Getting Started¶
pVACseq provides a set of example data to show the expected input and output files. You can download the data set by running the pvacseq download_example_data
command.
The example data output can be reproduced by running the following command:
pvacseq run \
<example_data_dir>/input.vcf \
Test \
HLA-A*02:01,HLA-B*35:01,DRB1*11:01 \
MHCflurry MHCnuggetsI MHCnuggetsII NNalign NetMHC PickPocket SMM SMMPMBEC SMMalign \
<output_dir> \
-e 8,9,10
A detailed description of all command options can be found on the Usage page.
Running pVACseq using Docker¶
A pVACtools Docker image is available on DockerHub using the
griffitlab/pvactools
tag. After installing Docker
you can start an interactive Docker instance by running the following command:
docker run -it griffithlab/pvactools
Version-specific images are available and can be run like so:
docker run -it griffithlab/pvactools:<version>
In order to have access to your local data inside of the Docker container you
will need to mount a local volume inside of the container. This is done using
the -v
flag. For example, you can mount your
/local/path/to/example_data_dir
in your container like so:
docker run -v /local/path/to/example_data_dir:/pvactools_example_data -it griffithlab/pvactools
This will mount the example_data_dir
inside the container as the
/pvacseq_example_data
directory. When you are inside of the container
you will now have access to all of the data that was inside of the
example_data_dir
from the /pvaseq_example_data
directory.
You will need to do the same thing for your /local/path/to/output_dir
so that any output
written by pVACseq will be accessible from your machine outside of your Docker
container.
docker run -v /local/path/to/example_data_dir:/pvacseq_example_data -v /local/path/to/output_dir:/pvacseq_output_data -it griffithlab/pvactools
You can now run your pVACseq command like so:
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 \
-e 8,9,10
--iedb-install-directory /opt/iedb
The output from your pVACseq run can be found under /pvacseq_output_data
inside of the container and /local/path/to/output_dir
on your local
machine.
Please note that our Docker container already includes installations of the IEDB class I and class II tools at /opt/iedb
(--iedb-install-directory /opt/iedb
).