Configuration¶

HCRProbeDesign stores reference genome index paths and default parameters in HCRconfig.yaml, located in the user data directory (~/.hcrprobedesign/ by default).

Data directory¶

All user data (configuration and Bowtie2 indices) lives in ~/.hcrprobedesign/. This directory is created automatically on first use and persists across package upgrades, so you won't lose your indices when running pip install -U hcrprobedesign.

Override the location by setting the HCRPROBEDESIGN_DATA_DIR environment variable:

export HCRPROBEDESIGN_DATA_DIR=/path/to/custom/dir

Migration from older versions¶

If you are upgrading from v0.3.0 or earlier (where data was stored inside the package directory), HCRProbeDesign will automatically detect and migrate your existing indices and species registrations on first run.

Example¶

species:
  mouse:
    bowtie2_index: indices/mm10/mm10
  human:
    bowtie2_index: /path/to/hg38/index_prefix

Viewing the current configuration¶

Run listReferences to display all registered species, default parameters, and the data directory location:

listReferences

Notes¶

• Paths can be absolute or relative to the data directory.
• buildGenomeIndex updates this file automatically.
• fetchMouseIndex also registers the mouse index for you.
• Use --config to write to a different config file when building indices.
• Use listReferences --config /path/to/HCRconfig.yaml to inspect a specific config file.