sragentlisted

# SRAgent: Sequence Read Archive Data and Publication Retrieval ## Overview SRAgent is an agentic workflow system for working with the NCBI Sequence Read Archive (SRA) and Gene Expression Omnibus (GEO) databases. It automates literature discovery, metadata extraction, and manuscript retrieval for genomics datasets. ## Setup Instructions ### 1. Install SRAgent SRAgent requires Python ≥3.11. Check to see if SRAgent is already installed: ```bash which SRAgent ``` If SRAgent is not installed, follow the instructions below. Install using `uv`: ```bash # Clone the repository git clone https://github.com/ArcInstitute/SRAgent.git cd SRAgent # Create and activate virtual environment with uv uv venv source .venv/bin/activate # Install the package uv pip install . ``` Verify installation: ```bash SRAgent --help ``` ### 2. Configure environment variables The following environment variables are required: - `OPENAI_API_KEY=sk-openai-...` - Needed to use OpenAI models - `ANTHROPIC_API_KEY=sk-ant-...` - Needed to use Claude models - `DYNACONF` - Needed to switch between Claude and OpenAI models - `EMAIL=user@example.com` - Needed for using the Entrez API - `NCBI_API_KEY=your-ncbi-key` - Optional for increased rate limits when using the Entrez API - `CORE_API_KEY=your-core-key` - Optional for paper downloads from the CORE API - `GCP_PROJECT_ID=your-project-id` - Needed for using Google BigQuery - `GOOGLE_APPLICATION_CREDENTIALS=/path/to/key.json` - Needed for usin