Mercurial > repos > iuc > jbrowse2

view test-data/out/02_remote/config.json @ 0:61add3f58f26 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 4fa86613193c985e0cb9a8fc795c56b8bc7b8532
author iuc
date Thu, 02 Oct 2025 10:19:44 +0000
parents
children
line wrap: on
line source

{
  "assemblies": [
    {
      "name": "hg19",
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "hg19-ReferenceSequenceTrack",
        "adapter": {
          "type": "BgzipFastaAdapter",
          "fastaLocation": {
            "uri": "https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz",
            "locationType": "UriLocation"
          },
          "faiLocation": {
            "uri": "https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz.fai",
            "locationType": "UriLocation"
          },
          "gziLocation": {
            "uri": "https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz.gzi",
            "locationType": "UriLocation"
          }
        }
      }
    }
  ],
  "configuration": {
    "disableAnalytics": false,
    "theme": {
      "palette": {
        "primary": {
          "main": "#0d233f"
        },
        "secondary": {
          "main": "#721e63"
        },
        "tertiary": {
          "main": "#135560"
        },
        "quaternary": {
          "main": "#ffb11d"
        }
      },
      "typography": {
        "fontSize": 10
      }
    }
  },
  "connections": [],
  "defaultSession": {
    "name": "hg19",
    "views": [
      {
        "type": "LinearGenomeView",
        "init": {
          "assembly": "hg19",
          "loc": "1",
          "tracks": [
            "f25077b166d61daa5cd442a5341a6778_0_0",
            "d356ba515264f7745079b8a8e25265e0_1_0",
            "4c55c087663d6bbdba9c10dba1371ef7_2_0",
            "0679f3e546fddf3021cce6cc4cdc5683_3_0",
            "717916f48c0481fcd916da20c9db8f3d_4_0",
            "b7b77cd71a6754bae52b38ac1bfcb1df_5_0",
            "d1c14592b12aa3d38a8c9114afb34f7d_6_0",
            "b99150c19ec943d2d90eeab328e8ac4e_7_0",
            "0e1a5cd1079b0cc284247c45ab58e154_8_0"
          ]
        }
      }
    ]
  },
  "tracks": [
    {
      "type": "QuantitativeTrack",
      "trackId": "f25077b166d61daa5cd442a5341a6778_0_0",
      "name": "SKBR3 pacbio coverage (NGMLR)",
      "adapter": {
        "type": "BigWigAdapter",
        "bigWigLocation": {
          "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/hg19/reads_lr_skbr3.fa_ngmlr-0.2.3_mapped.bam.regions.bw",
          "locationType": "UriLocation"
        }
      },
      "category": [
        "Default"
      ],
      "assemblyNames": [
        "hg19"
      ],
      "displays": [
        {
          "type": "LinearWiggleDisplay",
          "displayId": "f25077b166d61daa5cd442a5341a6778_0_0_LinearWiggleDisplay",
          "defaultRendering": "xyplot"
        }
      ],
      "metadata": {}
    },
    {
      "type": "MultiQuantitativeTrack",
      "trackId": "d356ba515264f7745079b8a8e25265e0_1_0",
      "name": "SKBR3 pacbio coverage (NGMLR) + 0 other track",
      "adapter": {
        "type": "MultiWiggleAdapter",
        "subadapters": [
          {
            "type": "BigWigAdapter",
            "name": "SKBR3 pacbio coverage (NGMLR)",
            "bigWigLocation": {
              "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/hg19/reads_lr_skbr3.fa_ngmlr-0.2.3_mapped.bam.regions.bw",
              "locationType": "UriLocation"
            }
          }
        ]
      },
      "category": [
        "Default"
      ],
      "assemblyNames": [
        "hg19"
      ],
      "displays": [
        {
          "type": "MultiLinearWiggleDisplay",
          "displayId": "d356ba515264f7745079b8a8e25265e0_1_0_MultiLinearWiggleDisplay",
          "defaultRendering": "multirowxy"
        }
      ],
      "metadata": {}
    },
    {
      "type": "AlignmentsTrack",
      "trackId": "4c55c087663d6bbdba9c10dba1371ef7_2_0",
      "name": "NA12878 Exome",
      "adapter": {
        "type": "BamAdapter",
        "bamLocation": {
