Installing and running HPO Annotation Q/C

This version of HpoAnnotQc uses phenol-1.3.2-SNAPSHOT, which needs to be installed locally with mvn install. Following this, to build HPO Annotation Q/C, clone the GitHub repository at https://github.com/monarch-initiative/hpoannotqc, and build HPO Workbench using maven.

$ git clone https://github.com/monarch-initiative/hpoannotqc.git
$ cd hpoannotqc
$ mvn clean package

This will create an executable jar file.

$ java -jar target/HpoAnnotQc.jar
    Usage: java -jar HpoAnnotQc.jar [-hV] [COMMAND]
    Variant-motif visualization tool.
    -h, --help      Show this help message and exit.
    -V, --version   Print version information and exit.
   Commands:
    download, D  download files
    big-file, B  Create phenotype.hpoa file
    gene2phen    Create genes to phenotypes file

We will update this as soon as phenol-1.3.2 is released in maven central.