jbrowse_config.json

{
  "assemblies": [
    {
      "name": "volvox",
      "aliases": [
        "vvx"
      ],
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "volvox_refseq",
        "metadata": {
          "date": "2020-08-20"
        },
        "formatAbout": {
          "hideUris": true,
          "config": "jexl:{extraField:'important data'}"
        },
        "adapter": {
          "type": "TwoBitAdapter",
          "twoBitLocation": {
            "uri": "test_data/volvox/volvox.2bit",
            "locationType": "UriLocation"
          }
        }
      },
      "refNameAliases": {
        "adapter": {
          "type": "FromConfigAdapter",
          "adapterId": "W6DyPGJ0UU",
          "features": [
            {
              "refName": "ctgA",
              "uniqueId": "alias1",
              "aliases": [
                "A",
                "contigA"
              ]
            },
            {
              "refName": "ctgB",
              "uniqueId": "alias2",
              "aliases": [
                "B",
                "contigB"
              ]
            }
          ]
        }
      }
    },
    {
      "name": "volvox_tripalauth",
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "volvox_tripalauth-ReferenceSequenceTrack",
        "adapter": {
          "type": "TwoBitAdapter",
          "twoBitLocation": {
            "uri": "test_data/volvox/volvox.2bit",
            "locationType": "UriLocation",
            "internetAccountId": "customTripalAuth"
          }
        }
      }
    }
  ],
  "connections": [],
  "defaultSession": {
    "name": "Integration test example",
    "views": [
      {
        "id": "integration_test",
        "type": "LinearGenomeView",
        "offsetPx": 2000,
        "bpPerPx": 0.05,
        "displayedRegions": [
          {
            "refName": "ctgA",
            "start": 0,
            "end": 50001,
            "assemblyName": "volvox"
          }
        ]
      }
    ],
    "widgets": {
      "hierarchicalTrackSelector": {
        "id": "hierarchicalTrackSelector",
        "type": "HierarchicalTrackSelectorWidget",
        "filterText": "",
        "view": "integration_test"
      }
    },
    "activeWidgets": {
      "hierarchicalTrackSelector": "hierarchicalTrackSelector"
    }
  },
  "tracks": [
    {
      "type": "QuantitativeTrack",
      "trackId": "tripalauth_bigwig",
      "name": "TripalAuth BigWig",
      "category": [
        "Authentication"
      ],
      "assemblyNames": [
        "volvox"
      ],
      "adapter": {
        "type": "BigWigAdapter",
        "bigWigLocation": {
          "locationType": "UriLocation",
          "uri": "test_data/volvox/volvox.bw",
          "internetAccountId": "ActivatingCrops"
        }
      }
    },
    {
      "type": "VariantTrack",
      "trackId": "tripalauth_vcf",
      "name": "TripalAuth VCF",
      "assemblyNames": [
        "volvox"
      ],
      "category": [
        "Authentication"
      ],
      "adapter": {
        "type": "VcfTabixAdapter",
        "vcfGzLocation": {
          "uri": "test_data/volvox/volvox.filtered.vcf.gz",
          "locationType": "UriLocation",
          "internetAccountId": "ActivatingCrops"
        },
        "index": {
          "location": {
            "uri": "test_data/volvox/volvox.filtered.vcf.gz.tbi",
            "locationType": "UriLocation",
            "internetAccountId": "ActivatingCrops"
          }
        }
      }
    },
    {
      "type": "QuantitativeTrack",
      "trackId": "noauth_bigwig",
      "name": "NoAuth BigWig",
      "category": [
        "Authentication"
      ],
      "assemblyNames": [
        "volvox"
      ],
      "adapter": {
        "type": "BigWigAdapter",
        "bigWigLocation": {
          "locationType": "UriLocation",
          "uri": "test_data/volvox/volvox.bw"
        }
      }
    },
    {
      "type": "VariantTrack",
      "trackId": "noauth_vcf",
      "name": "NoAuth VCF",
      "assemblyNames": [
        "volvox"
      ],
      "category": [
        "Authentication"
      ],
      "adapter": {
        "type": "VcfTabixAdapter",
        "vcfGzLocation": {
          "uri": "test_data/volvox/volvox.filtered.vcf.gz",
          "locationType": "UriLocation"
        },
        "index": {
          "location": {
            "uri": "test_data/volvox/volvox.filtered.vcf.gz.tbi",
            "locationType": "UriLocation"
          }
        }
      }
    }
  ],
  "internetAccounts": [
    {
      "type": "DrupalRestAuthModel",
      "internetAccountId": "ActivatingCrops",
      "name": "Activating Crops Tripal Authentication",
      "description": "Requires login to the Activating Crops website"
    }
  ],
  "plugins": [
    {
      "name": "DrupalRestAuthModel",
      "url": "http://localhost:9000/dist/drupal-rest-auth-model.umd.development.js"
    }
  ]
}