          "uri": "https://s3.amazonaws.com/1000genomes/phase3/data/NA12878/exome_alignment/NA12878.mapped.ILLUMINA.bwa.CEU.exome.20121211.bam",
          "locationType": "UriLocation"
        },
        "index": {
          "location": {
            "uri": "https://s3.amazonaws.com/1000genomes/phase3/data/NA12878/exome_alignment/NA12878.mapped.ILLUMINA.bwa.CEU.exome.20121211.bam.bai",
            "locationType": "UriLocation"
          },
          "indexType": "BAI"
        },
        "sequenceAdapter": {
          "type": "BgzipFastaAdapter",
          "fastaLocation": {
            "uri": "https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz",
            "locationType": "UriLocation"
          },
          "faiLocation": {
            "uri": "https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz.fai",
            "locationType": "UriLocation"
          },
          "gziLocation": {
            "uri": "https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz.gzi",
            "locationType": "UriLocation"
          }
        }
      },
      "category": [
        "Default"
      ],
      "assemblyNames": [
        "hg19"
      ],
      "displays": [
        {
          "type": "LinearAlignmentsDisplay",
          "displayId": "4c55c087663d6bbdba9c10dba1371ef7_2_0_LinearAlignmentsDisplay"
        }
      ],
      "metadata": {}
    },
    {
      "type": "AlignmentsTrack",
      "trackId": "0679f3e546fddf3021cce6cc4cdc5683_3_0",
      "name": "hg_isoforms.fasta_cram",
      "adapter": {
        "type": "CramAdapter",
        "cramLocation": {
          "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/hg19/alzheimers_isoseq/hq_isoforms.fasta.cram",
          "locationType": "UriLocation"
        },
        "craiLocation": {
          "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/hg19/alzheimers_isoseq/hq_isoforms.fasta.cram.crai",
          "locationType": "UriLocation"
        },
        "sequenceAdapter": {
          "type": "BgzipFastaAdapter",
          "fastaLocation": {
            "uri": "https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz",
            "locationType": "UriLocation"
          },
          "faiLocation": {
            "uri": "https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz.fai",
            "locationType": "UriLocation"
          },
          "gziLocation": {
            "uri": "https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz.gzi",
            "locationType": "UriLocation"
          }
        }
      },
      "category": [
        "Default"
      ],
      "assemblyNames": [
        "hg19"
      ],
      "displays": [
        {
          "type": "LinearAlignmentsDisplay",
          "displayId": "0679f3e546fddf3021cce6cc4cdc5683_3_0_LinearAlignmentsDisplay"
        }
      ],
      "metadata": {}
    },
    {
      "type": "HicTrack",
      "trackId": "717916f48c0481fcd916da20c9db8f3d_4_0",
      "name": "hg_isoforms.fasta_cram",
      "adapter": {
        "type": "HicAdapter",
        "hicLocation": {
          "uri": "https://jbrowse.org/genomes/hg19/intra_nofrag_30.hic",
          "locationType": "UriLocation"
        }
      },
      "category": [
        "Default"
      ],
      "assemblyNames": [
        "hg19"
      ],
      "displays": [
        {
          "type": "LinearHicDisplay",
          "displayId": "717916f48c0481fcd916da20c9db8f3d_4_0_LinearHicDisplay"
        }
      ],
      "metadata": {}
    },
    {
      "type": "VariantTrack",
      "trackId": "b7b77cd71a6754bae52b38ac1bfcb1df_5_0",
      "name": "HG002 dbVar variant calls",
      "adapter": {
        "type": "VcfTabixAdapter",
        "vcfGzLocation": {
          "uri": "https://ftp.ncbi.nlm.nih.gov/pub/dbVar/data/Homo_sapiens/by_study/vcf/nstd175.GRCh37.variant_call.vcf.gz",
          "locationType": "UriLocation"
        },
        "index": {
          "location": {
            "uri": "https://ftp.ncbi.nlm.nih.gov/pub/dbVar/data/Homo_sapiens/by_study/vcf/nstd175.GRCh37.variant_call.vcf.gz.tbi",
