Config.json to load synteny data (paf)

[abretaud]

Hi,
Working on the Galaxy tool for JBrowse2, I'd like it to generate a config.json showing a default view with 3 genomes and synteny data in PAF format.
The 3 (test) genomes are named merlin, merlon, and merlun (no imagination :D ), and I have a 'minimap2) PAF output of merlon on merlin, and merlun on merlon.
I also have a bigwig track on merlin (to make things more complicated hehe)

I have a generated config.json that looks like that:

{
  "assemblies": [
    {
      "name": "merlin.fa",
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "merlin.fa-ReferenceSequenceTrack",
        "adapter": {
          "type": "BgzipFastaAdapter",
          "fastaLocation": {
            "uri": "data/merlin.fa.fasta.gz",
            "locationType": "UriLocation"
          },
          "faiLocation": {
            "uri": "data/merlin.fa.fasta.gz.fai",
            "locationType": "UriLocation"
          },
          "gziLocation": {
            "uri": "data/merlin.fa.fasta.gz.gzi",
            "locationType": "UriLocation"
          }
        }
      }
    },
    {
      "name": "merlon.fa",
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "merlon.fa-ReferenceSequenceTrack",
        "adapter": {
          "type": "BgzipFastaAdapter",
          "fastaLocation": {
            "uri": "data/merlon.fa.fasta.gz",
            "locationType": "UriLocation"
          },
          "faiLocation": {
            "uri": "data/merlon.fa.fasta.gz.fai",
            "locationType": "UriLocation"
          },
          "gziLocation": {
            "uri": "data/merlon.fa.fasta.gz.gzi",
            "locationType": "UriLocation"
          }
        }
      }
    },
    {
      "name": "merlun.fa",
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "merlun.fa-ReferenceSequenceTrack",
        "adapter": {
          "type": "BgzipFastaAdapter",
          "fastaLocation": {
            "uri": "data/merlun.fa.fasta.gz",
            "locationType": "UriLocation"
          },
          "faiLocation": {
            "uri": "data/merlun.fa.fasta.gz.fai",
            "locationType": "UriLocation"
          },
          "gziLocation": {
            "uri": "data/merlun.fa.fasta.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": "Synteny",
    "views": [
      {
        "type": "LinearSyntenyView",
        "views": [
          {
            "type": "LinearGenomeView",
            "init": {
              "assembly": "merlin.fa",
              "loc": "Merlin",
              "tracks": [
                "17ca836dba3e0a2fd5f0f55f627b717a_0_0"
              ]
            }
          },
          {
            "type": "LinearGenomeView",
            "init": {
              "assembly": "merlon.fa",
              "loc": "Merlon",
              "tracks": [
                "d09def3ade05bd3391ecfecc68a526dd_0_0"
              ]
            }
          },
          {
            "type": "LinearGenomeView",
            "init": {
              "assembly": "merlun.fa",
              "loc": "Merlun",
              "tracks": [
                "91fc8aa321bbea45be2ea9e08db6a205_0_0"
              ]
            }
          }
        ],
        "tracks": [
          {
            "type": "SyntenyTrack",
            "trackId": "d09def3ade05bd3391ecfecc68a526dd_0_0",
            "name": "merlon_on_merlin.paf",
            "adapter": {
              "type": "PAFAdapter",
              "assemblyNames": [
                "merlin.fa",
                "merlon.fa"
              ],
              "pafLocation": {
                "uri": "data/d09def3ade05bd3391ecfecc68a526dd_0_0.paf"
              }
            },
            "category": [
              "Default"
            ],
            "assemblyNames": [
              "merlin.fa",
              "merlon.fa"
            ],
            "displays": [
              {
                "type": "LinearSyntenyDisplay",
                "displayId": "d09def3ade05bd3391ecfecc68a526dd_0_0_LinearSyntenyDisplay"
              }
            ],
            "metadata": {
              "dataset_id": "8bbb74f4ba8b6d59",
              "dataset_hid": "4",
              "dataset_size": "127 bytes",
