, bool]:
+    base = home or Path.home()
+
+    if model_name:
+        return model_name, model_name_to_target_dir(model_name, base), False
+
+    for candidate in AUTO_DETECT_ORDER:
+        root_dir = base / MODEL_DIRS[candidate]
+        skills_dir = root_dir / "skills"
+        if root_dir.exists() or skills_dir.exists():
+            return candidate, skills_dir, True
+
+    return (
+        DEFAULT_MODEL_NAME,
+        model_name_to_target_dir(DEFAULT_MODEL_NAME, base),
+        True,
+    )
+
+
+def _iter_skill_files(skills_root: Path):
+    for src_path in skills_root.rglob("*"):
+        if not src_path.is_file():
+            continue
+        rel_path = src_path.relative_to(skills_root)
+        if "__pycache__" in rel_path.parts:
+            continue
+        if rel_path == Path("__init__.py"):
+            continue
+        if src_path.suffix in {".pyc", ".pyo"}:
+            continue
+        yield src_path, rel_path
+
+
+def install_skills(
+    target_dir: Path, *, force: bool = False, dry_run: bool = False
+) -> tuple[int, int]:
+    copied = 0
+    skipped = 0
+    skills_tree = resources.files("skills")
+
+    if not dry_run:
+        target_dir.mkdir(parents=True, exist_ok=True)
+
+    with resources.as_file(skills_tree) as source_dir:
+        for src_path, rel_path in _iter_skill_files(Path(source_dir)):
+            dst_path = target_dir / rel_path
+            if dst_path.exists() and not force:
+                skipped += 1
+                continue
+            if not dry_run:
+                dst_path.parent.mkdir(parents=True, exist_ok=True)
+                shutil.copy2(src_path, dst_path)
+            copied += 1
+    return copied, skipped
+
+
+def main() -> int:
+    args = _parse_args()
+    if args.target_dir:
+        target_dir = args.target_dir
+        selected_model = "custom"
+        auto_detected = False
+    else:
+        selected_model, target_dir, auto_detected = detect_target_dir(args.model_name)
+
+    copied, skipped = install_skills(
+        target_dir=target_dir,
+        force=args.force,
+        dry_run=args.dry_run,
+    )
+
+    mode = "dry-run" if args.dry_run else "installed"
+    detect_note = "auto-detected" if auto_detected else "selected"
+    print(
+        f"{mode}: copied={copied} skipped={skipped} "
+        f"model={selected_model} ({detect_note}) target={target_dir}"
+    )
+    return 0
+
+
+if __name__ == "__main__":
+    raise SystemExit(main())

openbioskill-0.1.1/openbioskill.egg-info/PKG-INFO

@@ -0,0 +1,151 @@
+Metadata-Version: 2.1
+Name: openbioskill
+Version: 0.1.1
+Summary: OpenBio CLI and skill bundles.
+Author: Xiang Li
+License: MIT License
+        
+        Copyright (c) 2026 Xiang
+        
+        Permission is hereby granted, free of charge, to any person obtaining a copy
+        of this software and associated documentation files (the "Software"), to deal
+        in the Software without restriction, including without limitation the rights
+        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+        copies of the Software, and to permit persons to whom the Software is
+        furnished to do so, subject to the following conditions:
+        
+        The above copyright notice and this permission notice shall be included in all
+        copies or substantial portions of the Software.
+        
+        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+        SOFTWARE.
+        
+Keywords: bioinformatics,cli,skills
+Classifier: Development Status :: 3 - Alpha
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.12
+Description-Content-Type: text/markdown
+License-File: LICENSE
+
+# BioDeepagents CLI
+
+[![PyPI](https://img.shields.io/pypi/v/openbioskill?label=openbioskill&logo=pypi&logoColor=white)](https://pypi.org/project/openbioskill/)
+
+## PyPI Package
+
+The `openbioskill` package ships the bioinformatics skill bundle so you can manage and distribute skills via PyPI.
+
+Install from PyPI:
+
+```bash
+python3 -m pip install openbioskill
+```
+
+The package includes:
+- Bundled bioinformatics skills under `skills/`
+- A console entry point: `openbio`
+
+Install the bundled skills to the default model path (`~/.claude/skills`):
+
+```bash
+openbio install
+```
+
+`openbio install` auto-detects these targets (in order) when no flags are passed:
+- Cursor: `~/.cursor/skills`
+- Claude Code: `~/.claude/skills`
+- Codex: `~/.codex/skills`
+- Gemini CLI: `~/.gemini/skills`
+- Deepagents CLI: `~/.deepagents/skills`
+
+If none are detected, it falls back to `~/.claude/skills`.
