Installation

This document provides instructions to install and run SynFlow using Docker.

Requirements

• Docker version 20.x or higher

Pulling the Docker image

Before running SynFlow, you must first download the corresponding Docker image from the registry. This is done using the docker pull command. It ensures that you have the latest version of the image locally before launching the container.

docker pull ghcr.io/southgreenplatform/synflow:latest

Run the application

docker run -d --name synflow -p 8080:80 -p 3031:3031  -e SNAKEMAKE_CORES=4  ghcr.io/southgreenplatform/synflow:latest

Then open your browser and navigate to:

http://localhost:8080

Using your own data

If you want to modify the list shown in the Existing file section, you can create a JSON configuration file as illustrated in the example:

[
    { "organism": "Test", "url": "https://hpc.cirad.fr/bank/banana/synflow/" },
    { "organism": "Grapevine", "url": "https://hpc.cirad.fr/bank/vitis/Synflow/" }
]

In the Docker command, you need to add a CONFIG_FILE_PATH environment variable using the -e option and mount the new volume using the -v option.

docker run -d --name synflow  -p 8080:80 -p 3031:3031  -v  $(pwd)/config.json:/data/config.json -e CONFIG_FILE_PATH=/data/config.json  -e SNAKEMAKE_CORES=4  ghcr.io/southgreenplatform/synflow:latest

Support

If you encounter issues, feel free to open an Issue on GitHub.