AUGUST 2022 update for prod configsw

organisms/prod/Apis_mellifera/trackList.json

@@ -1,140 +1,149 @@
 {
-   "formatVersion" : 1,
-   "names" : {
-      "type" : "Hash",
-      "url" : "names/"
-   },
-   "tracks" : [
-      {
-         "category" : "Reference sequence",
-         "faiUrlTemplate" : "seq/GCF_000002195.4_Amel_4.5_genomic.fna.fai",
-         "key" : "Reference sequence",
-         "label" : "DNA",
-         "seqType" : "dna",
-         "storeClass" : "JBrowse/Store/Sequence/IndexedFasta",
-         "type" : "SequenceTrack",
-         "urlTemplate" : "seq/GCF_000002195.4_Amel_4.5_genomic.fna",
-         "useAsRefSeqStore" : 1
+  "formatVersion": 1,
+  "names": {
+    "type": "Hash",
+    "url": "names/"
+  },
+
+  "tracks": [
+    {
+      "category": "Reference sequence",
+      "faiUrlTemplate": "seq/GCF_000002195.4_Amel_4.5_genomic.fna.fai",
+      "key": "Reference sequence",
+      "label": "DNA",
+      "seqType": "dna",
+      "storeClass": "JBrowse/Store/Sequence/IndexedFasta",
+      "type": "SequenceTrack",
+      "unsafePopup": true,
+      "urlTemplate": "seq/GCF_000002195.4_Amel_4.5_genomic.fna",
+      "useAsRefSeqStore": 1
+    },
+    {
+      "category": "Apis mellifera Official Gene Set version 3.3",
+      "compress": 0,
+      "fmtDetailValue_Id": "function(id, feature) { var name2 = id.replace(/-R./, ''); if(feature.get('type')=='mRNA') { return ''+id+' (Click for Gene page)';} else {return id}}",
+      "key": "apimel_OGSv3.3 Gene",
+      "label": "apimel_current_models",
+      "menuTemplate": [
+        {
+          "label": "View details"
+        },
+        {
+          "action": "newWindow",
+          "iconClass": "dijitIconDatabase",
+          "label": "function(track,feature){ return 'Search HymenopteraMine for '+feature.get('id')}",
+          "title": "function(track,feature){ return 'Search HymenopteraMine for '+feature.get('id')}",
+          "url": "function(track,feature){ return 'http://128.206.116.3:8080/hymenopteramine/keywordSearchResults.do?searchTerm='+feature.get('id')+'&searchSubmit=Search'}"
+        }
+      ],
+      "metadata": {
+        "Data description": "Honey Bee Genome Sequencing Consortium. 2014. doi: 10.1186/1471-2164-15-86; https://i5k.nal.usda.gov/node/739241",
+        "Data provider": "BeeBase, http://hymenopteragenome.org/beebase/?q=consortium_datasets",
+        "Data source": "BeeBase, http://hymenopteragenome.org/beebase/?q=consortium_datasets",
+        "Method": "Honey Bee Genome Sequencing Consortium. 2014. doi: 10.1186/1471-2164-15-86; https://i5k.nal.usda.gov/node/739241",
+        "Publication status": "Published, Honey Bee Genome Sequencing Consortium. 2014. doi: 10.1186/1471-2164-15-86"
       },
-      {
-         "compress" : 0,
-         "fmtDetailValue_Id" : "function(id, feature) { var name2 = id.replace(/-R./, ''); if(feature.get('type')=='mRN:A') { return ''+id+' (Click for Gene page)';} else {return id}}",
-         "menuTemplate" : [
-             {
-                "label" : "View details",
-             },
-             {
-              "label": "function(track,feature){ return 'Search HymenopteraMine for '+feature.get('id')}",
-              "title": "function(track,feature){ return 'Search HymenopteraMine for '+feature.get('id')}",
-              "iconClass" : "dijitIconDatabase",
-              "action": "newWindow",
-              "url" : "function(track,feature){ return 'http://128.206.116.3:8080/hymenopteramine/keywordSearchResults.do?searchTerm='+feature.get('id')+'&searchSubmit=Search'}",
-              },
-        ],
-         "key" : "apimel_OGSv3.3 Gene",
-         "category":"Apis mellifera Official Gene Set version 3.3",
-         "metadata" : {
-         "Data description":"Honey Bee Genome Sequencing Consortium. 2014. doi: 10.1186/1471-2164-15-86; https://i5k.nal.usda.gov/node/739241",
-         "Data source":"BeeBase, http://hymenopteragenome.org/beebase/?q=consortium_datasets",
-         "Data provider":"BeeBase, http://hymenopteragenome.org/beebase/?q=consortium_datasets",
-         "Method":"Honey Bee Genome Sequencing Consortium. 2014. doi: 10.1186/1471-2164-15-86; https://i5k.nal.usda.gov/node/739241",
-         "Publication status":"Published, Honey Bee Genome Sequencing Consortium. 2014. doi: 10.1186/1471-2164-15-86"},
-         "label" : "apimel_current_models",
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
-         "style" : {
-            "arrowheadClass" : "trellis-arrowhead",
-            "className" : "container-16px",
-            "subfeatureClasses" : {
-               "CDS" : "primary_gene_set-cds",
-               "UTR" : "primary_gene_set-utr",
-               "exon" : "container-100pct",
-               "wholeCDS" : null
-            }
-         },
-         "trackType" : null,