+
+Install to a different model path:
+
+```bash
+openbio install --model-name codex
+openbio install --model-name deepagents-cli
+```
+
+## Skills
+
+Upstream skill sources and datasets:
+- [claude-scientific-skills](https://github.com/K-Dense-AI/claude-scientific-skills)
+- [ClawBio](https://github.com/ClawBio/ClawBio)
+- [Indexd Skills Datasets](https://agent.indexd.org/skills-datasets)
+
+Skills are sourced from BioClaw. The following skills are sourced from claude-scientific-skills:
+- Bioinformatics & Genomics
+- Sequence Analysis: Process DNA/RNA/protein sequences with BioPython and pysam
+- Single-Cell Analysis: Analyze 10X Genomics data with Scanpy, identify cell types, infer GRNs with Arboreto
+- Variant Annotation: Annotate VCF files with Ensembl VEP, query ClinVar for pathogenicity
+- Variant Database Management: Build scalable VCF databases with TileDB-VCF for incremental sample addition, efficient population-scale queries, and compressed storage of genomic variant data
+- Gene Discovery: Query NCBI Gene, UniProt, and Ensembl for comprehensive gene information
+- Network Analysis: Identify protein-protein interactions via STRING, map to pathways (KEGG, Reactome)
+
+| Skill | Description |
+| --- | --- |
+| [bio-orchestrator](skills/bio-orchestrator/SKILL.md) | Meta-agent that routes bioinformatics requests to specialised sub-skills. Handles file type detection, analysis planning, report generation, and reproducibility export. |
+...
+| [vcf-annotator](skills/vcf-annotator/SKILL.md) | Annotate VCF variants with VEP, ClinVar, gnomAD frequencies, and ancestry-aware context. Generates prioritised variant reports. |
+
+This project is basing on [deepagents](https://github.com/langchain-ai/deepagents) CLI, an open source coding assistant that runs in your terminal, similar to Claude Code.
+
+## Verified K-Dense Skills (146 total)
+- `iso-13485-certification` (author: K-Dense Inc.) – comprehensive ISO 13485:2016 QMS guidance with gap analysis tooling, clause-by-clause references, and templates for Quality Manuals, procedures, and Medical Device Files so teams can assess readiness and build compliant documentation.
+
+| Skills Source | Verified # | Total # | Verification Methods |
+| --- | --- | --- | --- |
+| `claude-scientific-skills` (K-Dense Inc.) | 146 | 147 (total skills in `skills/`) | Metadata-driven audit: only `SKILL.md` files with `skill-author: K-Dense Inc.` are promoted from `skills_unverified/claude-scientific-skills/` into `skills/`, ensuring each verified skill is explicitly claimed by the author. |
+
+*Key Features:**
+- **Built-in Tools**: File operations (read, write, edit, glob, grep), shell commands, web search, and subagent delegation
+- **Customizable Skills**: Add domain-specific capabilities through a progressive disclosure skill system
+- **Persistent Memory**: Agent remembers your preferences, coding style, and project context across sessions
+- **Project-Aware**: Automatically detects project roots and loads project-specific configurations 
+
+<img src="cli-banner.jpg" alt="deep agent" width="100%"/>
+
+
+## 🐳 Docker
+
+Build the CLI image from the repository root so both the CLI sources and the shared `deepagents` package are available to Docker:
+
+This project is a docker-compose hosted a deepagents-cli, and inside container some other agents(e.g. dsl) were also hosted. 
+
+```bash
+docker compose run --rm --service-ports --build flask-app
+```
+
+Copy the sample configuration into place and edit the credentials or tracing toggles you need:
+
+
+```bash
+docker run --rm -it -P \
+  -v "$(pwd)/workspace/:/workspace/project" \
+  --env-file ./.env \
+  deepagents-cli
+```
+Type naturally as you would in a chat interface. The agent will use its built-in tools, skills, and memory to help you with tasks.
+
+> [!WARNING]
+> **Human-in-the-Loop (HITL) Approval Required**
+>
+> Potentially destructive operations require user approval before execution:
+> - **File operations**: `write_file`, `edit_file`
+> - **Command execution**: `shell`, `execute`
+> - **External requests**: `web_search`, `fetch_url`
+> - **Delegation**: `task` (subagents)
+>
+> Each operation will prompt for approval showing the action details. Use `--auto-approve` to skip prompts:
+> ```bash
+> deepagents --auto-approve
+> ```