GUI

We have a simple GUI for VueGen that can be run locally or through a standalone executable.

Local GUI

To use the local GUI, you should clone this repository and install the required dependencies. You can do this by running the following command in the root directory of the cloned repository:

pip install '.[gui]'

Then, you should move to the gui folder and execute the app.py Python file:

python app.py

Bundled GUI

The bundle GUI with the VueGen package is available under the latest releases. You will need to unzip the file and run vuegen_gui in the unpacked main folder. Most dependencies are included into the bundle using PyInstaller.

Streamlit works out of the box as a purely Python based package. For the rest of report types you will have to have a Python 3.12 installation with the jupyter package installed, as quarto needs to start a kernel for execution. This is also true if you install quarto globally on your machine.

Tip

It is advisable to create a virtual environment to manage depenendencies and avoid conflicts with existing packages. You can use the virtual environment manager of your choice, such as poetry, conda, or pipenv. We recommend using miniforge to install Python and the conda package manager.

We assume you have installed the miniforge distribution for your machine (MacOS with arm64/ apple silicon or x86_64/ intel or Windows x86_64). Also, download the latest vuegen_gui bundle from the releases page according to your operating system.

You can create a new conda environment with Python 3.12 and the jupyter and vuegen package:

conda create -n vuegen_gui -c conda-forge -c bioconda python=3.12 jupyter vuegen

The exact Python version used for the release is specified on the releases page as we observed that sometimes the exact Python version is required to run the GUI.

Warning

If you have errors with the vuegen package, you can install it separately using pip, as explained in the installation section.

conda create -n vuegen_gui -c conda-forge -c bioconda python=3.12 jupyter
conda activate vuegen_gui
pip install vuegen

Then, activate the environment:

conda activate vuegen_gui

Now, you can list all conda environments to find the location of the vuegen_gui environment:

conda info -e

On MacOS, you need to add a bin to the path:

/Users/user/miniforge3/envs/vuegen_gui/bin

On Windows, you can use the path as displayed by conda info -e:

C:\Users\user\miniforge3\envs\vuegen_gui

Note

On Windows a base installation of miniforge with jupyter might work because the app can see your entire Path, which is not the case on MacOS.

More information regarding the app and builds can be found in the GUI README.