Add gene annotation track to IGV. Fix #1494.

refinery-platform · Nov 10, 2016 · 63ba0dd · 63ba0dd
1 parent 564e8b1
commit 63ba0dd
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Showing 2 changed files with 13 additions and 3 deletions.
diff --git a/refinery/core/views.py b/refinery/core/views.py
@@ -617,6 +617,8 @@ def visualize_genome(request):
               "fasta_url": url_base + genome + ".fa",
               "index_url": url_base + genome + ".fa.fai",
               "cytoband_url": url_base + "cytoBand.txt",
+              "bed_url": url_base + "refGene.bed",
+              "tbi_url": url_base + "refGene.bed.tbi",
               "node_ids_json": node_ids_json
           },
           context_instance=RequestContext(request))

diff --git a/refinery/templates/core/visualize/genome.html b/refinery/templates/core/visualize/genome.html
@@ -43,13 +43,21 @@
                         url: promise.relative_file_store_item_url,
                         format: promise.file_extension
                   };
-
                   if (promise.file_extension === "bam") {
                     igv_track.indexURL = promise.auxiliary_nodes[0];
                   }
-
                   return igv_track;
-
+                });
+                tracks.push({
+                    name: "Genes",
+                    type: "annotation",
+                    format: "bed",
+                    sourceType: "file",
+                    url: "{{ bed_url|escapejs }}",
+                    indexURL: "{{ tbi_url|escapejs }}",
+                    order: Number.MAX_VALUE,
+                    visibilityWindow: 300000000,
+                    displayMode: "EXPANDED"
                 });
                 var div = $("#igv")[0];
                 var options = {