toaSTR

toaSTR is a browser-based application for the analysis of short tandem repeats from massively parallel sequencing data. It runs on macOS, Windows, and Linux.

Original publication: https://www.fsigenetics.com/article/S1872-4973(18)30063-2/fulltext

Installation

This dockerized, standalone distribution of toaSTR is a multi-container application that depends on multiple services, including a MySQL database and a job queue system which processes the analysis tasks. The application’s services are configured in a Docker Compose file (docker-compose.yml) and automatically handled by the Docker platform. When toaSTR is started for the first time, it reads the init.sql file to initialize the toaSTR database.

1. Install Docker (macOS, Windows or Linux): https://docs.docker.com/get-docker/
2. Install Docker Compose (Linux users only): https://docs.docker.com/compose/install/
3. Clone or download this repository
4. Optionally configure the number of CPU cores used by toaSTR. Open the file docker-compose.yml in a text editor and search for the key theschwartz -> environment -> PARALLEL_WORKERS. Set the value to an appropriate number of CPU cores for your machine (default: 4).
5. Open a command prompt (terminal), navigate to the toastr directory and run docker-compose pull (Linux: sudo docker-compose pull) to pull the toaSTR service images from Docker Hub.

Usage

1. Start toaSTR: docker-compose up -d (Linux: sudo docker-compose up -d). On first start, please wait one minute to complete the database initialization before proceeding to the next step.
2. Open localhost:3000 in your browser and login with username admin and password toastrdocker. Please refer to the manual inside the app for usage instructions.
3. Stop toaSTR: docker-compose down (Linux: sudo docker-compose down)

Update

Stop toaSTR and run docker-compose pull (Linux: sudo docker-compose pull) from time to time to pull the most recent update.

Reset

In case you want to reset the application, run docker-compose down -v (Linux: sudo docker-compose down -v). Warning: This deletes all app data and configuration.

Support

Sebastian Ganschow sganschow@labcon-owl.de