Installation

pVACtools is written for Linux but some users have been able to run it successfully on Mac OS X. If you are using Windows you will need to set up a Linux environment, for example by setting up a virtual machine.

pVACtools requires Python 3.5. Before running any installation steps, check the Python version installed on your system:

python -V

If you don’t have Python 3.5 installed, we recommend using Conda to emulate a Python 3.5. environment. We’ve encountered problems with users that already have Python 2.x installed when they also try to install Python 3.5. The defaults will not be set correctly in that case. If you already have Python 2.x installed we strongly recommmend using Conda instead of installing Python 3.5 locally.

Once you have set up your Python 3.5 environment correctly you can use pip to install pVACtools. Make sure you have pip installed. pip is generally included in python distributions, but may need to be upgraded before use. See the instructions for installing or upgrading pip.

After you have pip installed, type the following command on your Terminal:

pip install pvactools[API]

You can check that pvactools has been installed under the default environment by listing all installed packages:

pip list

pip will fetch and install pVACtools and its dependencies for you. After installing, each tool of the pVACtools suite is available in its own command line tree directly from the Terminal.

If you have an old version of pVACtools installed you might want to consider upgrading to the latest version:

pip install pvactools[API] --upgrade

Installing MHCflurry

If you wish to run the MHCflurry prediction algorithm, you will need to install the mhcflurry python package on your system. This package is set as a dependency for the pvactools package so it should be installed automatically when you download or upgrade the pvactools package. You can install it manually by running:

pip install mhcflurry

Note

The mhcflurry package needs to be installed in the same python 3.5 conda environment as the pvactools package.

Next, you will need to download the download the MHCflurry datasets and trained models:

mhcflurry-downloads fetch

Note

The mhcflurry-downloads fetch command will need to be run manually, even if the mhcflurry package was already installed automatically as a dependency with the pvactools package.

You can check that the mhcflurry package was installed successfully by running:

mhcflurry-predict -h

This should pull up the help page for the MHCflurry predictor.

Installing MHCnuggets

If you wish to run the MHCnuggets prediction algorithm, you will need to install the mhcnuggets python package on your system. This package is set as a dependency for the pvactools package so it should be installed automatically when you download or upgrade the pvactools package. You can install it manually by running:

pip install mhcnuggets

Note

The mhcnuggets package needs to be installed in the same python 3.5 conda environment as the pvactools package.

You can check that the mhcnuggets package was installed successfully by running:

pip show mhcnuggets

This should show information about the mhcnuggets package.

Docker and CWL

A Docker container for pVACtools is available on DockerHub using the griffithlab/pvactools repo. CWL tool wrappers for pVACseq, pVACfuse, and pVACvector can be downloaded using the pvactools download_cwls command.

Download CWL tool wrappers

usage: pvactools download_cwls [-h] destination_directory

positional arguments:
  destination_directory
                        Directory for downloading CWLs

optional arguments:
  -h, --help            show this help message and exit