Sturgeon GUI

Graphical User Interface for the Sturgeon application The main function is to create and run a Docker command to start Sturgeon, have a graphic display on the current process, showing the latest plots/table, as well as signaling Sturgeon to stop.

System requirements

Hardware:

• NVIDIA CUDA graphics card
• GridION (not a hard requirement but used during development/testing)

Software:

• Docker
• NVIDIA Container Toolkit
  • Make sure to validate the installation sudo docker run --rm --gpus all nvidia/cuda:11.0.3-base-ubuntu20.04 nvidia-smi
• Java 11
• Bash
• Linux OS

Configuration

The configurations can be found in the following file: src/main/resources/Config.yml This contains the following settings:

• cnvPlot: Default name format of the CNV plots. The code does expect iteration_0 to be present in the name.
• confidencePlot: Default name format of the confidence plots. The code does expect iteration_0 to be present in the name.
• confidenceTable: Default name format of the confidence table. The code does expect iteration_0 to be present in the name.
• predictPlot: Default name format of the prediction plots. The code does expect iteration_0 to be present in the name.
• version: Version of the GUI.
• devMail: Mail address of the developer/maintainer of the GUI. Is shown when starting the tool so the operator has a contact point for questions/issues.
• refGenome: Path (host) to directory where the reference genome files are present.
• model: Path (host) to the model zip file used by Sturgeon to make predictions.
• sturgeonImage: Name of the Sturgeon image.
• wrapperScript: Path (container) where to find the R wrapper script to run. Currently only supports live_processing_fast5s_guppy_v6.5.R
• extraArgs: Extra arguments given to the Docker run call.
• wrapperFlagDir: Path (host) to the directory to write the wrapper flags to. These flags are used by Sturgeon to check if it is already running or if it needs to stop.
• defaultDir: Default directory to open the file explorer add when choosing the input pod5 folder.
• logDir: Directory (host) to write the log files to.
• samplePattern: Regex pattern to which a sample ID needs to adhere to. (Currently not being used)

How to install

Requirements:

• Java 11
• Maven
• Sturgeon (if you use this outside the production environment you might want to doublecheck src/main/resources/Config.yml if everything is aligning with your situation)

Build jar file:

# cd to sturgeon-gui folder and run the following:
mvn clean compile install
# Jar file can be found in the target folder and you can run it by:
java -jar target/sturgeon-gui.jar

Hints and known bugs:

• Due to hardware limitations of the GridION OS, only one sample can run at the time. This GUI has been made with this in mind.
• The layout of the GUI is not always stable. Usually resizing or restarting the GUI helps.
• The GUI and the docker back-end are not directly linked. Meaning if the GUI crashes or is forced quit, the container will keep running. Manually stop the container if needed.
• It is currently not possible to restart the GUI once a run is finished. For now just close the GUI and start it again.
• Check the log in the logDir (see config) for hints if errors have occurred.

Workflow

Color meaning:

• Grey = Lab process defined outside this repository.
• Blue = User interacting with the GUI as defined in the UserManual.
• Red = GUI processes.

Contact

Maintained by the Translation Bioinformatics group Developer: Alex Janse