Pvactools

Introduction

pVACtools is a cancer immunotherapy tools suite consisting of pVACseq, pVACbind, pVACfuse, pVACvector, and pVACview.

For more information, please check:
Docker hub: https://hub.docker.com/r/griffithlab/pvactools/
Home page: https://pvactools.readthedocs.io/en/latest/

Versions

3.0.1

Commands

pvacbind
pvacfuse
pvacseq
pvactools
pvacvector
pvacview

Module

You can load the modules by:

module load biocontainers
module load pvactools

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run pvactools on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=pvactools
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers pvactools

pvacseq download_example_data .

pvacseq run \
  pvacseq_example_data/input.vcf \
  Test \
  HLA-A*02:01,HLA-B*35:01,DRB1*11:01 \
  MHCflurry MHCnuggetsI MHCnuggetsII NNalign NetMHC PickPocket SMM SMMPMBEC SMMalign \
  pvacseq_output_data \
  -e1 8,9,10 \
  -e2 15 \
  --iedb-install-directory /opt/iedb