LIRICAL Runner for PhEval

This is the LIRICAL plugin for PhEval. With this plugin, you can leverage the prioritisation tool, LIRICAL, to run the PhEval pipeline seamlessly. he setup process for running the full PhEval Makefile pipeline differs from setting up for a single run. The Makefile pipeline creates directory structures for corpora and configurations to handle multiple run configurations. Detailed instructions on setting up the appropriate directory layout, including the input directory and test data directory, can be found here.

Installation

Install with pip:

pip install pheval.lirical

Alternatively clone the pheval.lirical repo and set up the poetry environment:

git clone https://github.com/monarch-initiative/pheval.lirical.git
cd pheval.lirical
poetry shell
poetry install

Configuring a single run:

Setting up the input directory

A config.yaml should be located in the input directory and formatted like so:

tool: LIRICAL
tool_version: 2.0.0-RC2
variant_analysis: True
gene_analysis: True
disease_analysis: True
tool_specific_configuration_options:
  mode: phenopacket
  lirical_jar_executable: lirical-cli-2.0.0-RC2/lirical-cli-2.0.0-RC2.jar
  exomiser_db_configurations:
    exomiser_database:
    exomiser_hg19_database: 2302_hg19_variants.mv.db
    exomiser_hg38_database:
  post_process:
    sort_order: descending

The bare minimum fields are filled to give an idea on the requirements.

The mode should specify the mode you want to run LIRICAL in (either manual or phenopacket) both of these options require phenopackets as an input.

The LIRICAL data files should be located in the input directory under a subdirectory named data If running LIRICAL with variant and/or gene analysis set to true, you will need to provide the relevant exomiser hg19/hg38 databases.

The lirical jar executable points to the location in the input directory.

The input directory should look something like so (removed some files for clarity):

.
├── 2302_hg19_variants.mv.db
├── config.yaml
├── data
│   ├── hg19_refseq.ser
│   ├── hg19_ucsc.ser
│   ├── hg38_refseq.ser
│   ├── hg38_ucsc.ser
│   ├── hgnc_complete_set.txt
│   ├── hp.json
│   ├── mim2gene_medgen
│   └── phenotype.hpoa
└── lirical-cli-2.0.0-RC2
    └── lirical-cli-2.0.0-RC2.jar

Setting up the testdata directory

The LIRICAL plugin for PhEval accepts phenopackets and vcf files as an input. The plugin can be run in only disease_analysis mode, where only phenopackets are required as an input, however, this must be specified in the config.yaml.

The testdata directory should include subdirectories named phenopackets and vcf if running with gene/variant prioritisation.

e.g.,

├── testdata_dir
   ├── phenopackets
   └── vcf

Run command

Once the testdata and input directories are correctly configured for the run, the pheval run command can be executed.

pheval run --input-dir /path/to/input_dir \
--testdata-dir /path/to/testdata_dir \
--runner liricalphevalrunner \
--output-dir /path/to/output_dir \
--version 13.2.0

Common errors

You may see an error that is related to the current setuptools being used:

pkg_resources.extern.packaging.requirements.InvalidRequirement: Expected closing RIGHT_PARENTHESIS
    requests (<3,>=2.12.*) ; extra == 'parse'
             ~~~~~~~~~~^

To fix the error, setuptools needs to be downgraded to version 66:

pip uninstall setuptools
pip install -U setuptools=="66"