CLI fenominal app: Downloading the hpo file

The fenominal command-line app requires a copy of hp.json, the main Human Phenotype Ontology file. The file can be manually downloaded from the HPO Website.

Alternatively, fenominal offers a convenience function to download all files to a local directory. By default, fenominal will download all four files into a newly created subdirectory called data in the current working directory. You can change this default with the -d or --data options (If you change this, then you will need to pass the location of your directory to all other fenominal commands using the -d flag). Download the files automatically as follows.

$ java -jar fenominal.jar download

fenominal will not download the files if they are already present unless the --overwrite argument is passed. For instance, the following command would download the four files to a directory called datafiles and would overwrite any previously downloaded files.

$ java -jar fenominal.jar download -d datafiles --overwrite

If you download the hp.json file manually or use any non-default name for the directory in which the file is located, you need to indicate the path of the directory using the -d argument for the parse command.