How to use UCSC plugin and tracks with normal tracks?

[Lilas-w]

I would like to add the UCSC plugin to my JBrowse configuration. Here is my configuration following the guide, but unfortunately, the UCSC tracks didn't show up:

{
  "plugins": [
    {
      "name": "UCSC",
      "url": "https://unpkg.com/jbrowse-plugin-ucsc/dist/jbrowse-plugin-ucsc.umd.production.min.js"
    }
  ],
  "assemblies": [
    {
      "name": "GRCh38.chr",
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "GRCh38.chr-ReferenceSequenceTrack",
        "adapter": {
          "type": "IndexedFastaAdapter",
          "fastaLocation": {
            "uri": "GRCh38.chr.fa",
            "locationType": "UriLocation"
          },
          "faiLocation": {
            "uri": "GRCh38.chr.fa.fai",
            "locationType": "UriLocation"
          }
        }
      }
    },
    {
      "name": "hg38",
      "aliases": ["GRCh38"],
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "P6R5xbRqRr",
        "adapter": {
          "type": "BgzipFastaAdapter",
          "fastaLocation": {
            "uri": "https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz"
          },
          "faiLocation": {
            "uri": "https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz.fai"
          },
          "gziLocation": {
            "uri": "https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz.gzi"
          }
        }
      },
      "refNameAliases": {
        "adapter": {
          "type": "RefNameAliasAdapter",
          "location": {
            "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/hg38_aliases.txt"
          }
        }
      }
    }
  ],
  "configuration": {
    "logoPath": {
      "uri": ""
    }
  },
  "connections": [],
  "defaultSession": {
    "name": "New Session"
  },
  "tracks": [
    {
      "type": "AlignmentsTrack",
      "trackId": "K562_DddB_merged_TRNAU1AP",
      "name": "K562_DddB_merged_TRNAU1AP",
      "adapter": {
        "type": "BamAdapter",
        "bamLocation": {
          "uri": "K562_DddB_merged_TRNAU1AP.bam",
          "locationType": "UriLocation"
        },
        "index": {
          "location": {
            "uri": "K562_DddB_merged_TRNAU1AP.bam.bai",
            "locationType": "UriLocation"
          },
          "indexType": "BAI"
        },
        "sequenceAdapter": {
          "type": "IndexedFastaAdapter",
          "fastaLocation": {
            "uri": "GRCh38.chr.fa",
            "locationType": "UriLocation"
          },
          "faiLocation": {
            "uri": "GRCh38.chr.fa.fai",
            "locationType": "UriLocation"
          }
        }
      },
      "assemblyNames": ["GRCh38.chr"]
    },
    {
      "type": "AlignmentsTrack",
      "trackId": "K562_DddB_merged_TRNAU1AP_cram",
      "name": "K562_DddB_merged_TRNAU1AP_cram",
      "adapter": {
        "type": "CramAdapter",
        "cramLocation": {
          "uri": "K562_DddB_merged_TRNAU1AP_cram.cram",
          "locationType": "UriLocation"
        },
        "craiLocation": {
          "uri": "K562_DddB_merged_TRNAU1AP_cram.cram.crai",
          "locationType": "UriLocation"
        },
        "sequenceAdapter": {
          "type": "IndexedFastaAdapter",
          "fastaLocation": {
            "uri": "GRCh38.chr.fa",
            "locationType": "UriLocation"
          },
          "faiLocation": {
            "uri": "GRCh38.chr.fa.fai",
            "locationType": "UriLocation"
          }
        }
      },
      "assemblyNames": ["GRCh38.chr"]
    },
    {
      "type": "FeatureTrack",
      "trackId": "K562_DddB_merged.footprint.corrected.DNase.bo05.bf.bed",
      "name": "K562_DddB_merged.footprint.corrected.DNase.bo05.bf.bed",
      "adapter": {
        "type": "BedTabixAdapter",
        "bedGzLocation": {
          "uri": "K562_DddB_merged.footprint.corrected.DNase.bo05.bf.bed.gz",
          "locationType": "UriLocation"
        },
        "index": {
          "location": {
            "uri": "K562_DddB_merged.footprint.corrected.DNase.bo05.bf.bed.gz.tbi",
            "locationType": "UriLocation"
          },
          "indexType": "TBI"
        }
      },
      "assemblyNames": ["GRCh38.chr"]
    },
    {
      "type": "FeatureTrack",
      "trackId": "genehancer_ucsc_hg38",
      "name": "UCSC GeneHancer",
      "category": ["Annotation"],
      "assemblyNames": ["hg38"],
      "adapter": {
        "type": "UCSCAdapter",
        "track": "geneHancerInteractionsDoubleElite"
      }
    }
  ]
}

And when I set the whole config.json file the same as example config, the UCSC tracks appear, but my normal tracks are missing.

I'm seeking assistance to resolve this issue and ensure that both the UCSC tracks and my custom tracks are visible in the JBrowse instance. Any guidance or suggestions would be highly appreciated.

[cmdcolin]

@Lilas-w I think you have maybe two issues

1. you have "two assemblies" basically both are grch38 but one is named "hg38" and one is named "GRCh38.chr". i would standardize in this case on "hg38" because of reason 2:
2. the UCSC plugin requests data from the UCSC api using the assembly name provided from the config, and in this case, UCSC is not aware of GRCh38.chr, but it is aware of hg38

potentially the UCSC plugin could make a fix for issue (2) if you wanted to remap the assembly names requested from the API. if you are interested in this, can you open a github issue on the plugin repo?

hope that helps!