This repository provides comprehensive documentation for the SoloMicrobe tool. It includes a detailed user guide for the web interface, instructions for using the command-line interface (CLI), and a Docker Compose file for easy local deployment.
To run the command-line interface or host the web application locally, an OpenCL-compatible device is required. OpenCL (Open Computing Language) enables parallel computing across heterogeneous systems and is essential for the high-performance computational tasks performed by Cas-OFFinder.
- OS: Linux (recommended); should work on macOS with minor changes.
- Disk / RAM: Enough space for reference genomes and alignment outputs
- Conda / mamba: to create the probeset environment from conda_environment.yml.
- Python: 3.11 (environment uses Python 3.11).
- Node.js / npm: Node >=16 and npm for the frontend
- Redis: a Redis server available for Celery broker/back-end (default redis://localhost:6379/1).
- Docker: docker / docker-compose if you prefer containerized deployment.
- Python pip deps: FastAPI, Uvicorn, Celery, Redis client, Biopython, pandas, numpy, requests, lxml, pydantic, etc. See requirements.txt.
- Alignment & utilities: samtools, gffread, RazerS3 — required for probe alignment and processing
Copyright (C) 2026 Mekonnen Abyot Melkamu and Jeongbin Park
This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.
You should have received a copy of the GNU Affero General Public License along with this program. If not, see https://www.gnu.org/licenses/.