              "dataset_edam_format": "<a target=\"_blank\" href=\"http://edamontology.org/format_2330\">paf</a>",
              "dataset_file_ext": "paf",
              "history_id": "59f92f7469c0d2ed",
              "history_user_email": "<a href=\"mailto:planemo@galaxyproject.org\">planemo@galaxyproject.org</a>",
              "history_user_id": "1",
              "history_display_name": "<a target=\"_blank\" href=\"http://localhost:8080/history/view/59f92f7469c0d2ed\">Unnamed history</a>",
              "metadata_dbkey": "?",
              "metadata_data_lines": "1",
              "tool_tool_id": "__DATA_FETCH__",
              "tool_tool_version": "0.1.0",
              "tool_tool": "<a target=\"_blank\" href=\"http://localhost:8080/datasets/8bbb74f4ba8b6d59/show_params\">__DATA_FETCH__</a>"
            }
          },
          {
            "type": "SyntenyTrack",
            "trackId": "91fc8aa321bbea45be2ea9e08db6a205_0_0",
            "name": "merlun_on_merlon.paf",
            "adapter": {
              "type": "PAFAdapter",
              "assemblyNames": [
                "merlon.fa",
                "merlun.fa"
              ],
              "pafLocation": {
                "uri": "data/91fc8aa321bbea45be2ea9e08db6a205_0_0.paf"
              }
            },
            "category": [
              "Default"
            ],
            "assemblyNames": [
              "merlon.fa",
              "merlun.fa"
            ],
            "displays": [
              {
                "type": "LinearSyntenyDisplay",
                "displayId": "91fc8aa321bbea45be2ea9e08db6a205_0_0_LinearSyntenyDisplay"
              }
            ],
            "metadata": {
              "dataset_id": "fd9ce4c2ba4cdd97",
              "dataset_hid": "5",
              "dataset_size": "127 bytes",
              "dataset_edam_format": "<a target=\"_blank\" href=\"http://edamontology.org/format_2330\">paf</a>",
              "dataset_file_ext": "paf",
              "history_id": "59f92f7469c0d2ed",
              "history_user_email": "<a href=\"mailto:planemo@galaxyproject.org\">planemo@galaxyproject.org</a>",
              "history_user_id": "1",
              "history_display_name": "<a target=\"_blank\" href=\"http://localhost:8080/history/view/59f92f7469c0d2ed\">Unnamed history</a>",
              "metadata_dbkey": "?",
              "metadata_data_lines": "1",
              "tool_tool_id": "__DATA_FETCH__",
              "tool_tool_version": "0.1.0",
              "tool_tool": "<a target=\"_blank\" href=\"http://localhost:8080/datasets/fd9ce4c2ba4cdd97/show_params\">__DATA_FETCH__</a>"
            }
          }
        ]
      }
    ]
  },
  "tracks": [
    {
      "type": "QuantitativeTrack",
      "trackId": "17ca836dba3e0a2fd5f0f55f627b717a_0_0",
      "name": "data.bw",
      "adapter": {
        "type": "BigWigAdapter",
        "bigWigLocation": {
          "uri": "data/17ca836dba3e0a2fd5f0f55f627b717a_0_0.bw",
          "locationType": "UriLocation"
        }
      },
      "category": [
        "Default"
      ],
      "assemblyNames": [
        "merlin.fa"
      ],
      "displays": [
        {
          "type": "LinearWiggleDisplay",
          "displayId": "17ca836dba3e0a2fd5f0f55f627b717a_0_0_LinearWiggleDisplay",
          "defaultRendering": "xyplot"
        }
      ],
      "metadata": {
        "dataset_id": "2d6b7d67c544c5cb",
        "dataset_hid": "8",
        "dataset_size": "81.6 KB",
        "dataset_edam_format": "<a target=\"_blank\" href=\"http://edamontology.org/format_3006\">bigwig</a>",
        "dataset_file_ext": "bigwig",
        "history_id": "59f92f7469c0d2ed",
        "history_user_email": "<a href=\"mailto:planemo@galaxyproject.org\">planemo@galaxyproject.org</a>",
        "history_user_id": "1",
        "history_display_name": "<a target=\"_blank\" href=\"http://localhost:8080/history/view/59f92f7469c0d2ed\">Unnamed history</a>",
        "metadata_dbkey": "?",
        "tool_tool_id": "__DATA_FETCH__",
        "tool_tool_version": "0.1.0",
        "tool_tool": "<a target=\"_blank\" href=\"http://localhost:8080/datasets/2d6b7d67c544c5cb/show_params\">__DATA_FETCH__</a>"
      }
    }
  ],
  "plugins": []
}

