SRAgent

SRAgent

[](https://doi.org/10.5281/zenodo.21539103)

Agentic workflows for obtaining data from the Sequence Read Archive.

Manuscript

**scBaseCount: An AI agent-curated, uniformly processed, and continually expanding single cell data repository**. Nicholas D Youngblut, Christopher Carpenter, Jaanak Prashar, Chiara Ricci-Tam, Rajesh Ilango, Noam Teyssier, Silvana Konermann, Patrick Hsu, Alexander Dobin, David P Burke, Hani Goodarzi, Yusuf H Roohani. bioRxiv 2025.02.27.640494; doi: [https://doi.org/10.1101/2025.02.27.640494](https://doi.org/10.1101/2025.02.27.640494)

Install

Option 1: Via conda

Create a conda environment [optional]:

mamba create -n sragent-env -y python=3.12 sra-tools=3.1 \
  && conda activate sragent-env

Clone the repository:

git clone https://github.com/ArcInstitute/SRAgent.git \
  && cd SRAgent

Option 2: Via UV

Create a uv venv:

uv venv

Source the venv:

source .venv/bin/activate

Install the package

Install the package:

pip install .

For development, install the package with the `dev` optional dependencies:

pip install -e ".[dev]"

Environmental variables

• OPENAI_API_KEY = API key for using the OpenAI API
  • required when using OpenAI models
  • See Configuring models information on setting models
• ANTHROPIC_API_KEY = API key for using the Anthropic API
  • required when using Claude models
• GOOGLE_API_KEY = API key for using the Google Gemini API
  • required when using Gemini models
• EMAIL = email for using the Entrez API
  • optional, but HIGHLY recommended
• NCBI_API_KEY = API key for using the Entrez API
  • optional, increases rate limits
• DYNACONF = switch between "test", "prod", "claude", and "gemini" environments
  • optional, default is "prod"
  • this affects the SQL database used and models selected
  • no database is