Installation¶
pVAC-Seq 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.
pVAC-Seq 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 pVAC-Seq. 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 (for Mac and Linux users) or the Command Prompt (for Windows users):
pip install pvacseq
You can check that pvacseq has been installed under the default environment by listing all installed packages:
pip list
pip will fetch and install pVAC-Seq and its dependencies for you. After installing, you can run pvacseq directly from the Terminal/Command Prompt.
If you have an old version of pVAC-Seq installed you might want to consider upgrading to the latest version:
pip install pvacseq --upgrade
Installing IEDB binding prediction tools (optional)¶
You may create a local install of the IEDB binding prediction tools by first downloading the archives for class I and class II from the IEDB website. If using both the Class I and the Class II tools, they both need to be installed into the same parent directory.
Note
IEDB requires tcsh. You can install it by running sudo apt-get install tcsh.
MHC Class I¶
tar -zxvf IEDB_MHC_I-2.15.tar.gz
cd mhc_i
./configure
Note
Running the configure script requires a Python 2 environment. If you are currently emulating a Python 3 environment with Conda you will need to run source deactivate before executing the configure script.
Open method/netmhc_4_0_executable/__init__.py and delete the first line (import pkg_resources).
If you want to use the NerMHCcons prediction algorithm you will need to change the shebang line of certain files to explicitly use python2.7. The files in question are:
method/netMHCcons-1.1/bin/pseudofindmethod/netMHC-3.4/netMHC
In these files change the shebang line to #! /usr/bin/env python2.7.
MHC Class II¶
tar -zxvf IEDB_MHC_II-2.15.tar.gz
cd mhc_ii
./configure.py
Note
Running the configure script requires a Python 2 environment. If you are currently emulating a Python 3 environment with Conda you will need to run source deactivate before executing the configure script.