Merge branch 'master' of mus.cacr.caltech.edu:htsworkflow

diff --git a/extra/ucsc_encode_submission/ucsc_gather.py b/extra/ucsc_encode_submission/ucsc_gather.py
index 1c0759fdf8c5542402501302c060ad16b753a068..90b4b3568b360ab120ad74c02c210cd5cbba822b 100755 (executable)
--- a/extra/ucsc_encode_submission/ucsc_gather.py
+++ b/extra/ucsc_encode_submission/ucsc_gather.py
@@ -638,9 +638,19 @@ class NameToViewMap(object):
             ('*.condor',                None),
             ('*.daf',                   None),
             ('*.ddf',                   None),
+
+            ('*ufflinks?0.9.3.genes.gtf',       'GeneDeNovo'),
+            ('*ufflinks?0.9.3.transcripts.gtf', 'TranscriptDeNovo'),
+            ('*GENCODE-v3c.exonFPKM.gtf',        'ExonsGencV3c'),
+            ('*GENCODE-v3c.genes.gtf',           'GeneGencV3c'),
+            ('*GENCODE-v3c.transcripts.gtf',     'TranscriptGencV3c'),
+            ('*GENCODE-v3c.TSS.gtf',             'TSS'),
+            ('*.junctions.bed6+3',                'Junctions'),
+            
             ('*.?ufflinks-0.9.0?genes.expr',       'GeneDeNovo'),
             ('*.?ufflinks-0.9.0?transcripts.expr', 'TranscriptDeNovo'),
             ('*.?ufflinks-0.9.0?transcripts.gtf',  'GeneModel'),
+
             ('*.GENCODE-v3c?genes.expr',       'GeneGCV3c'),
             ('*.GENCODE-v3c?transcript*.expr', 'TranscriptGCV3c'),
             ('*.GENCODE-v3c?transcript*.gtf',  'TranscriptGencV3c'),
@@ -661,6 +671,7 @@ class NameToViewMap(object):
             ('*.srf',                   None),
             ('*.wig',                   None),
             ('*.zip',                   None),
+            ('transfer_log',            None),
             ]
 
         self.views = {
@@ -676,6 +687,9 @@ class NameToViewMap(object):
             "GeneModel": {"MapAlgorithm": ma},
             "GeneDeNovo": {"MapAlgorithm": ma},
             "TranscriptDeNovo": {"MapAlgorithm": ma},
+            "ExonsGencV3c": {"MapAlgorithm": ma},
+            "GeneGencV3c": {"MapAlgorithm": ma},
+            "TSS": {"MapAlgorithm": ma},
             "GeneGCV3c": {"MapAlgorithm": ma},
             "TranscriptGCV3c": {"MapAlgorithm": ma},
             "TranscriptGencV3c": {"MapAlgorithm": ma},

diff --git a/htsworkflow/frontend/static/css/global.css b/htsworkflow/frontend/static/css/global.css
index fd840600e34187bf575e0585feea2ab3c265fa56..adc2539036b5c2622120bcfdd57f16ce1259a2fb 100644 (file)
--- a/htsworkflow/frontend/static/css/global.css
+++ b/htsworkflow/frontend/static/css/global.css
@@ -1,4 +1,4 @@
-body { margin:0; padding:0; font-size:12px; font-family:"Lucida Grande","DejaVu Sans","Bitstream Vera Sans",Verdana,Arial,sans-serif; color:#333; background:#fff; }
+body { margin:0; padding:0; font-size:14px; font-family:"Lucida Grande","DejaVu Sans","Bitstream Vera Sans",Verdana,Arial,sans-serif; color:#333; background:#fff; }
 
 /* LINKS */
 a:link, a:visited { color: #5b80b2; text-decoration:none; }

diff --git a/htsworkflow/frontend/templates/base.html b/htsworkflow/frontend/templates/base.html
index ba17cbda121d2c2bf6dd646df4c85450d01f77e9..22dad4bfea6f13007bfedded02373a82e3ee9800 100644 (file)
--- a/htsworkflow/frontend/templates/base.html
+++ b/htsworkflow/frontend/templates/base.html
@@ -5,7 +5,7 @@
       version="XHTML+RDFa 1.0"
       xmlns:xml="http://www.w3.org/1999/xhtml"
       xmlns:dc="http://purl.org/dc/elements/1.1/"
-      xmlns:xmls="http://www.w3.org/2001/XMLSchema#"
+      xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
       xmlns:libns="http://jumpgate.caltech.edu/wiki/LibraryOntology#"
       xml:lang="en"
 >

diff --git a/htsworkflow/frontend/templates/samples/library_detail.html b/htsworkflow/frontend/templates/samples/library_detail.html
index 1bbd65b2986caf766d832ac8fd86b294d992b8a5..0aa83d07528f2f7ea82a9499a8b1c28bf4b74011 100644 (file)
--- a/htsworkflow/frontend/templates/samples/library_detail.html
+++ b/htsworkflow/frontend/templates/samples/library_detail.html
@@ -98,7 +98,7 @@
     <span property="libns:made_by">{{ lib.made_by }}</span>
   <br/>
   <b>Creation Date</b>
-    <span property="libns:creation_date">{{ lib.creation_date }}</span>
+    <span property="libns:date" content="{{lib.creation_date|date:'Y-m-d'}}T00:00:00" datatype="xsd:dateTime">{{ lib.creation_date }}</span>
   <br/> 
   <b>Protocol Stopping Point</b>
     <span property="libns:stopping_point">{{ lib.stopping_point_name }}</span>
@@ -129,7 +129,7 @@
   <tbody>
     {% for result in eland_results %}
     <tr about="/flowcell/{{result.flowcell_id}}/lane/{{result.lane}}">
-      <td property="libns:run_date" contents="{{result.run_date}}" datatype="xmls:datetime">{{ result.run_date|date}}</td>
+      <td property="libns:date" content="{{result.run_date|date:'Y-m-d\TH:i:s'}}" datatype="xsd:dateTime">{{ result.run_date|date}}</td>
       <td>{{ result.cycle }}</td>
       <td property="libns:flowcell_id">{{ result.flowcell_id }}</td>
       <td property="libns:lane">{{ result.lane }}</td>
@@ -201,7 +201,7 @@
         <td>{{ lane.match_codes.U0|intcomma }}</td>
         <td>{{ lane.match_codes.U1|intcomma }}</td>
         <td>{{ lane.match_codes.U2|intcomma }}</td>
-        <td property="libns:sequence_unique_location" contents="{{lane.unique_reads}}" datatype="xmls:decimal">{{ lane.unique_reads|intcomma }}</td>
+        <td {% if lane.unique_reads %}property="libns:total_unique_locations" content="{{lane.unique_reads}}" datatype="xsd:decimal"{% endif %}>{{ lane.unique_reads|intcomma }}</td>
         <td>{{ lane.match_codes.R0|intcomma }}</td>
         <td>{{ lane.match_codes.R1|intcomma }}</td>
         <td>{{ lane.match_codes.R2|intcomma }}</td>