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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
        gwas_catalog_ingestion
        gwas_catalog_sumstat_preprocess
        ld_index
        locus_to_gene
        overlaps
        pics
        ukbiobank
        variant_annotation
        variant_index

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 gwas_catalog_sumstat_preprocess step, you can run:

gentropy step=gwas_catalog_sumstat_preprocess

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

gentropy step=gwas_catalog_sumstat_preprocess step.raw_sumstats_path=/path/to/raw_sumstats step.out_sumstats_path=/path/to/out_sumstats

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

  • 2024-01-12
  • 2025-01-22
  • Contributors
    • vivienho
    • web-flow
    • ireneisdoomed