Metadata-Version: 2.4
Name: BioDeep
Version: 0.1.0
Summary: BioDeepagents CLI and skill bundles.
Author: BioDeep
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: >=3.9
Description-Content-Type: text/markdown
License-File: LICENSE
Dynamic: license-file

# BioDeepagents CLI

## Skills

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. |
| [claw-ancestry-pca](skills/claw-ancestry-pca/SKILL.md) | Ancestry decomposition PCA against the Simons Genome Diversity Project. |
| [claw-metagenomics](skills/claw-metagenomics/SKILL.md) | Shotgun metagenomics profiling — taxonomy, resistome, and functional pathways. |
| [claw-semantic-sim](skills/claw-semantic-sim/SKILL.md) | Semantic Similarity Index for disease research literature using PubMedBERT embeddings. |
| [drug-photo](skills/drug-photo/SKILL.md) | Photo of a medication to get pharmacogenomic dosage guidance via a CPIC single-drug lookup. |
| [equity-scorer](skills/equity-scorer/SKILL.md) | Compute HEIM diversity and equity metrics from VCF or ancestry data. Generates heterozygosity, FST, PCA plots, and a composite HEIM Equity Score with markdown reports. |
| [genome-compare](skills/genome-compare/SKILL.md) | Compare your genome to George Church (PGP-1) and estimate ancestry composition. |
| [labstep](skills/labstep/SKILL.md) | Interact with the Labstep electronic lab notebook API using labstepPy. Query experiments, protocols, resources, inventory, and other lab entities. |
| [lit-synthesizer](skills/lit-synthesizer/SKILL.md) | Search PubMed and bioRxiv, summarise papers with LLM, build citation graphs, and generate literature review sections. |
| [nutrigx-advisor](skills/nutrigx_advisor/SKILL.md) | Personalised nutrition report from genetic data (23andMe, AncestryDNA, or VCF). |
| [pharmgx-reporter](skills/pharmgx-reporter/SKILL.md) | Pharmacogenomic report from DTC genetic data (23andMe/AncestryDNA). |
| [repro-enforcer](skills/repro-enforcer/SKILL.md) | Export any bioinformatics analysis as a reproducible bundle with Conda environment, Singularity container definition, and Nextflow pipeline. |
| [scrna-orchestrator](skills/scrna-orchestrator/SKILL.md) | Automate single-cell RNA-seq analysis with Scanpy or Seurat. QC, normalisation, clustering, DE analysis, and visualisation. |
| [seq-wrangler](skills/seq-wrangler/SKILL.md) | Sequence QC, alignment, and BAM processing. Wraps FastQC, BWA/Bowtie2, SAMtools for automated read-to-BAM pipelines. |
| [struct-predictor](skills/struct-predictor/SKILL.md) | Local protein structure prediction with AlphaFold, Boltz, or Chai. Compare predicted structures, compute RMSD, visualise 3D models. |
| [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.

*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 

deep agent

## 🐳 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
> ``` 
