Wrong URI while adding GFF track

While adding a new track to an assembly with the following command;

jbrowse add-track --trackType=FeatureTrack -n 'Annotation' --assemblyNames=CHL-ADG1  -l inPlace /mnt/www/pgdp-jbrowse2/jbrowse2/data/chl-adg1/ADG1_cp.gff.gz

It outputs this in the config.json as;

{
      "type": "FeatureTrack",
      "trackId": "ADG1_cp.gff",
      "name": "Annotation",
      "assemblyNames": [
        "CHL-ADG1"
      ],
      "adapter": {
        "type": "Gff3TabixAdapter",
        "gffGzLocation": {
          "uri": "ADG1_cp.gff.gz"
        },
        "index": {
          "location": {
            "uri": "ADG1_cp.gff.gz.tbi"
          },
          "indexType": "TBI"
        }
      }
    }

Which generates a HTTP 404 error due to file being not located. I solved the problem by adding the location of the file to the URIs manually.

{
      "type": "FeatureTrack",
      "trackId": "ADG1_cp.gff",
      "name": "Annotation",
      "assemblyNames": [
        "CHL-ADG1"
      ],
      "adapter": {
        "type": "Gff3TabixAdapter",
        "gffGzLocation": {
          "uri": "data/chl-adg1/ADG1_cp.gff.gz"
        },
        "index": {
          "location": {
            "uri": "data/chl-adg1/ADG1_cp.gff.gz.tbi"
          },
          "indexType": "TBI"
        }
      }
    }

Thank you, Ilayda

[cmdcolin]

To keep things organized, you can use --subDir which will copy the file to a subdirectory e.g.

jbrowse add-track myfile.bam --load copy --subDir bams

This will copy myfile.bam and myfile.bam.bai to a bams subdirectory, and output a track config like this

{
      "type": "AlignmentsTrack",
      "trackId": "volvox-sorted",
      "name": "volvox-sorted",
      "assemblyNames": [
        "volvox"
      ],
      "adapter": {
        "type": "BamAdapter",
        "bamLocation": {
          "uri": "test/volvox-sorted.bam"
        },
        "index": {
          "location": {
            "uri": "test/volvox-sorted.bam.bai"
          },
          "indexType": "BAI"
        },
        "sequenceAdapter": {
          "type": "IndexedFastaAdapter",
          "fastaLocation": {
            "uri": "volvox.fa"
          },
          "faiLocation": {
            "uri": "volvox.fa.fai"
          }
        }
      }
    }

It is true that it would get hard to organize the data directory properly without using something like --subDir, but let me know if that helps.

It is also allowed to use --load inPlace as you were using it if we fix the bug with it!

[cmdcolin]

To be clear, using --load inPlace data/chl-adg1/ADG1_cp.gff.gz.tbi and not --load inPlace /mnt/www/pgdp-jbrowse2/jbrowse2/data/chl-adg1/ADG1_cp.gff.gz …once we fix the bug