diff --git a/docs/computational/getting_started.md b/docs/computational/getting_started.md index b891a45..9504118 100644 --- a/docs/computational/getting_started.md +++ b/docs/computational/getting_started.md @@ -71,41 +71,39 @@ pip install -e openst The official [Docker image] is a great way to get up and running in a few minutes, as it comes with all dependencies pre-installed. Open up a terminal -and pull the image with: +and pull the image: ``` sh docker pull rajewsky/openst ``` -The `openst` executable is provided as an entry point and `serve` is the -default command. - -You can run a terminal for `openst` by running +#### Get a `bash` terminal +In a terminal: ```sh -docker run -it openst +docker run -it --rm --entrypoint bash openst ``` -Optionally, you might want to enable X11 redirection to enable GUI support (e.g., for the `openst manual_pairwise_aligner` tool). -Follow these steps: - -1. Install X Server on your host machine if not already installed. -2. Allow connections to your X Server by running the following command on your host: -```sh -xhost + +#### Attach a local folder to `docker`: +In a terminal: +```bash +docker run -it --rm -p 9876:9876 -v local_folder:/app/docker_folder openst ``` -3. Run the Docker container with the following additional options: -```sh -docker run -it --rm -e DISPLAY=$DISPLAY -v /tmp/.X11-unix:/tmp/.X11-unix openst + +Make sure to replace `local_folder` (and optionally `docker_folder`). + + +#### Support GUI (`openst manual_pairwise_aligner` or `napari`) +In a terminal: +```bash +docker run -it --rm -p 9876:9876 openst ``` -Now, you can execute PyQt5-based applications, and the GUI will be displayed on your host machine. +Then open [https://localhost:9876](https://localhost:9876) in a browser. +The video below shows an example launching `openst manual_pairwise_aligner` on +the browser (we recommend Google Chrome or similar). -!!! note - - Ensure that the X Server on your host allows connections (xhost +) before running the container, - - Make sure the necessary dependencies are installed on your host machine for PyQt5 applications. - - Remember to close the X Server connections after using the container: - ```sh - xhost - - ``` + - [Docker image]: https://hub.docker.com/r/rajewsky/openst/ \ No newline at end of file +[Docker image]: https://hub.docker.com/r/rajewsky/openst/ \ No newline at end of file diff --git a/docs/static/video/openst_docker_gui.webm b/docs/static/video/openst_docker_gui.webm new file mode 100755 index 0000000..335babf Binary files /dev/null and b/docs/static/video/openst_docker_gui.webm differ diff --git a/docs/stylesheets/extra.css b/docs/stylesheets/extra.css index 05febe8..6d2ca94 100644 --- a/docs/stylesheets/extra.css +++ b/docs/stylesheets/extra.css @@ -11,3 +11,7 @@ /* Adjust the margin-left value as needed */ margin-left: -20px; } + +video { + clip-path: inset(1px 1px); +} \ No newline at end of file