Installation

Tip

It is recommended to install VueGen inside 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.

Pip

VueGen is available on PyPI and can be installed using pip:

pip install vuegen

You can also install the package for development by cloning this repository and running the following command:

Warning

We assume you are in the root directory of the cloned repository when running this command. Otherwise, you need to specify the path to the vuegen directory.

pip install -e .

Conda

VueGen is also available on Bioconda and can be installed using conda:

conda install -c bioconda -c conda-forge vuegen

Dependencies

VueGen uses Quarto to generate various report types. The pip insallation includes quarto using the quarto-cli Python library. To test if quarto is installed in your computer, run the following command:

quarto check

Tip

If quarto is not installed, you can download the command-line interface from the Quarto website for your operating system.

For PDF reports, you need to have a LaTeX distribution installed. This can be done with quarto using the following command:

quarto install tinytex

Tip

Also, you can add the --quarto_checks argument to the VueGen command to check and install the required dependencies automatically.

Docker

If you prefer not to install VueGen on your system, a pre-configured Docker container is available. It includes all dependencies, ensuring a fully reproducible execution environment. See the Execution section for details on running VueGen with Docker. The official Docker images are available at quay.io/dtu_biosustain_dsp/vuegen. The Dockerfiles to build the images are available here.

Nextflow and nf-core

VueGen is also available as a nf-core module, customised for compatibility with the Nextflow environment. This module is designed to automate report generation from outputs produced by other modules, subworkflows, or pipelines. Asumming that you have nextflow and nf-core installed, you can use the following command to install the nf-core module:

nf-core modules install vuegen

Note

You can read the offical documentation for the nf-core module here. Also, the source code and additional details are available in the nf-VueGen repository.