Refgenie genome configuration file

Refgenie will read and write a genome configuration file in yaml format. In general, you shouldn't need to mess with the config file. You create one with refgenie init -c genome_config.yaml, then you add assets using either refgenie pull or refgenie build. You can also add your own custom assets with refgenie add, which is explained in using external assets. Refgenie will use the config file to remember what assets are available and where they are.

But here's how the config file works, in case for some reason you do need to edit some things by hand. Here's an example file to get you started:

genome_folder: /path/to/active/genomes
genome_server: http://refgenomes.databio.org
genome_archive: /path/to/archived/genomes
genomes:
  hg38:
    genome_description: ...
    assets:
      bowtie2_index:
        path: indexed_bowtie2
        asset_description: ...
      hisat2_index: 
        path: indexed_hisat2
        asset_description: ...
  mm10:
    genome_description: ...
    assets:
      bowtie2_index:
        path: indexed_bowtie2
  rCRS:
    genome_description: ...
    assets:
      bowtie2_index:
        path: indexed_bowtie2
      indexed_bowtie2:
        path: indexed_bowtie2
      indexed_hisat2:
        path: indexed_hisat2
      indexed_kallisto:
        path: indexed_kallisto

Details of config attributes

  • genome_folder: Path to parent folder refgenie-managed assets.
  • genome_server: URL to a refgenieserver instance (currently only 1 URL allowed).
  • genome_archive: (optional; used by refgenieserver) Path to folder where asset archives will be stored.
  • genomes: A list of genomes, each genome has a list of assets. Any relative paths in the asset path attributes are considered relative to the genome folder in the config file (or the file itself if not folder path is specified), with the genome name as an intervening path component, e.g. folder/mm10/indexed_bowtie2.

So, for example:

genomes:
  hg38:                <---- genome key
    bowtie2:           <---- asset key
      path: blahblah   <---- relative to genome folder
      asset_description: freeform text (currently manual)
      asset_checksum: 12345
      asset_size: 15MB
      archive_size: 12MB

For genomes that are managed by refgenie (that is, they were built or pulled with refgenie), these asset attributes will be automatically populated. You can edit them and refgenie will respect your edits (unless you re-build or re-pull the asset, which will overwrite those fields). You can also add your own assets and refgenie won't touch them. For more info, see using external assets.

Genome config versions

Up to version 0.4.4, refgenie used a config file version that lacked the assets level in the hierarchy (so, assets were listed directly under the genome). Starting with version 0.5.0, we moved the assets down a layer to accommodate other genome-level attributes we intend to use in the future (like a description, checksums, other provenance information). Earlier refgenie config files will need to be updated.