SIMBA🦁 Downstream toolkit

This repository contains the source code of the python shiny app which is recommended to be used for the downstream analysis of the output of the SIMBA🦁 pipeline. Available instances can be found at at https://exbio.wzw.tum.de/cost/overview/.

Offline Usage

Docker

The app can be run using the docker image bigdatainbiomedicine/simba-downstream. The image can be pulled from the docker hub using the following command:

docker run -p <port>:8080 bigdatainbiomedicine/simba-downstream

Assuming that the port 1234 is used, the app can be accessed at http://localhost:1234.

Local

The app can also be run locally. The following steps are required to run the app locally:

1. Clone the repository:

git clone https://github.com/Mye-InfoBank/SIMBA-Downstream.git

2. Install the required packages:

pip install -r requirements.txt

3. Run the app:

cd src
uvicorn app:app --host 0.0.0.0 --port <port>

Assuming that the port 1234 is used, the app can be accessed at http://localhost:1234.