Installation

You can install VaxPress using Pip, Conda, or Singularity. Pip is the recommended method for advanced users. The Conda package simplifies the installation of necessary dependencies. The Singularity container image runs just out of the box if your computing environment already has Singularity installed.

Note

Optional Installation of LinearDesign

VaxPress can be integrated with LinearDesign for optimal coding sequence design that offers superior performance and versatility. To access these features, install LinearDesign separately. For information, see Installing LinearDesign.

Installing VaxPress using Pip

Installing

# Create a virtual environment for VaxPress
python -m venv /path/to/vaxpress-env

# Activate the virtual environment
source /path/to/vaxpress-env/bin/activate

# Install VaxPress alone
pip install vaxpress

# Alternatively, install VaxPress with LinearFold (only for non-commercial uses)
pip install 'vaxpress[nonfree]'

Running

# Activate the virtual environment
source /path/to/vaxpress-env/bin/activate

# Run VaxPress
vaxpress -h

Note

Optional Dependencies for Installations using Pip

If you wish to activate the iCodon predicted stability (--iCodon-weight) in the fitness function, ensure you have working installations of R, rpy2 (version >= 3.0) and iCodon. For detailed installation instructions, visit iCodon’s GitHub page.

Installing VaxPress using Conda

Installing

conda create -n vaxpress -y -c changlabsnu -c bioconda -c conda-forge vaxpress

Running

# Activate the environment
conda activate vaxpress

# Run VaxPress
vaxpress -h

Running VaxPress via Singularity

To run VaxPress via Singularity, you will need to install the Singularity CE first.

Downloading the Image

Download the container image from the GitHub project page and place it in a directory of your choice.

Running

singularity run vaxpress.sif -h

Warning

For ease of use, it’s advised to store the VaxPress container image and all your input/output files in a directory within your home directory. If placed elsewhere, you might have to use the --bind option with Singularity each time you run the container. For detailed guidance, refer to the Singularity documentation.

Installing LinearDesign

To utilize the --lineardesign options, you need to have LinearDesign installed in addition to VaxPress. For installation guidance, visit the LinearDesign GitHub page. Indicate the path to the LinearDesign directory using the --lineardesign-dir option in the command line. This path will be stored in the configuration file and will be activated as the default for subsequent runs.

Further information on the --lineardesign options can be found in Using LinearDesign for Optimization Initialization.