Set-up
phenopacket2prompt requires at least Java 17. To build it from scratch, Apache Maven is also required.
Installation
Most users should download the prebuilt executable file from the Releases page of the GutHub repository.
It is also possible to build the application from source using standard Maven and Java tools.
git clone https://github.com/monarch-initiative/phenopacket2prompt.git
cd phenopacket2prompt
maven package
java -jar target/phenopacket2prompt.jar [OPTIONS]
Setup
Downloading necessary input files
For more information about the HPO, see
Koehler et al. (2021).
To run the commands, we need to download the latest copy of the Human Phenotype Ontology hp.json file as well as the
hp-international.obo file. We can do this by runing the download command to get the necessary files. Adjust the path to the phenopacket2prompt.jar
file as necessary, the default is target/phenopacket2prompt.
Obtaining phenopackets
This app is designed to work with the collection of GA4GH phenopackets obtained from the phenopacket-store repository. Obtain the latest release of these files from the Releases page of the repository and unpack (unzip or ungzip) the repository.