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Common bean PHGv2 build

Scripts and notes for building a common bean PHG using v2 architecture.

Prerequisites

  • Conda package management system
  • CBSU working environment
    • Uses module load java/21.0.1 for PHGv2 steps

Repo structure

  • data/
    • fa_keyfile.csv - files to pull from CBSUBLFS1.
    • phg_environment.yml - Conda environment setup.
  • src/
    • utitl_config.sh - defining global parameters.
    • util_functions.sh - helper functions.
  • ./00_setup_and_download.sh:
    • creates working directories and retrieves assemblies.
    • sets up PHGv2 conda environment
    • initializes TileDB instances for data storage
  • ./01_build_load.sh:
    • Main PHGv2 code to build and load VCF data 🚧