The tool can be downloaded by running git clone https://github.com/whalleyt/bacterial_vaccine_design. This directory contains the bare bones to run the tool within docker containers.
The Docker containers can be downloaded as follows:
docker pull twhalley93/loctree3:latest
docker pull twhalley93/bvd:latest
The Dockerfiles, along with the source code of the entire script (should you wish to run the code locally) can be found here. please consider using the Dockerfiles provided, this is because a number of tools have to be manually downloaded manually due to licensing constraints.
The tool can be ran using nextflow as follows:
nextflow pipeline.nf --fasta_folder <folder> --outdir <outdir>
Help can be accessed by nextflow pipeline -h.
All tools intgegrated in this software, and the source code are published under the GNU GPL; with the exception of NetMHCIpan and NetMHCIIpan. Please find the academic license in the NETMHC_LICENSE file. If you are a non-academic user, please contact the authors of NetMHC before proceeding. They can be found at: [email protected].
The license documentation can be found in LICENSE.
please feel free to contact us at [email protected], alternatively make a pull request.