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 🚧