Docker 

Installation 

We introduce how to install optinist. We have developed optinist python(backend) and typescript(frontend), so you need to make both environment. Please follow instructions below.

1. Make Docker Image Container 

Install Tools 

Install Docker

Make Docker Image 

Pull the latest docker image from docker hub.

docker pull oistncu/optinist

Start docker container.

# Notes:
# - Set your saving directory to `/your/saving/dir`.
# - The "command line continuation character" should be replaced by your platform.
#   - Unix Shells ... \
#   - Windows Command Prompt ... ^
#   - Windows PowerShell ... `

docker run -it --shm-size=2G \
  -v /your/saving/dir:/app/studio_data \
  --env OPTINIST_DIR="/app/studio_data" \
  --name optinist_container -d -p 8000:8000 --restart=unless-stopped \
  oistncu/optinist:latest \
  poetry run python main.py --host 0.0.0.0 --port 8000

Note

Please set /your/saving/dir to your local directory. Without this, OptiNiSt’s data will lost when you stop docker container or reboot your PC. By the command above (-v option), you can mount your local directory to docker container.
If you want to keep the snakemake directory (which contains the conda environment etc.) on the host machine, add the following option: -v /your/snakemake/dir:/app/.snakemake

2. Access to Backend 

Launch browser, and go to http://localhost:8000

Done!