-         "type" : "ColorByType/View/Track/ColorByTypeDraggable",
-         "urlTemplate" : "tracks/apimel_current_models/{refseq}/trackData.json"
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
+        "subfeatureClasses": {
+          "CDS": "primary_gene_set-cds",
+          "UTR": "primary_gene_set-utr",
+          "exon": "container-100pct",
+          "wholeCDS": null
+        }
       },
-      {
-         "autoscale" : "local",
-         "bicolor_pivot" : "zero",
-         "category" : "Reference Assembly",
-         "key" : "Gaps in assembly",
-         "label" : "Gaps in assembly",
-         "metadata" : {
-            "Track contact" : "The i5k workspace@NAL",
-            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
-            "Track legend" : "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
-         },
-         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
-         "style" : {
-            "neg_color" : "white",
-            "pos_color" : "black"
-         },
-         "type" : "JBrowse/View/Track/Wiggle/Density",
-         "urlTemplate" : "bigwig/GCF_000002195.4_Amel_4.5_genomic.fna.gaps.bigwig"
+      "trackType": null,
+      "type": "FeatureTrack",
+      "unsafePopup": true,
+      "urlTemplate": "tracks/apimel_current_models/{refseq}/trackData.json"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "zero",
+      "category": "Reference Assembly",
+      "key": "Gaps in assembly",
+      "label": "Gaps in assembly",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of gaps in the reference assembly.  Basecalls of N are colored black. All other regions are left blank"
       },
-      {
-         "autoscale" : "local",
-         "bicolor_pivot" : "0.5",
-         "category" : "Reference Assembly",
-         "key" : "GC Content",
-         "label" : "GC Content",
-         "metadata" : {
-            "Track contact" : "The i5k workspace@NAL",
-            "Track description" : "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
-            "Track legend" : "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
-         },
-         "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
-         "style" : {
-            "neg_color" : "rgba(255,255,0,50)",
-            "pos_color" : "rgba(0,0,255,50)"
-         },
-         "type" : "JBrowse/View/Track/Wiggle/Density",
-         "urlTemplate" : "bigwig/GCF_000002195.4_Amel_4.5_genomic.fna.gc.bigwig"
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "white",
+        "pos_color": "black"
       },
-      {
-         "category" : "NCBI Annotation Release 103",
-         "compress" : 0,
-         "key" : "NCBI_Annotation_Release_103_Pseudogene",
-         "label" : "NCBI_Annotation_Release_103_Pseudogene",
-         "metadata" : {
-            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Apis_mellifera/README_CURRENT_RELEASE",
-            "Data provider" : "NCBI",
-            "Data source" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/002/195/GCF_000002195.4_Amel_4.5/GCF_000002195.4_Amel_4.5_genomic.gff.gz",
-            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
-         },
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
-         "style" : {
-            "arrowheadClass" : "trellis-arrowhead",
-            "className" : "container-16px",
-            "description" : "product, note, description",
-            "subfeatureClasses" : {
-               "CDS" : "primary_gene_set-cds",
-               "UTR" : "primary_gene_set-utr",
-               "exon" : "container-100pct",
-               "wholeCDS" : null
-            }
-         },
-         "trackType" : "HTMLFeatures",
-         "type" : "HTMLFeatures",
-         "urlTemplate" : "tracks/NCBI_Annotation_Release_103_Pseudogene/{refseq}/trackData.json"
+      "type": "JBrowse/View/Track/Wiggle/Density",
+      "unsafePopup": true,
+      "urlTemplate": "bigwig/GCF_000002195.4_Amel_4.5_genomic.fna.gaps.bigwig"
+    },
+    {
+      "autoscale": "local",
+      "bicolor_pivot": "0.5",
+      "category": "Reference Assembly",
+      "key": "GC Content",
+      "label": "GC Content",
+      "metadata": {
+        "Track contact": "The i5k workspace@NAL",
+        "Track description": "This track was created as part of the data proccessing workflow used to create the Web Apollo instance.",
+        "Track legend": "Visualization of GC/AT content in the reference assembly.  Bases called as G or C are scored 1 and colored blue; A and T bases are scored 0 and colored yellow. Ambiguous bases (N) are left blank. At zoom levels in which individual bases can not be resolved, scores are averaged for visualization. The pivot point is 0.5, or 50% G+C or A+T. The score at any position may be seen by moving the cursor to that position in the track."
