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conda_conventions.md

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Conda conventions at Clinical Genomics

  • Avoid installing anything in the conda default environment (base) if possible
  • Naming conventions for conda environments:
    • Production: [env_type=P]_[logical_name]_[creation_date]
    • Development: [env_type=D]_[logical_name]_[creation_date]_[signature]
      • env_type: Allowed environment types are D (develop) or P (production).
      • creation_date: YYMMDD.
      • logical_name: Whatever makes sense.
      • signature: Something to show who created the environment. Use the two- or three letter name akronyms assigned to you.
  • List your production environment and dependent processes at the bottom of this page.
  • It is considered unpolite to change or delete someone elses environment without involving the person which created the environment.

Move environments from devel to prod

When it is time to move your development environment to production - make a copy of it and rename it following the above conventions e.g.:

$ conda create --name P_mip-6.0_180129 --clone D_mip-6.0_180101_hs

Production conda environments

  • base
    • Process: MIP
  • mip_cnvnator
    • Process: MIP
  • mip_peddy
    • Process: MIP