Clean up example browsers.

myhelix · Oct 28, 2014 · 86657d9 · 86657d9
1 parent aaaf3b2
commit 86657d9
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Showing 7 changed files with 166 additions and 695 deletions.
diff --git a/test37-compiled.html → example-browsers/human37.html b/test37-compiled.html → example-browsers/human37.html
@@ -8,7 +8,7 @@
 </style>
 
 <title>Human GRCh37 :: Dalliance</title> 
-<script language="javascript" src="build/dalliance-all.js"></script>
+<script language="javascript" src="../build/dalliance-all.js"></script>
 
 <script language="javascript">
   var b = new Browser({
@@ -81,21 +81,16 @@
                 ],
 
     setDocumentTitle: true,
-    uiPrefix: '',
+    uiPrefix: '../',
 
     fullScreen: true,
 
-    browserLinks: {
-        Ensembl: 'http://ncbi36.ensembl.org/Homo_sapiens/Location/View?r=${chr}:${start}-${end}',
-        UCSC: 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr${chr}:${start}-${end}',
-        Sequence: 'http://www.derkholm.net:8080/das/hg19comp/sequence?segment=${chr}:${start},${end}'
-    }
-  });
-
-  b.hubs = [
+    hubs: [
             'http://www.biodalliance.org/datasets/testhub/hub.txt',
             'http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/hub.txt'
-           ];
+           ]
+  });
+
 
   b.addFeatureInfoPlugin(function(f, info) {
       info.add('Testing', 'This is a test!');
@@ -106,32 +101,12 @@
     link.href = 'http://www.ensembl.org/Homo_sapiens/Location/View?r=' + chr + ':' + min + '-' + max;
   });
 
-/*
-  var geneDescriptions;
-  connectBigTab(new URLFetchable('http://www.biodalliance.org/datasets/ensg-to-desc.bt'), function(bt) {
-    geneDescriptions = bt;
-  });
-
-b.addFeatureInfoPlugin(function(f, info) {
-  if (f.geneId) {
-    var desc = makeElement('div', 'Loading...');
-    info.add('Description', desc);
-    geneDescriptions.index.lookup(f.geneId, function(res, err) {
-      if (err) {
-        console.log(err);
-      } else {
-        desc.textContent = res;
-      }
-    });
-  }
-}); */
-
 </script>
 </head>
 
 <body>
 <a href='http://www.ensembl.org/' id='enslink' target='_newtab'>Link to Ensembl</a>
-<div id='svgHolder'>Dalliance genome browser goes here.  Unless you have an ancient web browser or something.</div>
+<div id='svgHolder'>Failed to load the Biodalliance genome browser.  Have you run "gulp"?</div>
 </body>
 </html>
 