This render like this when loaded by JBrowse:

So the problems I see:

• The first paf data triggers this strange error about CytobandAdapter
• The second paf data is not displayed at all

Is there something I should do in config.json to make everything work as expected? Or is there a bug somewhere?

[abretaud]

Sample data is there: galaxyproject/tools-iuc@651c660

[cmdcolin]

Hello. The configuration of synteny views does not have a simplified "init" type field, so the configuration can be a bit complex. In the config below, the two main things I did were

1. You cannot declare new tracks that way in the defaultSession section of the config. I moved it to the normal top level "tracks" array in the config

2. I used this "levels" concept to show the melin_vs_merlon in the space between view 1 and 2, and then then merlon_vs_merlun between view 2 and 3

Here is an example what it might look like. I stripped down and simplified coded identifiers to emphasize the changes

{
  "assemblies": [
    {
      "name": "merlin.fa",
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "merlin.fa-ReferenceSequenceTrack",
        "adapter": {
          "type": "BgzipFastaAdapter",
          "uri": "data/merlin.fa.fasta.gz"
        }
      }
    },
    {
      "name": "merlon.fa",
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "merlon.fa-ReferenceSequenceTrack",
        "adapter": {
          "type": "BgzipFastaAdapter",
          "uri": "data/merlon.fa.fasta.gz"
        }
      }
    },
    {
      "name": "merlun.fa",
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "merlun.fa-ReferenceSequenceTrack",
        "adapter": {
          "type": "BgzipFastaAdapter",
          "uri": "data/merlun.fa.fasta.gz"
        }
      }
    }
  ],
  "defaultSession": {
    "name": "Synteny",
    "views": [
      {
        "type": "LinearSyntenyView",
        "views": [
          {
            "type": "LinearGenomeView",
            "init": {
              "assembly": "merlin.fa",
              "loc": "Merlin",
              "tracks": ["merlin_quant"]
            }
          },
          {
            "type": "LinearGenomeView",
            "init": {
              "assembly": "merlon.fa",
              "loc": "Merlon",
              "tracks": ["merlon_on_merlin_synteny"]
            }
          },
          {
            "type": "LinearGenomeView",
            "init": {
              "assembly": "merlun.fa",
              "loc": "Merlun",
              "tracks": ["merlun_on_merlon_synteny"]
            }
          }
        ],
        "levels": [
          {
            "id": "level0_uniqueid",
            "type": "LinearSyntenyViewHelper",
            "tracks": [
              {
                "id": "level0_uniqueid_track0",
                "type": "SyntenyTrack",
                "configuration": "merlon_on_merlin_synteny",
                "displays": [
                  {
                    "id": "level0_uniqueid_track0_display0",
                    "type": "LinearSyntenyDisplay",
                    "configuration": "merlon_on_merlin_synteny-LinearSyntenyDisplay"
                  }
                ]
              }
            ],
            "height": 100,
            "level": 0
          },
          {
            "id": "level1_uniqueid",
            "type": "LinearSyntenyViewHelper",
            "tracks": [
              {
                "id": "level1_uniqueid_track0",
                "type": "SyntenyTrack",
                "configuration": "merlun_on_merlon_synteny",
                "displays": [
                  {
                    "id": "level1_uniqueid_track0_display0",
                    "type": "LinearSyntenyDisplay",
                    "configuration": "merlun_on_merlon_synteny-LinearSyntenyDisplay"
                  }
                ]
              }
            ],
            "height": 100,
            "level": 1
          }
        ]
      }
    ]
  },
  "tracks": [
    {
      "type": "QuantitativeTrack",
      "trackId": "merlin_quant",
      "name": "data.bw",
      "adapter": {
        "type": "BigWigAdapter",
        "uri": "data/merlin_quant.bw"
      },
      "assemblyNames": ["merlin.fa"]
    },
    {
      "type": "SyntenyTrack",
      "trackId": "merlon_on_merlin_synteny",
      "name": "merlon_on_merlin.paf",
      "adapter": {
        "type": "PAFAdapter",
        "assemblyNames": ["merlin.fa", "merlon.fa"],
        "uri": "data/merlon_on_merlin_synteny.paf"
      },
      "assemblyNames": ["merlin.fa", "merlon.fa"]
    },
    {
      "type": "SyntenyTrack",
      "trackId": "merlun_on_merlon_synteny",
      "name": "merlun_on_merlon.paf",
      "adapter": {
        "type": "PAFAdapter",
        "assemblyNames": ["merlon.fa", "merlun.fa"],
        "uri": "data/merlun_on_merlon_synteny.paf"
      },
      "assemblyNames": ["merlon.fa", "merlun.fa"]
    }
  ]
}

One way that you can try to inspect how defaultSessions are generated is to export the config from a live instance ("File->Export Session") and then you can view the resulting JSON file. That JSON can be imported into the defaultSession section. Some of the those contents are hard to programmatically generate but hopefully it can help show e.g. the "levels" concept in the synteny view

[cmdcolin]

note that I did not explicitly live test the above config in any way so there could be typos, but the basic idea should be valid

[abretaud]

Thanks a lot! It works now, I've commited the changed to the galaxy wrapper :)