            "locationType": "UriLocation"
          },
          "indexType": "TBI"
        }
      },
      "category": [
        "Default"
      ],
      "assemblyNames": [
        "hg19"
      ],
      "displays": [
        {
          "type": "LinearVariantDisplay",
          "displayId": "b7b77cd71a6754bae52b38ac1bfcb1df_5_0_LinearVariantDisplay"
        }
      ],
      "formatDetails": {},
      "metadata": {}
    },
    {
      "type": "VariantTrack",
      "trackId": "d1c14592b12aa3d38a8c9114afb34f7d_6_0",
      "name": "truthset_somaticSVs_COLO829",
      "adapter": {
        "type": "VcfAdapter",
        "vcfLocation": {
          "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/hg19/COLO829/truthset_somaticSVs_COLO829.vcf",
          "locationType": "UriLocation"
        }
      },
      "category": [
        "Default"
      ],
      "assemblyNames": [
        "hg19"
      ],
      "displays": [
        {
          "type": "LinearVariantDisplay",
          "displayId": "d1c14592b12aa3d38a8c9114afb34f7d_6_0_LinearVariantDisplay"
        }
      ],
      "formatDetails": {},
      "metadata": {}
    },
    {
      "type": "FeatureTrack",
      "trackId": "b99150c19ec943d2d90eeab328e8ac4e_7_0",
      "name": "Gencode v36 (GRCh37 liftover)",
      "adapter": {
        "type": "Gff3TabixAdapter",
        "gffGzLocation": {
          "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/hg19/gencode/gencode.v36lift37.annotation.sort.gff3.gz",
          "locationType": "UriLocation"
        },
        "index": {
          "location": {
            "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/hg19/gencode/gencode.v36lift37.annotation.sort.gff3.gz.tbi",
            "locationType": "UriLocation"
          },
          "indexType": "TBI"
        }
      },
      "category": [
        "Default"
      ],
      "assemblyNames": [
        "hg19"
      ],
      "displays": [
        {
          "type": "LinearBasicDisplay",
          "displayId": "b99150c19ec943d2d90eeab328e8ac4e_7_0_LinearBasicDisplay",
          "renderer": {
            "type": "SvgFeatureRenderer",
            "showLabels": true,
            "showDescriptions": true,
            "labels": {
              "name": "jexl:get(feature,'name') || get(feature,'id')",
              "description": "jexl:get(feature,'note') || get(feature,'description')"
            },
            "displayMode": "normal",
            "maxHeight": 600
          }
        }
      ],
      "formatDetails": {
        "depth": 1
      },
      "metadata": {}
    },
    {
      "type": "FeatureTrack",
      "trackId": "0e1a5cd1079b0cc284247c45ab58e154_8_0",
      "name": "wgEncodeDukeMapabilityRegionsExcludable",
      "adapter": {
        "type": "BedTabixAdapter",
        "bedGzLocation": {
          "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/hg19/mappability/wgEncodeDukeMapabilityRegionsExcludable.bed.gz",
          "locationType": "UriLocation"
        },
        "index": {
          "location": {
            "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/hg19/mappability/wgEncodeDukeMapabilityRegionsExcludable.bed.gz.tbi",
            "locationType": "UriLocation"
          },
          "indexType": "TBI"
        }
      },
      "category": [
        "Default"
      ],
      "assemblyNames": [
        "hg19"
      ],
      "displays": [
        {
          "type": "LinearBasicDisplay",
          "displayId": "0e1a5cd1079b0cc284247c45ab58e154_8_0_LinearBasicDisplay",
          "renderer": {
            "type": "SvgFeatureRenderer",
            "showLabels": true,
            "showDescriptions": true,
            "labels": {
              "name": "jexl:get(feature,'name') || get(feature,'id')",
              "description": "jexl:get(feature,'note') || get(feature,'description')"
            },
            "displayMode": "normal",
            "maxHeight": 600
          }
        }
      ],
      "formatDetails": {
        "depth": 1
      },
      "metadata": {}
    }
  ],
  "plugins": []
}