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

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 --upgrade

Docker and CWL

A Docker container for pVACtools is available on DockerHub using the mgibio/pvactools repo. CWL tool wrappers for pVACseq, pVACfuse, and pVACvector can be downloaded using the pvactools download_cwls command. The CWLs do not support the –iedb-install-directory or –additional-input-file-list options.

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