CLI fenominal app: Setup

This page describes how to build and use the cli application.

Prerequisites

fenominal was written with Java version 17. If you want to build fenominal from source, then the build process described below requires Git and maven.

Build

Go the GitHub page of fenominal, and clone the project. Build the executable from source with maven, and then test the build.

$ git clone https://github.com/monarch-initiative/fenominal
$ cd fenominal
$ ./mvnw package
$ java -jar fenominal-cli/target/fenominal-cli-0.7.10.jar
    Usage: fenominal [-hV] [COMMAND]
    phenotype/disease NER
        -h, --help      Show this help message and exit.
        -V, --version   Print version information and exit.
    Commands:
        download, D  Download files for fenominal
        parse, P     Parse text