Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Failed to load latest commit information.
.github/ISSUE_TEMPLATE
docs
lib Fix help text Oct 8, 2018
tests
tools
utils Update VAF cutoff default to 0.25 Oct 3, 2018
.gitignore pvacseq.egg-info/ updated to pvactools.egg-info/ in .gitignore Jun 7, 2018
.travis.yml
LICENSE License file added Aug 13, 2015
README.md fix minor typos and grammar in readme Jan 31, 2018
environment.yml
readthedocs.yml
setup.py

README.md

pVACtools

pVACtools is a cancer immunotherapy suite consisting of the following tools:

pVACseq

A cancer immunotherapy pipeline for identifying and prioritizing neoantigens from a list of tumor mutations.

pVACfuse

A tool for detecting neoantigens resulting from gene fusions.

pVACvector

A tool designed to aid specifically in the construction of DNA vector-based cancer vaccines.

Coming Soon

pVACclient

A browser-based user interface that assists users in launching, managing, reviewing, and visualizing the results of pVACtools processes.

pVACapi

The pVACapi will provide a HTTP REST interface to the pVACtools suite.

Citation

Jasreet Hundal, Beatriz M. Carreno, Allegra A. Petti, Gerald P. Linette, Obi L. Griffith, Elaine R. Mardis, and Malachi Griffith. pVAC-Seq: A genome-guided in silico approach to identifying tumor neoantigens. Genome Medicine. 2016, 8:11, DOI: 10.1186/s13073-016-0264-5. PMID: 26825632.

License

This project is licensed under NPOSL-3.0.

Installation

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/upgraded, 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

You can also check the installed version:

pvactools -v

pip will fetch and install pVACtools and its dependencies for you. After installing, each tool of the pVACtools suite is available with 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

Documentation

The pVACtools documentation can be found on ReadTheDocs.

Contact

Bug reports or feature requests can be submitted on the pVACtools Github page. You may also contact us by email at help@pvactools.org.