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Project description
AI-MARRVEL Runner for PhEval
This is the AI-MARRVEL plugin for PhEval. With this plugin, you can leverage the tool, AI-MARRVEL, to run the PhEval pipeline seamlessly. Detailed instructions on setting up the appropriate directory layout, including the input directory and test data directory, can be found here.
Installation
git clone https://github.com/yaseminbridges/pheval.ai_marrvel.git
cd pheval.ai_marrvel
poetry install
poetry shell
Configuring a single run:
Setting up the input directory
A config.yaml
should be located in the input directory and formatted like so:
tool: AI-MARRVEL
tool_version: 1.0.0
variant_analysis: True
gene_analysis: True
disease_analysis: False
tool_specific_configuration_options:
The AI-MARRVEL data dependencies should also be unpacked into the input directory. The overall structure of the input directory should look something like:
.
├── annotate
├── bcf_annotate
├── config.yaml
├── download.err
├── filter_vep
├── merge_expand
├── mod5_diffusion
├── model_inputs
├── omim_annotate
├── phrank
├── predict_new
├── var_tier
└── vep
The testdata directory should include the subdirectory named phenopackets
- which should contain phenopackets and vcf
- which should contain the gzipped VCF files.
e.g.,
├── testdata_dir
├── phenopackets
└── vcf
Run command
pheval run --input-dir /path/to/input_dir \
--runner aimarrvelrunner \
--output-dir /path/to/output_dir \
--testdata-dir /path/to/testdata_dir
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