# Built-in misha genome registry.
#
# Used as the lowest-priority fallback by gdb.build_genome() and friends.
# Resolution order is documented in ?gdb.build_genome.
#
# Schema:
#   genome:
#     <name>:
#       source: ucsc | ncbi | s3 | manual | local
#       <source-specific fields>
#
# Per-source required fields:
#   ucsc:    assembly
#   ncbi:    accession (must match ^GC[FA]_[0-9]+\.[0-9]+$)
#            optional chrom_naming: sequence_name (default) | ucsc | accession
#   s3:      assembly (mapped to gdb.create_genome())
#   local:   path (existing groot)
#   manual:  fasta (string or list); optional genes/genes_format/annots_file/
#            annots_names/rmsk/cpgIsland/cytoband
#
# A bare string value is shorthand for "source: local, path: <string>"
# (compatible with tgdb/misha.yaml).

genome:
  hg19:    {source: ucsc, assembly: hg19}
  hg38:    {source: ucsc, assembly: hg38}
  mm9:     {source: ucsc, assembly: mm9}
  mm10:    {source: ucsc, assembly: mm10}
  mm39:    {source: ucsc, assembly: mm39}
  rn6:     {source: ucsc, assembly: rn6}
  rn7:     {source: ucsc, assembly: rn7}
  dm6:     {source: ucsc, assembly: dm6}
  ce11:    {source: ucsc, assembly: ce11}
  sacCer3: {source: ucsc, assembly: sacCer3}
  danRer11: {source: ucsc, assembly: danRer11}