       },
-      {
-         "category" : "NCBI Annotation Release 103",
-         "compress" : 0,
-         "key" : "NCBI_Annotation_Release_103_Gene",
-         "label" : "NCBI_Annotation_Release_103_Gene",
-         "metadata" : {
-            "Data description" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/Apis_mellifera/README_CURRENT_RELEASE",
-            "Data provider" : "NCBI",
-            "Data source" : "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/002/195/GCF_000002195.4_Amel_4.5/GCF_000002195.4_Amel_4.5_genomic.gff.gz",
-            "Method" : "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
-         },
-         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
-         "trackType" : "ColorByType/View/Track/ColorByTypeDraggable",
-         "type" : "FeatureTrack",
-         "urlTemplate" : "tracks/NCBI_Annotation_Release_103_Gene/{refseq}/trackData.json"
-      }
-   ]
+      "scoreType": "avgScore",
+      "storeClass": "JBrowse/Store/SeqFeature/BigWig",
+      "style": {
+        "neg_color": "rgba(255,255,0,50)",
+        "pos_color": "rgba(0,0,255,50)"
+      },
+      "type": "JBrowse/View/Track/Wiggle/Density",
+      "unsafePopup": true,
+      "urlTemplate": "bigwig/GCF_000002195.4_Amel_4.5_genomic.fna.gc.bigwig"
+    },
+    {
+      "category": "NCBI Annotation Release 103",
+      "compress": 0,
+      "key": "NCBI_Annotation_Release_103_Pseudogene",
+      "label": "NCBI_Annotation_Release_103_Pseudogene",
+      "metadata": {
+        "Data description": "ftp://ftp.ncbi.nlm.nih.gov/genomes/Apis_mellifera/README_CURRENT_RELEASE",
+        "Data provider": "NCBI",
+        "Data source": "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/002/195/GCF_000002195.4_Amel_4.5/GCF_000002195.4_Amel_4.5_genomic.gff.gz",
+        "Method": "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "style": {
+        "arrowheadClass": "trellis-arrowhead",
+        "className": "{type}",
+        "description": "product, note, description",
+        "subfeatureClasses": {
+          "CDS": "primary_gene_set-cds",
+          "UTR": "primary_gene_set-utr",
+          "exon": "container-100pct",
+          "wholeCDS": null
+        }
+      },
+      "trackType": null,
+      "type": "FeatureTrack",
+      "unsafePopup": true,
+      "urlTemplate": "tracks/NCBI_Annotation_Release_103_Pseudogene/{refseq}/trackData.json"
+    },
+    {
+      "category": "NCBI Annotation Release 103",
+      "compress": 0,
+      "key": "NCBI_Annotation_Release_103_Gene",
+      "label": "NCBI_Annotation_Release_103_Gene",
+      "metadata": {
+        "Data description": "ftp://ftp.ncbi.nlm.nih.gov/genomes/Apis_mellifera/README_CURRENT_RELEASE",
+        "Data provider": "NCBI",
+        "Data source": "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/002/195/GCF_000002195.4_Amel_4.5/GCF_000002195.4_Amel_4.5_genomic.gff.gz",
+        "Method": "http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/"
+      },
+      "storeClass": "JBrowse/Store/SeqFeature/NCList",
+      "trackType": null,
+      "type": "FeatureTrack",
+      "unsafePopup": true,
+      "urlTemplate": "tracks/NCBI_Annotation_Release_103_Gene/{refseq}/trackData.json"
+    }
+  ]
 }