Configuration

Genomepy uses many configurable options. The default setting for several options can be overwritten using a config file.

You can create new config file with genomepy config generate, or find the location of your current config file with genomepy config file.

Configurable options

The config file uses the YAML format, wherein each configurable option is given as a key: value pair, and anything after the comment symbol # is ignored.

These keys are currently supported:

  • bgzip: determines if newly installed assembly data is compressed or not.

    • Options: true or false.

    • Default: false

  • cache_exp_genomes: expiration time (in seconds) for the cache used in genomepy search. (Re)building this cache is slow, but must be done periodically to get the latest assemblies. This setting does not affect your installed assembly data.

    • Options: an integer or scientific number, or None for infinite.

    • Default: 6.048e5 (1 week)

  • cache_exp_other: expiration time (in seconds) for the cache used in short term activities (e.g. mygene.info queries). This setting does not affect your installed assembly data.

    • Options: an integer or scientific number, or None for infinite.

    • Default: 3.6e3 (1 hour)

  • genomes_dir: the path where assembly data will be installed.

    • Default: ~/.local/share/genomes/

  • plugin: the list of currently active plugins. See command genomepy plugin show for options. genomepy plugin can also be used to easily change this list.