From 2026d7b56b49039817e235119aa7e31b0828024d Mon Sep 17 00:00:00 2001
From: Yasemin Bridges <y.bridges@qmul.ac.uk>
Date: Wed, 4 Oct 2023 11:52:37 +0100
Subject: [PATCH] updating README.md

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+# GADO Runner for PhEval
+This is the GADO plugin for PhEval. With this plugin, you can leverage the gene prioritisation tool, GADO, to run the PhEval pipeline seamlessly. The 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
+
+Clone the pheval.gado repo and set up the poetry environment:
+
+```sh
+git clone https://github.com/yaseminbridges/pheval.gado.git
+
+cd pheval.gado
+
+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:
+
+```yaml
+tool: GADO
+tool_version: 1.0.1
+variant_analysis: False
+gene_analysis: True
+disease_analysis: False
+tool_specific_configuration_options:
+  gado_jar: GadoCommandline-1.0.1/GADO.jar
+  hpo_ontology: hp.obo
+  hpo_predictions_info: predictions_auc_bonf.txt
+  genes: hpo_prediction_genes.txt
+  hpo_predictions: genenetwork_bonf_spiked/genenetwork_bonf_spiked.dat
+```
+
+The bare minimum fields are filled to give an idea on the requirements, as GADO is gene prioritisation tool, only `gene_analysis` should be set to `True` in the config. An example config has been provided pheval.gado/config.yaml.
+
+All GADO input data files required for running (specified in the `tool_specific_configuration_options`) should be located in the input directory.
+The `gado_jar` points to the name of the GADO jar file which should also be located in the input directory.
+
+The overall structure of the input directory should look something like so:
+
+```tree
+.
+├── GadoCommandline-1.0.1
+├── config.yaml
+├── predictions_auc_bonf.txt
+├── hp.obo
+├── hpo_prediction_genes.txt
+└── genenetwork_bonf_spiked
+   └── genenetwork_bonf_spiked.dat
+```
+### Setting up the testdata directory
+
+The GADO plugin for PhEval accepts phenopackets as an input for running GADO. 
+
+The testdata directory should include a subdirectory named phenopackets:
+
+```tree
+├── testdata_dir
+   └── phenopackets
+```
+
+## Run command
+
+Once the testdata and input directories are correctly configured for the run, the pheval run command can be executed.
+
+```sh
+pheval run --input-dir /path/to/input_dir \
+--testdata-dir /path/to/testdata_dir \
+--runner gadophevalrunner \
+--output-dir /path/to/output_dir \
+--version 1.0.1
+```