sdrf:setup

Install and configure SDRF annotation dependencies via Conda, Pip, or uv.

11|9|Updated Mar 18, 2026

Search Tags:#pip #bioinformatics #setup #conda #dependency #sdrf

Ready to run

npx skills add https://github.com/bigbio/sdrf-skills --skill sdrf-setup

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: sdrf:setup
Source: https://github.com/bigbio/sdrf-skills/tree/main/skills/sdrf-setup
Command: npx skills add https://github.com/bigbio/sdrf-skills --skill sdrf-setup

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

The skill helps users set up the SDRF annotation environment by installing required packages, configuring submodules, and verifying the installation, eliminating manual guesswork.

Core Features & Use Cases

Detect available package managers and suggest appropriate install commands.
Provide step‑by‑step commands for Conda, Pip, or uv installations.
Verify tool versions and optionally initialize or update the SDRF specification submodule.
Guide users on configuring MCP servers for full annotation capabilities.

Quick Start

Ask the assistant to set up SDRF dependencies using the preferred package manager.

Frequently Asked Questions about sdrf:setup

High-intent search queries and answers about installing and using this skill.

FAQPage Schema

How do I install SDRF annotation dependencies using Conda or Pip?▼

To install SDRF annotation dependencies, you can use Conda, Pip, or uv. The setup process detects available package managers and provides step-by-step commands utilizing environment.yml or requirements.txt to configure the necessary bioinformatics packages.

What is the best way to configure SDRF tools for bioinformatics workflows?▼

The best way to configure SDRF tools is by running a guided setup that detects your package manager, installs required dependencies from environment.yml or requirements.txt, and optionally initializes the SDRF specification submodule for annotation workflows.

Do I need Conda to set up SDRF annotation tools, or can I use uv?▼

You do not need Conda specifically to set up SDRF annotation tools; the setup supports Conda, Pip, and uv. It automatically detects your available package manager and suggests the appropriate installation commands for your environment.

Why is SDRF setup not working when initializing submodules?▼

SDRF setup may fail during submodule initialization if access to the terminal is restricted or the SDRF specification submodule cannot be reached. Ensure you have terminal access to run package manager commands and verify tool versions before initializing.

How does MCP server configuration work with SDRF dependencies?▼

MCP server configuration for SDRF dependencies involves verifying tool versions and initializing submodules to enable full annotation capabilities. The setup guides users through checking MCP server status after installing required packages via Conda, Pip, or uv.