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pvactools on Biowulf

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

A cancer immunotherapy pipeline for identifying and prioritizing neoantigens from a list of tumor mutations.
A tool for detecting neoantigens resulting from gene fusions.
A tool designed to aid specifically in the construction of DNA vector-based cancer vaccines.


Important Notes

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load pvactools
[+] Loading pvactools 1.0.2

[user@cn3144 ~]$ pvacseq run -e 11 --iedb-install-directory /usr/local/apps/pvacseq/ out.vcf Test HLA-C*07:02  NNalign NetMHC NetMHCIIpan NetMHCcons `pwd`

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Batch job
Most jobs should be run as batch jobs.

Create a batch input file (e.g. pvactools.sh). For example:

#! /bin/bash
set -e


cd /data/$USER/somedir

module load pvactools
pvacseq run -e 8,9,10,11 --fasta-size=50 final.vcf Test ${allele} \
    {NNalign,NetMHC,NetMHCIIpan,NetMHCcons,NetMHCpan,PickPocket,SMM,SMMPMBEC,SMMalign} outdir

Submit this job using the Slurm sbatch command.

sbatch [--mem=#] pvactools.sh
Swarm of Jobs
A swarm of jobs is an easy way to submit a set of independent commands requiring identical resources.

Create a swarmfile (e.g. pvactools.swarm). For example:

pvacseq run -e 11 --iedb-install-directory /usr/local/apps/pvacseq/ out1.vcf Test1 HLA-C*07:02  \
       {NNalign,NetMHC,NetMHCIIpan,NetMHCcons,NetMHCpan,PickPocket,SMM,SMMPMBEC,SMMalign} out1
pvacseq run -e 11 --iedb-install-directory /usr/local/apps/pvacseq/ out2.vcf Test2 HLA-C*07:02  \
       {NNalign,NetMHC,NetMHCIIpan,NetMHCcons,NetMHCpan,PickPocket,SMM,SMMPMBEC,SMMalign} out2

Submit this job using the swarm command.

swarm -f pvactools.swarm [-g #]  --module pvactools
-g # Number of Gigabytes of memory required for each process (1 line in the swarm command file)
--module pvactools Loads the pvactools module for each subjob in the swarm