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Run step in CLI

To run a step in the command line interface (CLI), you need to know the step's name. To list what steps are avaiable in your current environment, simply run gentropy with no arguments. This will list all the steps:

You must specify 'step', e.g, step=<OPTION>
Available options:
        clump
        colocalisation
        eqtl_catalogue
        finngen_studies
        finngen_sumstat_preprocess
        gene_index
        gwas_catalog_ingestion
        gwas_catalog_sumstat_preprocess
        ld_index
        locus_to_gene
        overlaps
        pics
        ukbiobank
        variant_annotation
        variant_index
        variant_to_gene

Set the environment variable HYDRA_FULL_ERROR=1 for a complete stack trace.

As indicated, you can run a step by specifying the step's name with the step argument. For example, to run the gene_index step, you can run:

gentropy step=gene_index

In most occassions, some mandatory values will be required to run the step. For example, the gene_index step requires the step.target_path and step.gene_index_path argument to be specified. You can complete the necessary arguments by adding them to the command line:

gentropy step=gene_index step.target_path=/path/to/target step.gene_index_path=/path/to/gene_index

You can find more about the available steps in the documentation.

  • 2024-01-12
  • 2024-02-05
  • Contributors
    • ireneisdoomed