Installation

Installation from source

Note

For the installation from source, the user needs to clone the git repository of immunopepper. This can be done by running the following command:

git clone https://github.com/ratschlab/immunopepper.git

It is recommended to set up a separate virtual or conda environment to install immunopepper.

The python version in the environment should be >= 3.9

conda create -n immunopepper python=3.9
conda activate immunopepper

The user should also check if gcc is installed on the system, as it is required for the installation of the tool. This can be checked by running the following command:

gcc --version

The rest of the installation can be performed by running:

conda install cython
conda install -c bioconda 'pyvcf3==1.0.3'
make install

After installation, please consult the help screen for further usage options:

immunopepper -h

Prerequisites

ImmunoPepper takes a splicing graph as input. This splicing graph has to be generated using the SplAdder pipeline. Further information about SplAdder is available on its GitHub page or the Online documentation.

Mode cancerspecif

In this mode Java needs to be installed. The user can check if Java is installed by running the following command:

java -version

Mode mhcbind

If the mode mhcbind wants to be run, the user needs to clone the mhcbind github repository inside the main immunopepper folder.

This can be done by running the following command:

git clone https://github.com/openvax/mhctools.git

Mode pepquery

If the mode pepquery wants to be run, the user needs to download and install the PepQuery software in its local computer.

Instructions for the installation of the software can be seen in the PepQuery documentation.