Add GRCm39 as Assembly track

[adaware-loxo]

Is your feature request related to a problem? Please describe.

I want to add GRCm39 as reference assembly to the existing hg19 and hg38.

Describe the solution you'd like

Reference from ticket #4117, could you point me to a config.json which has GRCm39 added ?

Describe alternatives you've considered

If config.json with GRCm39 does not exist then could you please mention what part of config json do I need to edit or add to make changes to incorporate it? Thanks

[cmdcolin]

an example of a mm39 config.json exists here (for a human vs mouse synteny demo)

jbrowse-components/test_data/hs1_vs_mm39/config.json

Lines 28 to 43 in 42442fe

	{
	"name": "mm39",
	"sequence": {
	"type": "ReferenceSequenceTrack",
	"trackId": "mm39-ReferenceSequenceTrack",
	"adapter": {
	"type": "TwoBitAdapter",
	"twoBitLocation": {
	"uri": "https://hgdownload.soe.ucsc.edu/goldenPath/mm39/bigZips/mm39.2bit"
	},
	"chromSizesLocation": {
	"uri": "https://hgdownload.soe.ucsc.edu/goldenPath/mm39/bigZips/mm39.chrom.sizes"
	}
	}
	}
	}

[cmdcolin]

note that this config refers directly to files on the UCSC server so it fetches data remotely.

you could also download them to your server

other options include adding refNameAliases which would look maybe something like

{
      "name": "mm39",
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "mm39-ReferenceSequenceTrack",
        "adapter": {
          "type": "TwoBitAdapter",
          "twoBitLocation": {
            "uri": "https://hgdownload.soe.ucsc.edu/goldenPath/mm39/bigZips/mm39.2bit"
          },
          "chromSizesLocation": {
            "uri": "https://hgdownload.soe.ucsc.edu/goldenPath/mm39/bigZips/mm39.chrom.sizes"
          }
        }
      },
      "refNameAliases": {
        "adapter": {
          "type": "RefNameAliasAdapter",
          "location": {
            "uri": "https://hgdownload.soe.ucsc.edu/goldenPath/mm39/bigZips/mm39.chromAlias.txt"
          }
        }
      }
    }

[cmdcolin]

note: converted issue to discussion :) (see https://github.com/GMOD/jbrowse-components/discussions)

[adaware-loxo]

Thank you so much!