pvactools
Link to section 'Introduction' of 'pvactools' Introduction
pVACtools is a cancer immunotherapy tools suite consisting of pVACseq, pVACbind, pVACfuse, pVACvector, and pVACview.
Docker hub: https://hub.docker.com/r/griffithlab/pvactools/
Home page: https://pvactools.readthedocs.io/en/latest/
Link to section 'Versions' of 'pvactools' Versions
- 3.0.1
Link to section 'Commands' of 'pvactools' Commands
- pvacbind
- pvacfuse
- pvacseq
- pvactools
- pvacvector
- pvacview
Link to section 'Module' of 'pvactools' Module
You can load the modules by:
module load biocontainers
module load pvactools
Link to section 'Example job' of 'pvactools' Example job
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