diff --git a/example-browsers/human38.html b/example-browsers/human38.html
@@ -0,0 +1,86 @@
+<!DOCTYPE html> 
+
+<html>
+
+<head>
+
+<style>
+</style>
+
+<title>Human GRCh38 :: Dalliance</title> 
+<script language="javascript" src="../build/dalliance-all.js"></script>
+
+<script language="javascript">
+var b = new Browser({
+   chr:                 '22',
+    viewStart:           30300000,
+    viewEnd:             30500000,
+    cookieKey:           'human-grc_h38',
+
+    coordSystem: {
+      speciesName: 'Human',
+      taxon: 9606,
+      auth: 'GRCh',
+      version: '38',
+      ucscName: 'hg38'
+    },
+
+    chains: {
+
+      hg19ToHg38: new Chainset('http://www.derkholm.net:8080/das/hg19ToHg38/', 'GRCh37', 'GRCh38',
+                               {
+                                  speciesName: 'Human',
+                                  taxon: 9606,
+                                  auth: 'GRCh',
+                                  version: 37,
+                                  ucscName: 'hg19'
+                               })
+    },
+
+    sources:          [{name:                 'Genome',
+                       twoBitURI:            'http://www.biodalliance.org/datasets/hg38.2bit',
+                       tier_type: 'sequence'}
+
+
+                      ,{name: 'GENCODE',
+                       desc: 'Gene structures from GENCODE 20',
+                       bwgURI: 'http://www.biodalliance.org/datasets/GRCh38/gencode.v20.annotation.bb',
+                       stylesheet_uri: 'http://www.biodalliance.org/stylesheets/gencode2.xml',
+                       collapseSuperGroups: true,
+                       trixURI: 'http://www.biodalliance.org/datasets/GRCh38/gencode.v20.annotation.ix'}
+
+                      ,{name: 'GENCODEv19',
+                       desc: 'Gene structures from GENCODE 19',
+                       bwgURI: 'http://www.biodalliance.org/datasets/gencode.bb',
+                       stylesheet_uri: 'http://www.biodalliance.org/stylesheets/gencode.xml',
+                       collapseSuperGroups: true,
+                       pennant: 'http://genome.ucsc.edu/images/19.jpg',
+                       trixURI: 'http://www.biodalliance.org/datasets/gene-index.ix',
+                       mapping: 'hg19ToHg38'}
+
+                      ,{name: 'Repeats',
+                        desc: 'Repeat annotation from UCSC', 
+                        bwgURI: 'http://www.biodalliance.org/datasets/GRCh38/repeats.bb',
+                        stylesheet_uri: 'http://www.biodalliance.org/stylesheets/bb-repeats2.xml'}
+    ],
+
+    prefix: '../',
+    fullScreen: true,
+
+    browserLinks: {
+      Ensembl: 'http://www.ensembl.org/Homo_sapiens/Location/View?r=${chr}:${start}-${end}',
+      UCSC: 'http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr${chr}:${start}-${end}',
+      Sequence: 'http://www.derkholm.net:8080/das/hg19comp/sequence?segment=${chr}:${start},${end}'
+    },
+
+    hubs: ['http://ngs.sanger.ac.uk/production/ensembl/regulation/hub.txt', {url: 'http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/hub.txt', genome: 'hg19', mapping: 'hg19ToHg38'}],
+  });
+
+</script>
+</head>
+
+<body>
+<div id='svgHolder'>Failed to load the Biodalliance genome browser.  Have you run "gulp"?</div>
+</body>
+</html>
+
diff --git a/example-browsers/mouse38.html b/example-browsers/mouse38.html
@@ -0,0 +1,67 @@
+<!DOCTYPE html> 
+
+<html>
+
+<head>
+
+<style>
+</style>
+
+<title>Mouse GRCm38 :: Dalliance</title> 
+<script language="javascript" src="../build/dalliance-all.js"></script>
+
+<script language="javascript">
+
+var b = new Browser({
+      chr:        '19',
+      viewStart:  30000000,
+      viewEnd:    30100000,
+      cookieKey:  'mouse38',
+
+      coordSystem: {
+          speciesName: 'Mouse',
+          taxon: 10090,
+          auth: 'GRCm',
+          version: 38,
+          ucscName: 'mm10'
+      },
+
+
+    chains: {
+      mm9ToMm10: new Chainset('http://www.derkholm.net:8080/das/mm9ToMm10/', 'NCBIM37', 'GRCm38',
+                               {
+                                  speciesName: 'Mouse',
+                                  taxon: 10090,
+                                  auth: 'NCBIM',
+                                  version: 37,
+                                  ucscName: 'mm9'
+                               })
+    }, 
+
+
+      sources:      [{name: 'Genome',
+                     twoBitURI:  'http://www.biodalliance.org/datasets/GRCm38/mm10.2bit',
+                     desc: 'Mouse reference genome build GRCm38',
+                     tier_type: 'sequence',
+                     provides_entrypoints: true}
+                      ,{name: 'Genes',
+                        desc: 'Gene structures from GENCODE M2',
+                        bwgURI: 'http://www.biodalliance.org/datasets/GRCm38/gencodeM2.bb',
+                        stylesheet_uri: 'http://www.biodalliance.org/stylesheets/gencode.xml',
+                        collapseSuperGroups: true,
+                        trixURI: 'http://www.biodalliance.org/datasets/GRCm38/gencodeM2.ix'}
+                      ,{name: 'Repeats',
+                        desc: 'Repeat annotation from UCSC', 
+                        bwgURI: 'http://www.biodalliance.org/datasets/GRCm38/repeats.bb',
+                        stylesheet_uri: 'http://www.biodalliance.org/stylesheets/bb-repeats2.xml'}],
+        uiPrefix: '../',
+        fullScreen: true                    
+});
+</script>
+</head>
+
+<body>
+<div id='svgHolder'>Failed to load the Biodalliance genome browser.  Have you run "gulp"?</div>
+</body>
+</html>
+
diff --git a/test-mouse.html b/test-mouse.html