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VacciBody CLI

The vaccibody command line interface is designed to run the following commands:

  • Peptides/Proteome matcher
  • WIP

Getting started

To build the solution from the source run make.

  • make init - build the solution on linux - generates the binary and the peptides/proteome matches file output.
  • make build - build the solution on linux and generates the binary on /Resources folder.
  • make run - run the solution and generates the peptides/proteome matches on the /Resources folder. (Note: provide the files /Resources/peptides.fasta + /Resources/proteome.fasta on the build step).
  • make clean - deletes the container
/Resources/peptides.fasta
/Resources/proteome.fasta

Usage

USAGE: vaccibody <subcommand>

OPTIONS:
  -h, --help              Show help information.

SUBCOMMANDS:
  match                   Scan a list of short peptides against the proteome and returns the matches

See 'vaccibody help <subcommand>' for detailed help.

Example:

vaccibody match "/peptides.fasta" "/proteome.fasta"

match command returns the peptides/proteome matches in json format on the root path.

Building on XCode

To build on mac run make mac - the process will download the dependencies and generate the XCode project file.

To run the unit tests the project requires the following environment variables:

PROTEOME_FILE_PATH=/Resources/proteome.fasta
PEPTIDES_FILE_PATH=/Resources/peptides.fasta